Starting phenix.real_space_refine on Tue Dec 31 05:52:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6m66_30114/12_2024/6m66_30114.cif Found real_map, /net/cci-nas-00/data/ceres_data/6m66_30114/12_2024/6m66_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_30114/12_2024/6m66_30114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6m66_30114/12_2024/6m66_30114.map" model { file = "/net/cci-nas-00/data/ceres_data/6m66_30114/12_2024/6m66_30114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6m66_30114/12_2024/6m66_30114.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: C, B, E, D, G, F Time building chain proxies: 5.36, per 1000 atoms: 0.36 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=2, 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 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: 3.72 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 1.57 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: 4.01 Time building geometry restraints manager: 4.22 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: 7293 14.27 - 28.53: 1273 28.53 - 42.80: 420 42.80 - 57.07: 78 57.07 - 71.33: 14 Dihedral angle restraints: 9078 sinusoidal: 3527 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 9075 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: 2.02 - 2.60: 200 2.60 - 3.17: 12494 3.17 - 3.75: 25062 3.75 - 4.32: 31781 4.32 - 4.90: 48750 Nonbonded interactions: 118287 Sorted by model distance: nonbonded pdb=" SG CYS D 84 " pdb=" SG CYS D 246 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS G 84 " pdb=" SG CYS G 246 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS C 84 " pdb=" SG CYS C 246 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS E 84 " pdb=" SG CYS E 246 " model vdw 2.024 3.760 nonbonded pdb=" SG CYS F 84 " pdb=" SG CYS F 246 " model vdw 2.024 3.760 ... (remaining 118282 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.560 Check model and map are aligned: 0.140 Set scattering table: 0.160 Process input model: 30.460 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 15309 Z= 0.343 Angle : 1.076 8.681 20825 Z= 0.566 Chirality : 0.060 0.226 2471 Planarity : 0.010 0.080 2520 Dihedral : 16.352 71.333 5460 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 9.42 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.002 TRP E 127 HIS 0.004 0.001 HIS A 106 PHE 0.028 0.002 PHE E 109 TYR 0.017 0.002 TYR F 309 ARG 0.002 0.001 ARG B 254 *********************** 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 : 1.755 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: 0.7613 (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: 0.3186 time to fit residues: 111.4034 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 : 1.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 153 optimal weight: 7.9990 chunk 137 optimal weight: 3.9990 chunk 76 optimal weight: 8.9990 chunk 47 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 73 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 chunk 165 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 134 HIS A 207 ASN A 319 HIS B 134 HIS B 207 ASN B 319 HIS ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS C 207 ASN C 319 HIS ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 134 HIS D 207 ASN D 319 HIS E 134 HIS E 207 ASN E 319 HIS F 134 HIS F 207 ASN F 319 HIS G 134 HIS G 207 ASN G 319 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15309 Z= 0.305 Angle : 0.883 8.493 20825 Z= 0.435 Chirality : 0.052 0.227 2471 Planarity : 0.007 0.053 2520 Dihedral : 6.792 22.771 1981 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.17), residues: 1827 helix: -1.67 (0.13), residues: 1155 sheet: -4.79 (0.38), residues: 84 loop : -3.05 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 127 HIS 0.003 0.001 HIS B 134 PHE 0.018 0.001 PHE B 109 TYR 0.030 0.002 TYR E 234 ARG 0.005 0.000 ARG C 128 *********************** 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 190 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 190 time to evaluate : 1.798 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: 0.8335 (mm110) cc_final: 0.8096 (mm110) REVERT: A 128 ARG cc_start: 0.9415 (ttp-110) cc_final: 0.9211 (ttp-110) REVERT: A 141 PHE cc_start: 0.7718 (m-10) cc_final: 0.7497 (m-80) REVERT: A 272 ILE cc_start: 0.9519 (pt) cc_final: 0.9081 (tt) REVERT: B 56 GLN cc_start: 0.8356 (mm-40) cc_final: 0.7937 (mm110) REVERT: B 128 ARG cc_start: 0.9545 (tmm-80) cc_final: 0.9273 (ttp-110) REVERT: B 141 PHE cc_start: 0.7517 (m-10) cc_final: 0.7316 (m-80) REVERT: B 272 ILE cc_start: 0.9497 (pt) cc_final: 0.9133 (tt) REVERT: C 36 LYS cc_start: 0.8883 (tmmt) cc_final: 0.8644 (tptt) REVERT: C 56 GLN cc_start: 0.8225 (mm110) cc_final: 0.7676 (mm110) REVERT: C 152 ARG cc_start: 0.5827 (ttt180) cc_final: 0.5505 (ptt90) REVERT: C 272 ILE cc_start: 0.9511 (pt) cc_final: 0.9262 (tt) REVERT: D 37 MET cc_start: 0.7942 (ttp) cc_final: 0.7738 (mtp) REVERT: D 128 ARG cc_start: 0.9565 (tmm-80) cc_final: 0.9330 (ttp-110) REVERT: D 141 PHE cc_start: 0.7695 (m-10) cc_final: 0.7443 (m-80) REVERT: D 152 ARG cc_start: 0.5344 (ttt180) cc_final: 0.5058 (ptt90) REVERT: E 56 GLN cc_start: 0.8223 (mm110) cc_final: 0.7929 (mm110) REVERT: E 128 ARG cc_start: 0.9487 (tmm-80) cc_final: 0.9155 (ttp-110) REVERT: E 272 ILE cc_start: 0.9553 (pt) cc_final: 0.9247 (tt) REVERT: F 128 ARG cc_start: 0.9414 (ttp-110) cc_final: 0.9201 (ttp-110) REVERT: F 141 PHE cc_start: 0.7733 (m-10) cc_final: 0.7519 (m-80) REVERT: F 152 ARG cc_start: 0.5664 (ttt180) cc_final: 0.5444 (ptt90) REVERT: G 152 ARG cc_start: 0.5750 (ttt180) cc_final: 0.5468 (ptt90) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.3223 time to fit residues: 86.7604 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 : 1.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 91 optimal weight: 20.0000 chunk 51 optimal weight: 20.0000 chunk 137 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 45 optimal weight: 0.6980 chunk 165 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 chunk 147 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 332 ASN B 280 ASN B 332 ASN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN C 332 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 332 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 332 ASN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 332 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.3254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15309 Z= 0.188 Angle : 0.799 9.547 20825 Z= 0.384 Chirality : 0.048 0.211 2471 Planarity : 0.007 0.056 2520 Dihedral : 6.149 21.534 1981 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.54 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.93 (0.18), residues: 1827 helix: -1.13 (0.14), residues: 1134 sheet: -4.33 (0.47), residues: 84 loop : -2.99 (0.22), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 127 HIS 0.002 0.001 HIS D 106 PHE 0.020 0.001 PHE C 141 TYR 0.031 0.001 TYR D 234 ARG 0.005 0.000 ARG A 217 *********************** 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 176 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 2.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8261 (mm110) cc_final: 0.7953 (mm110) REVERT: A 128 ARG cc_start: 0.9413 (ttp-110) cc_final: 0.9169 (ttp-110) REVERT: A 141 PHE cc_start: 0.7653 (m-10) cc_final: 0.7389 (m-80) REVERT: A 272 ILE cc_start: 0.9518 (pt) cc_final: 0.9231 (tt) REVERT: B 128 ARG cc_start: 0.9554 (tmm-80) cc_final: 0.9293 (ttp-110) REVERT: C 56 GLN cc_start: 0.8145 (mm110) cc_final: 0.7582 (mm110) REVERT: C 272 ILE cc_start: 0.9472 (pt) cc_final: 0.9269 (tt) REVERT: D 56 GLN cc_start: 0.8392 (mt0) cc_final: 0.8094 (mm110) REVERT: D 141 PHE cc_start: 0.7630 (m-10) cc_final: 0.7399 (m-80) REVERT: D 152 ARG cc_start: 0.5331 (ttt180) cc_final: 0.5036 (ptt90) REVERT: D 217 ARG cc_start: 0.9160 (mtt180) cc_final: 0.8725 (mpp80) REVERT: D 272 ILE cc_start: 0.9479 (pt) cc_final: 0.9203 (tt) REVERT: E 56 GLN cc_start: 0.8181 (mm110) cc_final: 0.7862 (mm110) REVERT: E 128 ARG cc_start: 0.9536 (tmm-80) cc_final: 0.9248 (ttp-110) REVERT: E 272 ILE cc_start: 0.9516 (pt) cc_final: 0.9272 (tt) REVERT: F 56 GLN cc_start: 0.8219 (mt0) cc_final: 0.7966 (mm110) REVERT: F 128 ARG cc_start: 0.9418 (ttp-110) cc_final: 0.9152 (ttp-110) REVERT: F 272 ILE cc_start: 0.9511 (pt) cc_final: 0.9162 (tt) REVERT: G 56 GLN cc_start: 0.8459 (mt0) cc_final: 0.8216 (mm-40) REVERT: G 152 ARG cc_start: 0.5649 (ttt180) cc_final: 0.5404 (ptt90) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.3227 time to fit residues: 83.5108 Evaluate side-chains 125 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 163 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 79 optimal weight: 9.9990 chunk 111 optimal weight: 0.9980 chunk 166 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 157 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 56 GLN ** 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 56 GLN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7525 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15309 Z= 0.187 Angle : 0.774 9.699 20825 Z= 0.371 Chirality : 0.048 0.185 2471 Planarity : 0.007 0.067 2520 Dihedral : 5.821 19.791 1981 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.18 % Allowed : 3.38 % Favored : 96.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.18), residues: 1827 helix: -0.68 (0.14), residues: 1162 sheet: -4.31 (0.51), residues: 84 loop : -2.96 (0.23), residues: 581 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 127 HIS 0.002 0.000 HIS E 106 PHE 0.023 0.001 PHE B 141 TYR 0.018 0.001 TYR B 234 ARG 0.004 0.000 ARG F 217 *********************** 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 176 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 173 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8224 (mm110) cc_final: 0.7920 (mm110) REVERT: A 128 ARG cc_start: 0.9407 (ttp-110) cc_final: 0.9162 (ttp-110) REVERT: B 56 GLN cc_start: 0.8047 (mm110) cc_final: 0.7397 (mm-40) REVERT: B 128 ARG cc_start: 0.9500 (tmm-80) cc_final: 0.9144 (ttp80) REVERT: B 272 ILE cc_start: 0.9445 (pt) cc_final: 0.9166 (pt) REVERT: C 56 GLN cc_start: 0.8119 (mm110) cc_final: 0.7740 (mm-40) REVERT: C 141 PHE cc_start: 0.7484 (m-10) cc_final: 0.7126 (m-80) REVERT: C 272 ILE cc_start: 0.9472 (pt) cc_final: 0.9260 (pt) REVERT: D 56 GLN cc_start: 0.8323 (mt0) cc_final: 0.8039 (mm110) REVERT: D 128 ARG cc_start: 0.9366 (ttp-110) cc_final: 0.9150 (ttp-110) REVERT: D 141 PHE cc_start: 0.7688 (m-10) cc_final: 0.7412 (m-80) REVERT: D 152 ARG cc_start: 0.5262 (ttt180) cc_final: 0.4993 (ptt90) REVERT: D 217 ARG cc_start: 0.9234 (mtt180) cc_final: 0.8632 (mpp80) REVERT: D 272 ILE cc_start: 0.9495 (pt) cc_final: 0.9129 (tt) REVERT: E 52 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.8812 (pp) REVERT: E 128 ARG cc_start: 0.9551 (tmm-80) cc_final: 0.9239 (ttp-110) REVERT: F 128 ARG cc_start: 0.9404 (ttp-110) cc_final: 0.9137 (ttp-110) REVERT: G 122 LEU cc_start: 0.9504 (mt) cc_final: 0.9258 (tt) REVERT: G 152 ARG cc_start: 0.5612 (ttt180) cc_final: 0.5369 (ptt90) REVERT: G 272 ILE cc_start: 0.9514 (pt) cc_final: 0.9182 (tt) REVERT: G 280 ASN cc_start: 0.9060 (t0) cc_final: 0.8715 (t0) outliers start: 3 outliers final: 0 residues processed: 176 average time/residue: 0.2535 time to fit residues: 68.0871 Evaluate side-chains 120 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 119 time to evaluate : 2.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 146 optimal weight: 0.9980 chunk 99 optimal weight: 0.2980 chunk 2 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 150 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 89 optimal weight: 7.9990 chunk 157 optimal weight: 0.5980 chunk 44 optimal weight: 0.0980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 ASN D 56 GLN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 332 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.4219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15309 Z= 0.168 Angle : 0.758 9.565 20825 Z= 0.369 Chirality : 0.046 0.184 2471 Planarity : 0.006 0.054 2520 Dihedral : 5.473 18.980 1981 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.19), residues: 1827 helix: -0.46 (0.15), residues: 1148 sheet: -4.27 (0.50), residues: 84 loop : -2.78 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 127 HIS 0.002 0.000 HIS B 106 PHE 0.032 0.001 PHE E 334 TYR 0.030 0.002 TYR G 234 ARG 0.007 0.000 ARG G 128 *********************** 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 184 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 184 time to evaluate : 1.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.8334 (mm110) cc_final: 0.8041 (mm-40) REVERT: B 56 GLN cc_start: 0.8099 (mm110) cc_final: 0.7436 (mm-40) REVERT: B 128 ARG cc_start: 0.9359 (tmm-80) cc_final: 0.9129 (ttp-110) REVERT: B 272 ILE cc_start: 0.9368 (pt) cc_final: 0.9026 (pt) REVERT: C 56 GLN cc_start: 0.8118 (mm110) cc_final: 0.7741 (mm-40) REVERT: C 128 ARG cc_start: 0.9309 (ttp-110) cc_final: 0.9054 (ttp-110) REVERT: C 272 ILE cc_start: 0.9444 (pt) cc_final: 0.9223 (pt) REVERT: D 128 ARG cc_start: 0.9351 (ttp-110) cc_final: 0.9099 (ttp-110) REVERT: D 141 PHE cc_start: 0.7799 (m-10) cc_final: 0.7434 (m-80) REVERT: D 152 ARG cc_start: 0.5283 (ttt180) cc_final: 0.5006 (ptt90) REVERT: D 217 ARG cc_start: 0.9198 (mtt180) cc_final: 0.8826 (mtm180) REVERT: E 56 GLN cc_start: 0.8034 (mm110) cc_final: 0.7572 (mm-40) REVERT: E 128 ARG cc_start: 0.9575 (tmm-80) cc_final: 0.9283 (ttp-110) REVERT: E 272 ILE cc_start: 0.9388 (pt) cc_final: 0.9138 (pt) REVERT: F 56 GLN cc_start: 0.7924 (mm110) cc_final: 0.7483 (mm-40) REVERT: F 128 ARG cc_start: 0.9377 (ttp-110) cc_final: 0.9097 (ttp-110) REVERT: F 272 ILE cc_start: 0.9504 (pt) cc_final: 0.9274 (pt) REVERT: G 152 ARG cc_start: 0.5540 (ttt180) cc_final: 0.5307 (ptt90) outliers start: 0 outliers final: 0 residues processed: 184 average time/residue: 0.2426 time to fit residues: 69.5258 Evaluate side-chains 127 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 1.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 59 optimal weight: 4.9990 chunk 158 optimal weight: 0.1980 chunk 34 optimal weight: 3.9990 chunk 103 optimal weight: 20.0000 chunk 43 optimal weight: 0.0050 chunk 176 optimal weight: 3.9990 chunk 146 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 58 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 overall best weight: 2.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 207 ASN ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 ASN ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 207 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 ASN ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 207 ASN ** F 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 207 ASN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 207 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 15309 Z= 0.222 Angle : 0.761 9.350 20825 Z= 0.373 Chirality : 0.048 0.191 2471 Planarity : 0.006 0.056 2520 Dihedral : 5.502 18.485 1981 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.19), residues: 1827 helix: -0.12 (0.15), residues: 1155 sheet: -4.42 (0.51), residues: 84 loop : -2.84 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 127 HIS 0.002 0.000 HIS E 106 PHE 0.029 0.001 PHE C 141 TYR 0.026 0.002 TYR G 234 ARG 0.006 0.001 ARG G 128 *********************** 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 163 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 1.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.9418 (ttp-110) cc_final: 0.9158 (ttp-110) REVERT: B 56 GLN cc_start: 0.8247 (mm110) cc_final: 0.7561 (mm-40) REVERT: B 128 ARG cc_start: 0.9424 (tmm-80) cc_final: 0.9198 (ttp-110) REVERT: B 272 ILE cc_start: 0.9418 (pt) cc_final: 0.9045 (pt) REVERT: C 56 GLN cc_start: 0.8248 (mm110) cc_final: 0.7887 (mm-40) REVERT: C 128 ARG cc_start: 0.9333 (ttp-110) cc_final: 0.9036 (ttp-110) REVERT: C 272 ILE cc_start: 0.9535 (pt) cc_final: 0.9194 (pt) REVERT: D 128 ARG cc_start: 0.9377 (ttp-110) cc_final: 0.9152 (ttp-110) REVERT: D 152 ARG cc_start: 0.5321 (ttt180) cc_final: 0.5021 (ptt90) REVERT: D 217 ARG cc_start: 0.9195 (mtt180) cc_final: 0.8667 (mpp80) REVERT: F 56 GLN cc_start: 0.8066 (mm110) cc_final: 0.7572 (mm-40) REVERT: F 128 ARG cc_start: 0.9393 (ttp-110) cc_final: 0.9120 (ttp-110) REVERT: F 272 ILE cc_start: 0.9555 (pt) cc_final: 0.9292 (pt) REVERT: G 56 GLN cc_start: 0.8441 (mm110) cc_final: 0.8072 (mm-40) REVERT: G 152 ARG cc_start: 0.5600 (ttt180) cc_final: 0.5358 (ptt90) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2405 time to fit residues: 60.7598 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 : 2.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 169 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 100 optimal weight: 0.0770 chunk 128 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 148 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 175 optimal weight: 8.9990 chunk 109 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 chunk 80 optimal weight: 8.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.4308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15309 Z= 0.275 Angle : 0.821 10.355 20825 Z= 0.402 Chirality : 0.051 0.231 2471 Planarity : 0.006 0.057 2520 Dihedral : 5.777 21.566 1981 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.30 % Favored : 90.70 % Rotamer: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.20), residues: 1827 helix: -0.07 (0.15), residues: 1183 sheet: -4.55 (0.51), residues: 84 loop : -2.65 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP D 127 HIS 0.003 0.001 HIS A 106 PHE 0.034 0.002 PHE D 141 TYR 0.025 0.002 TYR E 234 ARG 0.004 0.001 ARG G 128 *********************** 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 157 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 157 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.9441 (ttp-110) cc_final: 0.9189 (ttp-110) REVERT: B 128 ARG cc_start: 0.9476 (tmm-80) cc_final: 0.9151 (ttp-110) REVERT: C 56 GLN cc_start: 0.8404 (mm110) cc_final: 0.7891 (mm-40) REVERT: C 272 ILE cc_start: 0.9537 (pt) cc_final: 0.9152 (pt) REVERT: D 128 ARG cc_start: 0.9378 (ttp-110) cc_final: 0.9102 (tmm-80) REVERT: E 56 GLN cc_start: 0.8253 (mm110) cc_final: 0.7661 (mm-40) REVERT: E 128 ARG cc_start: 0.9583 (tmm-80) cc_final: 0.9272 (ttp-110) REVERT: E 272 ILE cc_start: 0.9445 (pt) cc_final: 0.9153 (pt) REVERT: F 56 GLN cc_start: 0.8261 (mm110) cc_final: 0.7675 (mm-40) REVERT: F 128 ARG cc_start: 0.9384 (ttp-110) cc_final: 0.9119 (ttp-110) REVERT: F 272 ILE cc_start: 0.9572 (pt) cc_final: 0.9243 (pt) REVERT: G 56 GLN cc_start: 0.8510 (mm110) cc_final: 0.8180 (mm-40) REVERT: G 152 ARG cc_start: 0.5703 (ttt180) cc_final: 0.5390 (ptt90) outliers start: 0 outliers final: 0 residues processed: 157 average time/residue: 0.2323 time to fit residues: 57.0682 Evaluate side-chains 95 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 108 optimal weight: 0.8980 chunk 70 optimal weight: 7.9990 chunk 104 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 34 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 119 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 16 optimal weight: 7.9990 chunk 137 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 106 HIS ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15309 Z= 0.186 Angle : 0.781 9.543 20825 Z= 0.375 Chirality : 0.049 0.213 2471 Planarity : 0.006 0.089 2520 Dihedral : 5.576 20.513 1981 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.20), residues: 1827 helix: 0.12 (0.15), residues: 1176 sheet: -4.45 (0.51), residues: 84 loop : -2.68 (0.24), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 127 HIS 0.001 0.000 HIS E 106 PHE 0.025 0.001 PHE D 109 TYR 0.023 0.002 TYR B 234 ARG 0.014 0.001 ARG F 254 *********************** 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 174 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 174 time to evaluate : 1.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.9435 (ttp-110) cc_final: 0.9167 (ttp-110) REVERT: B 56 GLN cc_start: 0.8248 (mm110) cc_final: 0.7561 (mm-40) REVERT: B 128 ARG cc_start: 0.9465 (tmm-80) cc_final: 0.9257 (ttp-110) REVERT: B 272 ILE cc_start: 0.9334 (pt) cc_final: 0.9091 (pt) REVERT: C 56 GLN cc_start: 0.8280 (mm110) cc_final: 0.7777 (mm-40) REVERT: C 272 ILE cc_start: 0.9504 (pt) cc_final: 0.9192 (pt) REVERT: D 128 ARG cc_start: 0.9419 (ttp-110) cc_final: 0.9160 (ttp-110) REVERT: E 56 GLN cc_start: 0.8239 (mm110) cc_final: 0.7661 (mm-40) REVERT: E 128 ARG cc_start: 0.9472 (tmm-80) cc_final: 0.9264 (ttp-110) REVERT: E 272 ILE cc_start: 0.9419 (pt) cc_final: 0.9152 (pt) REVERT: F 56 GLN cc_start: 0.8253 (mm110) cc_final: 0.7720 (mm-40) REVERT: F 128 ARG cc_start: 0.9396 (ttp-110) cc_final: 0.9132 (ttp-110) REVERT: F 272 ILE cc_start: 0.9501 (pt) cc_final: 0.9150 (pt) REVERT: G 56 GLN cc_start: 0.8442 (mm110) cc_final: 0.8151 (mm-40) REVERT: G 152 ARG cc_start: 0.5649 (ttt180) cc_final: 0.5346 (ptt90) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.2588 time to fit residues: 69.0832 Evaluate side-chains 108 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 159 optimal weight: 0.4980 chunk 168 optimal weight: 4.9990 chunk 153 optimal weight: 5.9990 chunk 163 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 50 optimal weight: 8.9990 chunk 147 optimal weight: 5.9990 chunk 154 optimal weight: 0.4980 chunk 162 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** F 280 ASN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7492 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15309 Z= 0.173 Angle : 0.772 9.622 20825 Z= 0.368 Chirality : 0.048 0.181 2471 Planarity : 0.006 0.065 2520 Dihedral : 5.414 20.094 1981 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.16 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.20), residues: 1827 helix: 0.27 (0.16), residues: 1127 sheet: -4.38 (0.51), residues: 84 loop : -2.49 (0.23), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 127 HIS 0.001 0.000 HIS B 106 PHE 0.020 0.001 PHE D 109 TYR 0.019 0.001 TYR B 234 ARG 0.008 0.001 ARG F 254 *********************** 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 171 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 1.763 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ARG cc_start: 0.9450 (ttp-110) cc_final: 0.9185 (ttp80) REVERT: B 36 LYS cc_start: 0.8990 (tmmt) cc_final: 0.8654 (tmtt) REVERT: B 128 ARG cc_start: 0.9496 (tmm-80) cc_final: 0.9269 (ttp-110) REVERT: C 56 GLN cc_start: 0.8202 (mm110) cc_final: 0.7757 (mm-40) REVERT: C 272 ILE cc_start: 0.9491 (pt) cc_final: 0.9196 (pt) REVERT: D 128 ARG cc_start: 0.9433 (ttp-110) cc_final: 0.9148 (ttp-110) REVERT: E 37 MET cc_start: 0.7625 (mtp) cc_final: 0.7412 (ttt) REVERT: E 56 GLN cc_start: 0.8256 (mm110) cc_final: 0.7694 (mm-40) REVERT: E 128 ARG cc_start: 0.9477 (tmm-80) cc_final: 0.9261 (ttp-110) REVERT: E 272 ILE cc_start: 0.9386 (pt) cc_final: 0.9102 (pt) REVERT: F 56 GLN cc_start: 0.8189 (mm110) cc_final: 0.7684 (mm-40) REVERT: F 128 ARG cc_start: 0.9399 (ttp-110) cc_final: 0.9122 (ttp-110) REVERT: F 272 ILE cc_start: 0.9479 (pt) cc_final: 0.9106 (pt) REVERT: G 56 GLN cc_start: 0.8447 (mm110) cc_final: 0.8172 (mm-40) REVERT: G 152 ARG cc_start: 0.5534 (ttt180) cc_final: 0.5241 (ptt90) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.2476 time to fit residues: 66.5467 Evaluate side-chains 119 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 1.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 107 optimal weight: 0.4980 chunk 172 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 120 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 280 ASN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.4902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15309 Z= 0.199 Angle : 0.779 9.632 20825 Z= 0.373 Chirality : 0.049 0.198 2471 Planarity : 0.006 0.056 2520 Dihedral : 5.413 19.797 1981 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.20), residues: 1827 helix: 0.37 (0.16), residues: 1134 sheet: -4.50 (0.50), residues: 84 loop : -2.37 (0.24), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 127 HIS 0.002 0.001 HIS E 106 PHE 0.023 0.001 PHE D 109 TYR 0.026 0.002 TYR E 234 ARG 0.008 0.001 ARG D 217 ********************** 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 166 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 36 LYS cc_start: 0.9075 (tmmt) cc_final: 0.8675 (tmtt) REVERT: B 128 ARG cc_start: 0.9514 (tmm-80) cc_final: 0.9265 (ttp-110) REVERT: C 56 GLN cc_start: 0.8352 (mm110) cc_final: 0.7945 (mm-40) REVERT: C 217 ARG cc_start: 0.8867 (ttm170) cc_final: 0.8260 (mtp85) REVERT: C 272 ILE cc_start: 0.9507 (pt) cc_final: 0.9186 (pt) REVERT: D 128 ARG cc_start: 0.9425 (ttp-110) cc_final: 0.9109 (ttp-110) REVERT: E 56 GLN cc_start: 0.8291 (mm110) cc_final: 0.7676 (mm-40) REVERT: E 128 ARG cc_start: 0.9494 (tmm-80) cc_final: 0.9284 (ttp-110) REVERT: E 272 ILE cc_start: 0.9398 (pt) cc_final: 0.9100 (pt) REVERT: F 56 GLN cc_start: 0.8216 (mm110) cc_final: 0.7749 (mm-40) REVERT: F 128 ARG cc_start: 0.9386 (ttp-110) cc_final: 0.9116 (ttp-110) REVERT: F 272 ILE cc_start: 0.9475 (pt) cc_final: 0.9099 (pt) REVERT: G 56 GLN cc_start: 0.8407 (mm110) cc_final: 0.8169 (mm-40) REVERT: G 152 ARG cc_start: 0.5573 (ttt180) cc_final: 0.5261 (ptt90) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.2807 time to fit residues: 71.8572 Evaluate side-chains 108 residues out of total 1687 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 182 random chunks: chunk 114 optimal weight: 6.9990 chunk 153 optimal weight: 8.9990 chunk 44 optimal weight: 0.7980 chunk 133 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 60 optimal weight: 0.0270 chunk 148 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 overall best weight: 1.2442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** F 280 ASN ** G 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 280 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.099454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.078324 restraints weight = 63777.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.080103 restraints weight = 41309.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.081233 restraints weight = 30727.510| |-----------------------------------------------------------------------------| r_work (final): 0.3726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.5075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 15309 Z= 0.169 Angle : 0.774 10.463 20825 Z= 0.369 Chirality : 0.048 0.226 2471 Planarity : 0.006 0.055 2520 Dihedral : 5.281 19.397 1981 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.20), residues: 1827 helix: 0.40 (0.15), residues: 1127 sheet: -4.44 (0.51), residues: 84 loop : -2.40 (0.24), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 127 HIS 0.003 0.000 HIS B 106 PHE 0.022 0.001 PHE A 109 TYR 0.023 0.001 TYR E 234 ARG 0.007 0.000 ARG D 217 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2521.05 seconds wall clock time: 48 minutes 36.93 seconds (2916.93 seconds total)