Starting phenix.real_space_refine on Thu Jun 4 17:09:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zhr_60114/06_2026/8zhr_60114.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zhr_60114/06_2026/8zhr_60114.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zhr_60114/06_2026/8zhr_60114.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zhr_60114/06_2026/8zhr_60114.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zhr_60114/06_2026/8zhr_60114.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zhr_60114/06_2026/8zhr_60114.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 72 5.16 5 C 8883 2.51 5 N 2436 2.21 5 O 2612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14005 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2261 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 280} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 3946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3946 Classifications: {'peptide': 493} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 462} Chain: "F" Number of atoms: 3837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3837 Classifications: {'peptide': 485} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 3, 'PTRANS': 22, 'TRANS': 459} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "A" Number of atoms: 3946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3946 Classifications: {'peptide': 493} Link IDs: {'PCIS': 3, 'PTRANS': 27, 'TRANS': 462} Chain: "F" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'H6P': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.93, per 1000 atoms: 0.21 Number of scatterers: 14005 At special positions: 0 Unit cell: (95.04, 141.12, 251.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 72 16.00 P 2 15.00 O 2612 8.00 N 2436 7.00 C 8883 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 126 " distance=2.03 Simple disulfide: pdb=" SG CYS E 166 " - pdb=" SG CYS E 220 " distance=2.03 Simple disulfide: pdb=" SG CYS B 51 " - pdb=" SG CYS B 125 " distance=2.03 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 219 " distance=2.03 Simple disulfide: pdb=" SG CYS B 247 " - pdb=" SG CYS A 247 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS A 265 " distance=2.02 Simple disulfide: pdb=" SG CYS F 52 " - pdb=" SG CYS F 126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 166 " - pdb=" SG CYS F 220 " distance=2.03 Simple disulfide: pdb=" SG CYS A 51 " - pdb=" SG CYS A 125 " distance=2.04 Simple disulfide: pdb=" SG CYS A 165 " - pdb=" SG CYS A 219 " 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: 1.25 Conformation dependent library (CDL) restraints added in 673.4 milliseconds 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3278 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 23 sheets defined 22.9% alpha, 32.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'E' and resid 90 through 94 removed outlier: 3.768A pdb=" N ARG E 94 " --> pdb=" O ALA E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 106 Processing helix chain 'E' and resid 117 through 121 Processing helix chain 'E' and resid 239 through 243 Processing helix chain 'E' and resid 245 through 322 Proline residue: E 257 - end of helix Processing helix chain 'B' and resid 102 through 105 Processing helix chain 'B' and resid 116 through 120 Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 245 through 323 removed outlier: 3.977A pdb=" N VAL B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) Proline residue: B 252 - end of helix Proline residue: B 261 - end of helix removed outlier: 3.872A pdb=" N THR B 323 " --> pdb=" O ARG B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 419 Processing helix chain 'B' and resid 436 through 440 removed outlier: 4.002A pdb=" N ILE B 440 " --> pdb=" O PRO B 437 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 107 Processing helix chain 'F' and resid 117 through 121 Processing helix chain 'F' and resid 239 through 243 removed outlier: 3.632A pdb=" N ARG F 243 " --> pdb=" O PRO F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 319 Proline residue: F 257 - end of helix removed outlier: 3.885A pdb=" N ILE F 317 " --> pdb=" O ARG F 313 " (cutoff:3.500A) Processing helix chain 'F' and resid 325 through 337 Processing helix chain 'F' and resid 425 through 428 Processing helix chain 'A' and resid 85 through 88 removed outlier: 3.576A pdb=" N GLN A 88 " --> pdb=" O THR A 85 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 85 through 88' Processing helix chain 'A' and resid 103 through 106 Processing helix chain 'A' and resid 116 through 120 Processing helix chain 'A' and resid 237 through 241 Processing helix chain 'A' and resid 246 through 322 Proline residue: A 252 - end of helix Proline residue: A 261 - end of helix Processing helix chain 'A' and resid 416 through 419 Processing sheet with id=AA1, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AA2, first strand: chain 'E' and resid 40 through 43 removed outlier: 6.257A pdb=" N SER E 69 " --> pdb=" O VAL E 75 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N VAL E 75 " --> pdb=" O SER E 69 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 190 through 191 removed outlier: 6.789A pdb=" N VAL E 204 " --> pdb=" O THR E 169 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N THR E 169 " --> pdb=" O VAL E 204 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N ALA E 206 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N ARG E 167 " --> pdb=" O ALA E 206 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL E 208 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLU E 165 " --> pdb=" O VAL E 208 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N MET E 210 " --> pdb=" O HIS E 163 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N HIS E 163 " --> pdb=" O MET E 210 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY E 156 " --> pdb=" O HIS E 163 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N GLU E 165 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N VAL E 154 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ARG E 167 " --> pdb=" O VAL E 152 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL E 152 " --> pdb=" O ARG E 167 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N TRP F 179 " --> pdb=" O ILE F 187 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 186 through 187 removed outlier: 4.146A pdb=" N TRP E 179 " --> pdb=" O ILE E 187 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU E 229 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N VAL F 152 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER E 234 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL F 154 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N SER E 236 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY F 156 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VAL F 152 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ARG F 167 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL F 154 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLU F 165 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY F 156 " --> pdb=" O HIS F 163 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TYR F 202 " --> pdb=" O GLY F 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 186 through 187 removed outlier: 4.146A pdb=" N TRP E 179 " --> pdb=" O ILE E 187 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU E 229 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N VAL F 152 " --> pdb=" O THR E 232 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N SER E 234 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N VAL F 154 " --> pdb=" O SER E 234 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N SER E 236 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLY F 156 " --> pdb=" O SER E 236 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N VAL F 152 " --> pdb=" O ARG F 167 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ARG F 167 " --> pdb=" O VAL F 152 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N VAL F 154 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLU F 165 " --> pdb=" O VAL F 154 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLY F 156 " --> pdb=" O HIS F 163 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N TYR F 202 " --> pdb=" O GLY F 170 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL F 195 " --> pdb=" O ALA F 203 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 32 through 33 Processing sheet with id=AA7, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA8, first strand: chain 'B' and resid 150 through 156 removed outlier: 5.407A pdb=" N ARG B 162 " --> pdb=" O ARG B 154 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ARG B 162 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 209 " --> pdb=" O ARG B 162 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU B 164 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL B 207 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ILE B 166 " --> pdb=" O THR B 205 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N THR B 205 " --> pdb=" O ILE B 166 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ARG B 168 " --> pdb=" O VAL B 203 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL B 203 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 185 through 186 removed outlier: 4.202A pdb=" N TRP B 178 " --> pdb=" O ALA B 186 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 341 through 343 removed outlier: 6.204A pdb=" N HIS B 326 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N GLU B 389 " --> pdb=" O HIS B 326 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A 325 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU A 389 " --> pdb=" O CYS A 500 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 516 through 517 removed outlier: 6.496A pdb=" N PHE A 463 " --> pdb=" O ILE A 472 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N THR A 474 " --> pdb=" O VAL A 461 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL A 461 " --> pdb=" O THR A 474 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A 325 " --> pdb=" O ALA B 327 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N HIS B 326 " --> pdb=" O TYR B 387 " (cutoff:3.500A) removed outlier: 8.540A pdb=" N GLU B 389 " --> pdb=" O HIS B 326 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL B 461 " --> pdb=" O THR B 474 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR B 474 " --> pdb=" O VAL B 461 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N PHE B 463 " --> pdb=" O ILE B 472 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 374 through 376 removed outlier: 3.635A pdb=" N TRP B 398 " --> pdb=" O MET B 426 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 32 through 34 removed outlier: 3.981A pdb=" N GLY F 103 " --> pdb=" O LYS F 108 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N ALA F 110 " --> pdb=" O ARG F 101 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N ARG F 101 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG F 112 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ILE F 99 " --> pdb=" O ARG F 112 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 40 through 42 removed outlier: 6.037A pdb=" N ILE F 40 " --> pdb=" O LYS F 142 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU F 65 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL F 78 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N TRP F 67 " --> pdb=" O VAL F 76 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 338 through 339 Processing sheet with id=AB7, first strand: chain 'F' and resid 338 through 339 removed outlier: 5.899A pdb=" N ASN F 475 " --> pdb=" O HIS F 481 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N HIS F 481 " --> pdb=" O ASN F 475 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 383 through 385 removed outlier: 4.435A pdb=" N TYR F 441 " --> pdb=" O LEU F 451 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 31 through 33 removed outlier: 7.540A pdb=" N SER A 107 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS A 101 " --> pdb=" O SER A 107 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AC2, first strand: chain 'A' and resid 150 through 157 removed outlier: 5.911A pdb=" N ARG A 162 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N HIS A 156 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N GLY A 160 " --> pdb=" O HIS A 156 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N GLU A 164 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N VAL A 207 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 5.341A pdb=" N ILE A 166 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR A 205 " --> pdb=" O ILE A 166 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ARG A 168 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N VAL A 203 " --> pdb=" O ARG A 168 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 175 through 177 Processing sheet with id=AC4, first strand: chain 'A' and resid 216 through 217 Processing sheet with id=AC5, first strand: chain 'A' and resid 374 through 376 698 hydrogen bonds defined for protein. 1827 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: 2.87 Time building geometry restraints manager: 1.65 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: 4637 1.34 - 1.46: 2768 1.46 - 1.58: 6809 1.58 - 1.69: 3 1.69 - 1.81: 106 Bond restraints: 14323 Sorted by residual: bond pdb=" O16 H6P F 601 " pdb=" P17 H6P F 601 " ideal model delta sigma weight residual 1.697 1.641 0.056 2.00e-02 2.50e+03 7.71e+00 bond pdb=" O16 H6P F 601 " pdb=" P13 H6P F 601 " ideal model delta sigma weight residual 1.594 1.642 -0.048 2.00e-02 2.50e+03 5.78e+00 bond pdb=" C28 H6P F 601 " pdb=" O29 H6P F 601 " ideal model delta sigma weight residual 1.442 1.397 0.045 2.00e-02 2.50e+03 5.00e+00 bond pdb=" C31 H6P F 601 " pdb=" O33 H6P F 601 " ideal model delta sigma weight residual 1.440 1.398 0.042 2.00e-02 2.50e+03 4.46e+00 bond pdb=" CB CYS B 265 " pdb=" SG CYS B 265 " ideal model delta sigma weight residual 1.808 1.748 0.060 3.30e-02 9.18e+02 3.31e+00 ... (remaining 14318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 19171 2.16 - 4.32: 210 4.32 - 6.48: 18 6.48 - 8.64: 2 8.64 - 10.80: 3 Bond angle restraints: 19404 Sorted by residual: angle pdb=" C GLY E 131 " pdb=" N ASP E 132 " pdb=" CA ASP E 132 " ideal model delta sigma weight residual 121.70 130.89 -9.19 1.80e+00 3.09e-01 2.61e+01 angle pdb=" N VAL A 256 " pdb=" CA VAL A 256 " pdb=" C VAL A 256 " ideal model delta sigma weight residual 112.35 106.58 5.77 1.41e+00 5.03e-01 1.67e+01 angle pdb=" N LEU B 258 " pdb=" CA LEU B 258 " pdb=" C LEU B 258 " ideal model delta sigma weight residual 111.82 116.21 -4.39 1.16e+00 7.43e-01 1.44e+01 angle pdb=" N ILE B 257 " pdb=" CA ILE B 257 " pdb=" C ILE B 257 " ideal model delta sigma weight residual 110.36 106.47 3.89 1.05e+00 9.07e-01 1.37e+01 angle pdb=" P13 H6P F 601 " pdb=" O16 H6P F 601 " pdb=" P17 H6P F 601 " ideal model delta sigma weight residual 135.28 124.48 10.80 3.00e+00 1.11e-01 1.30e+01 ... (remaining 19399 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.17: 8292 31.17 - 62.33: 360 62.33 - 93.50: 37 93.50 - 124.67: 0 124.67 - 155.83: 2 Dihedral angle restraints: 8691 sinusoidal: 3598 harmonic: 5093 Sorted by residual: dihedral pdb=" CB CYS E 52 " pdb=" SG CYS E 52 " pdb=" SG CYS E 126 " pdb=" CB CYS E 126 " ideal model delta sinusoidal sigma weight residual 93.00 163.69 -70.69 1 1.00e+01 1.00e-02 6.42e+01 dihedral pdb=" CB CYS F 52 " pdb=" SG CYS F 52 " pdb=" SG CYS F 126 " pdb=" CB CYS F 126 " ideal model delta sinusoidal sigma weight residual 93.00 145.75 -52.75 1 1.00e+01 1.00e-02 3.79e+01 dihedral pdb=" CB CYS B 265 " pdb=" SG CYS B 265 " pdb=" SG CYS A 265 " pdb=" CB CYS A 265 " ideal model delta sinusoidal sigma weight residual 93.00 131.45 -38.45 1 1.00e+01 1.00e-02 2.08e+01 ... (remaining 8688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1485 0.039 - 0.079: 425 0.079 - 0.118: 184 0.118 - 0.158: 26 0.158 - 0.197: 1 Chirality restraints: 2121 Sorted by residual: chirality pdb=" CA ILE B 257 " pdb=" N ILE B 257 " pdb=" C ILE B 257 " pdb=" CB ILE B 257 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.70e-01 chirality pdb=" CA ILE F 343 " pdb=" N ILE F 343 " pdb=" C ILE F 343 " pdb=" CB ILE F 343 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE E 221 " pdb=" N ILE E 221 " pdb=" C ILE E 221 " pdb=" CB ILE E 221 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 2118 not shown) Planarity restraints: 2514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 436 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO B 437 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO B 437 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 437 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 260 " 0.034 5.00e-02 4.00e+02 5.19e-02 4.31e+00 pdb=" N PRO B 261 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 186 " 0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 187 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 187 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 187 " 0.026 5.00e-02 4.00e+02 ... (remaining 2511 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 86 2.46 - 3.07: 9652 3.07 - 3.68: 21429 3.68 - 4.29: 32005 4.29 - 4.90: 55160 Nonbonded interactions: 118332 Sorted by model distance: nonbonded pdb=" OH TYR B 126 " pdb=" NE2 GLN B 128 " model vdw 1.855 3.120 nonbonded pdb=" OG1 THR E 232 " pdb=" OD2 ASP F 149 " model vdw 2.126 3.040 nonbonded pdb=" OH TYR E 134 " pdb=" OE1 GLU B 63 " model vdw 2.147 3.040 nonbonded pdb=" O GLU F 86 " pdb=" NH1 ARG F 94 " model vdw 2.163 3.120 nonbonded pdb=" N GLU E 86 " pdb=" OE1 GLU E 86 " model vdw 2.165 3.120 ... (remaining 118327 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.160 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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 : 0.004 0.060 14333 Z= 0.166 Angle : 0.584 10.796 19424 Z= 0.309 Chirality : 0.044 0.197 2121 Planarity : 0.004 0.062 2514 Dihedral : 16.852 155.834 5383 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.59 % Favored : 96.30 % Rotamer: Outliers : 0.20 % Allowed : 19.52 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.20), residues: 1757 helix: 3.21 (0.28), residues: 304 sheet: -0.83 (0.21), residues: 549 loop : -0.61 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 301 TYR 0.012 0.001 TYR B 126 PHE 0.018 0.001 PHE A 67 TRP 0.013 0.001 TRP F 332 HIS 0.005 0.001 HIS F 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (14323) covalent geometry : angle 0.58150 / 0.31 (19404) SS BOND : bond 0.00568 / 0.43 ( 10) SS BOND : angle 1.86236 / 1.19 ( 20) hydrogen bonds : bond 0.11818 / 7.85 ( 669) hydrogen bonds : angle 6.07783 / 4.19 ( 1827) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 207 time to evaluate : 0.574 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: F 150 LEU cc_start: 0.7982 (mp) cc_final: 0.7740 (mp) outliers start: 3 outliers final: 1 residues processed: 209 average time/residue: 0.6836 time to fit residues: 155.3064 Evaluate side-chains 100 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 99 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 GLN A 273 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.111277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.077867 restraints weight = 40761.110| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 4.20 r_work: 0.3266 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14333 Z= 0.167 Angle : 0.657 14.070 19424 Z= 0.333 Chirality : 0.045 0.237 2121 Planarity : 0.005 0.068 2514 Dihedral : 6.603 120.617 1952 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.24 % Favored : 96.64 % Rotamer: Outliers : 3.54 % Allowed : 21.48 % Favored : 74.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.20), residues: 1757 helix: 3.54 (0.26), residues: 305 sheet: -0.76 (0.20), residues: 570 loop : -0.47 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 94 TYR 0.015 0.002 TYR E 127 PHE 0.016 0.002 PHE F 128 TRP 0.021 0.002 TRP F 67 HIS 0.007 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (14323) covalent geometry : angle 0.65674 / 0.33 (19404) SS BOND : bond 0.00751 / 0.57 ( 10) SS BOND : angle 1.00675 / 0.58 ( 20) hydrogen bonds : bond 0.03920 / 2.63 ( 669) hydrogen bonds : angle 5.04705 / 3.55 ( 1827) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 117 time to evaluate : 0.530 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: B 134 ASP cc_start: 0.8130 (t0) cc_final: 0.7845 (t0) REVERT: B 202 MET cc_start: 0.8573 (mtt) cc_final: 0.8340 (mtt) REVERT: B 378 ARG cc_start: 0.8695 (ttm170) cc_final: 0.8464 (ttp-110) REVERT: B 416 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8418 (pp) REVERT: F 43 MET cc_start: 0.7565 (mmm) cc_final: 0.7182 (mmm) REVERT: F 49 ASP cc_start: 0.8126 (OUTLIER) cc_final: 0.7924 (t0) REVERT: F 202 TYR cc_start: 0.8161 (m-80) cc_final: 0.7915 (m-80) REVERT: F 281 PHE cc_start: 0.9192 (t80) cc_final: 0.8856 (t80) REVERT: F 282 ARG cc_start: 0.9167 (mmt-90) cc_final: 0.8590 (mmt-90) REVERT: F 414 LYS cc_start: 0.9068 (OUTLIER) cc_final: 0.8618 (ttmm) REVERT: A 89 MET cc_start: 0.8672 (mmm) cc_final: 0.8177 (mmt) REVERT: A 92 TYR cc_start: 0.7927 (m-80) cc_final: 0.7593 (m-80) REVERT: A 202 MET cc_start: 0.7056 (OUTLIER) cc_final: 0.6694 (ppp) outliers start: 54 outliers final: 19 residues processed: 158 average time/residue: 0.5482 time to fit residues: 95.6593 Evaluate side-chains 114 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 91 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 426 MET Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 390 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 14 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 15 optimal weight: 0.2980 chunk 95 optimal weight: 5.9990 chunk 173 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 156 optimal weight: 0.7980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 182 ASN F 326 HIS A 365 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.107581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.072786 restraints weight = 41082.148| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 4.37 r_work: 0.3156 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 14333 Z= 0.245 Angle : 0.660 8.741 19424 Z= 0.338 Chirality : 0.046 0.169 2121 Planarity : 0.005 0.064 2514 Dihedral : 6.668 122.644 1952 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.96 % Favored : 96.93 % Rotamer: Outliers : 4.19 % Allowed : 21.55 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.20), residues: 1757 helix: 3.76 (0.26), residues: 305 sheet: -0.62 (0.20), residues: 567 loop : -0.50 (0.21), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 211 TYR 0.016 0.002 TYR A 387 PHE 0.033 0.002 PHE A 67 TRP 0.019 0.002 TRP F 332 HIS 0.005 0.001 HIS A 427 Details of bonding type rmsd/Z covalent geometry : bond 0.00551 / 0.25 (14323) covalent geometry : angle 0.65871 / 0.34 (19404) SS BOND : bond 0.00455 / 0.31 ( 10) SS BOND : angle 1.20801 / 0.70 ( 20) hydrogen bonds : bond 0.03879 / 2.65 ( 669) hydrogen bonds : angle 5.12418 / 3.59 ( 1827) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 87 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 43 MET cc_start: 0.9148 (mmm) cc_final: 0.8843 (mmm) REVERT: B 70 GLN cc_start: 0.8817 (pt0) cc_final: 0.8562 (pt0) REVERT: B 134 ASP cc_start: 0.8278 (t0) cc_final: 0.7922 (t0) REVERT: B 202 MET cc_start: 0.8572 (mtt) cc_final: 0.8360 (mtt) REVERT: B 319 ARG cc_start: 0.8882 (tmm160) cc_final: 0.8485 (ttp-110) REVERT: F 43 MET cc_start: 0.7824 (mmm) cc_final: 0.7424 (mmm) REVERT: F 49 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7845 (t0) REVERT: F 63 MET cc_start: 0.4488 (OUTLIER) cc_final: 0.4277 (tpp) REVERT: F 67 TRP cc_start: 0.6699 (m100) cc_final: 0.6321 (m100) REVERT: F 281 PHE cc_start: 0.9190 (t80) cc_final: 0.8820 (t80) REVERT: F 282 ARG cc_start: 0.9155 (mmt-90) cc_final: 0.8575 (mmt-90) REVERT: F 293 MET cc_start: 0.9146 (mmm) cc_final: 0.8862 (pp-130) REVERT: F 414 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8577 (ttmm) REVERT: A 53 LEU cc_start: -0.1384 (OUTLIER) cc_final: -0.2058 (mt) REVERT: A 202 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.7079 (ppp) REVERT: A 312 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8586 (tm-30) outliers start: 64 outliers final: 20 residues processed: 141 average time/residue: 0.4837 time to fit residues: 76.1794 Evaluate side-chains 99 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 90 optimal weight: 0.7980 chunk 146 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 173 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 167 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 119 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 350 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.124449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.089901 restraints weight = 40437.039| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 4.32 r_work: 0.3197 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14333 Z= 0.146 Angle : 0.610 14.631 19424 Z= 0.306 Chirality : 0.045 0.232 2121 Planarity : 0.005 0.065 2514 Dihedral : 6.278 112.393 1952 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 4.06 % Allowed : 22.27 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.20), residues: 1757 helix: 3.83 (0.27), residues: 305 sheet: -0.54 (0.20), residues: 575 loop : -0.39 (0.21), residues: 877 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 286 TYR 0.017 0.001 TYR A 387 PHE 0.026 0.001 PHE A 67 TRP 0.019 0.001 TRP F 332 HIS 0.003 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (14323) covalent geometry : angle 0.60854 / 0.31 (19404) SS BOND : bond 0.00409 / 0.29 ( 10) SS BOND : angle 1.23017 / 0.76 ( 20) hydrogen bonds : bond 0.03509 / 2.40 ( 669) hydrogen bonds : angle 4.97034 / 3.49 ( 1827) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 88 time to evaluate : 0.573 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: E 43 MET cc_start: 0.9108 (mmm) cc_final: 0.8810 (mmm) REVERT: E 246 GLN cc_start: 0.8246 (OUTLIER) cc_final: 0.7971 (tm-30) REVERT: B 70 GLN cc_start: 0.8757 (pt0) cc_final: 0.8518 (pt0) REVERT: B 105 ARG cc_start: 0.8845 (mtm-85) cc_final: 0.8389 (pmm-80) REVERT: B 202 MET cc_start: 0.8565 (mtt) cc_final: 0.8356 (mtt) REVERT: B 279 LEU cc_start: 0.6686 (OUTLIER) cc_final: 0.6419 (tp) REVERT: B 319 ARG cc_start: 0.8898 (tmm160) cc_final: 0.8473 (ttp-110) REVERT: F 43 MET cc_start: 0.7963 (mmm) cc_final: 0.7567 (mmm) REVERT: F 49 ASP cc_start: 0.8320 (OUTLIER) cc_final: 0.7871 (t0) REVERT: F 63 MET cc_start: 0.4162 (OUTLIER) cc_final: 0.3939 (tpp) REVERT: F 259 LEU cc_start: 0.6074 (OUTLIER) cc_final: 0.5809 (tp) REVERT: F 293 MET cc_start: 0.9163 (mmm) cc_final: 0.8889 (pp-130) REVERT: F 414 LYS cc_start: 0.9058 (OUTLIER) cc_final: 0.8608 (ttmm) REVERT: A 53 LEU cc_start: -0.2307 (OUTLIER) cc_final: -0.2511 (mt) REVERT: A 89 MET cc_start: 0.7747 (mmt) cc_final: 0.7469 (mmt) REVERT: A 92 TYR cc_start: 0.7854 (m-80) cc_final: 0.7610 (m-80) REVERT: A 153 MET cc_start: 0.8986 (mtm) cc_final: 0.8757 (mtt) REVERT: A 202 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.6928 (ppp) REVERT: A 217 MET cc_start: 0.8030 (mmm) cc_final: 0.7825 (mmm) REVERT: A 312 GLU cc_start: 0.8820 (mm-30) cc_final: 0.8554 (tm-30) REVERT: A 416 ILE cc_start: 0.8893 (OUTLIER) cc_final: 0.8645 (pp) outliers start: 62 outliers final: 23 residues processed: 136 average time/residue: 0.4962 time to fit residues: 75.5587 Evaluate side-chains 113 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 81 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain F residue 49 ASP Chi-restraints excluded: chain F residue 63 MET Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 416 ILE Chi-restraints excluded: chain A residue 450 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 2 optimal weight: 6.9990 chunk 34 optimal weight: 0.4980 chunk 88 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 13 optimal weight: 0.1980 chunk 80 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 48 optimal weight: 0.6980 chunk 133 optimal weight: 50.0000 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** F 374 ASN ** 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 = 0.4118 r_free = 0.4118 target = 0.124017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.088780 restraints weight = 40399.808| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 4.50 r_work: 0.3168 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 14333 Z= 0.157 Angle : 0.608 11.370 19424 Z= 0.301 Chirality : 0.045 0.217 2121 Planarity : 0.005 0.064 2514 Dihedral : 6.082 106.685 1952 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 3.86 % Allowed : 22.72 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.20), residues: 1757 helix: 3.87 (0.26), residues: 304 sheet: -0.43 (0.20), residues: 569 loop : -0.36 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG E 322 TYR 0.016 0.001 TYR A 387 PHE 0.021 0.001 PHE A 67 TRP 0.019 0.001 TRP F 332 HIS 0.003 0.001 HIS F 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.16 (14323) covalent geometry : angle 0.60747 / 0.30 (19404) SS BOND : bond 0.00401 / 0.29 ( 10) SS BOND : angle 1.16846 / 0.68 ( 20) hydrogen bonds : bond 0.03451 / 2.38 ( 669) hydrogen bonds : angle 4.88478 / 3.43 ( 1827) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 85 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 43 MET cc_start: 0.9108 (mmm) cc_final: 0.8851 (mmm) REVERT: E 190 VAL cc_start: 0.9460 (OUTLIER) cc_final: 0.9161 (p) REVERT: E 246 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7966 (tm-30) REVERT: B 70 GLN cc_start: 0.8820 (pt0) cc_final: 0.8564 (pt0) REVERT: B 134 ASP cc_start: 0.8200 (t0) cc_final: 0.7855 (t0) REVERT: B 135 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8332 (pt0) REVERT: B 202 MET cc_start: 0.8552 (mtt) cc_final: 0.8345 (mtt) REVERT: B 279 LEU cc_start: 0.6716 (OUTLIER) cc_final: 0.6436 (tp) REVERT: B 282 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8223 (tp30) REVERT: B 319 ARG cc_start: 0.8932 (tmm160) cc_final: 0.8485 (ttp-110) REVERT: F 43 MET cc_start: 0.8011 (mmm) cc_final: 0.7636 (mmm) REVERT: F 58 MET cc_start: 0.6949 (pp-130) cc_final: 0.6488 (pp-130) REVERT: F 63 MET cc_start: 0.4233 (ttp) cc_final: 0.4025 (tpp) REVERT: F 259 LEU cc_start: 0.6186 (OUTLIER) cc_final: 0.5776 (tt) REVERT: F 293 MET cc_start: 0.9138 (mmm) cc_final: 0.8890 (pp-130) REVERT: A 92 TYR cc_start: 0.7863 (m-80) cc_final: 0.7652 (m-80) REVERT: A 202 MET cc_start: 0.7250 (OUTLIER) cc_final: 0.7037 (ppp) REVERT: A 217 MET cc_start: 0.8053 (mmm) cc_final: 0.7838 (mmm) REVERT: A 312 GLU cc_start: 0.8832 (mm-30) cc_final: 0.8515 (tm-30) outliers start: 59 outliers final: 33 residues processed: 133 average time/residue: 0.4684 time to fit residues: 70.3151 Evaluate side-chains 121 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 81 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 135 GLU Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 268 TRP Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 371 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 450 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 153 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 117 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 158 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 66 optimal weight: 0.6980 chunk 73 optimal weight: 0.9980 chunk 41 optimal weight: 0.0670 chunk 78 optimal weight: 20.0000 chunk 67 optimal weight: 4.9990 overall best weight: 1.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.107071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.072406 restraints weight = 40686.300| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 4.23 r_work: 0.3154 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14333 Z= 0.213 Angle : 0.635 11.465 19424 Z= 0.314 Chirality : 0.045 0.181 2121 Planarity : 0.005 0.063 2514 Dihedral : 6.198 109.955 1952 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.41 % Favored : 96.53 % Rotamer: Outliers : 4.26 % Allowed : 22.72 % Favored : 73.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.20), residues: 1757 helix: 3.82 (0.27), residues: 305 sheet: -0.44 (0.20), residues: 570 loop : -0.36 (0.21), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 322 TYR 0.017 0.002 TYR A 387 PHE 0.025 0.002 PHE F 281 TRP 0.019 0.002 TRP F 332 HIS 0.004 0.001 HIS F 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.21 (14323) covalent geometry : angle 0.63380 / 0.31 (19404) SS BOND : bond 0.00448 / 0.31 ( 10) SS BOND : angle 1.22704 / 0.72 ( 20) hydrogen bonds : bond 0.03501 / 2.43 ( 669) hydrogen bonds : angle 4.98273 / 3.49 ( 1827) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 85 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 58 MET cc_start: 0.9208 (ptp) cc_final: 0.8931 (ptp) REVERT: E 190 VAL cc_start: 0.9477 (OUTLIER) cc_final: 0.9195 (p) REVERT: E 246 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7977 (tm-30) REVERT: E 293 MET cc_start: 0.8843 (ppp) cc_final: 0.8563 (ppp) REVERT: B 70 GLN cc_start: 0.8845 (pt0) cc_final: 0.8562 (pt0) REVERT: B 105 ARG cc_start: 0.8790 (mtm-85) cc_final: 0.8567 (mtm-85) REVERT: B 279 LEU cc_start: 0.6773 (OUTLIER) cc_final: 0.6490 (tp) REVERT: B 282 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8238 (tp30) REVERT: B 319 ARG cc_start: 0.8909 (tmm160) cc_final: 0.8513 (ttp-110) REVERT: F 43 MET cc_start: 0.8060 (mmm) cc_final: 0.7712 (mmm) REVERT: F 58 MET cc_start: 0.7012 (pp-130) cc_final: 0.6612 (pp-130) REVERT: F 259 LEU cc_start: 0.6214 (OUTLIER) cc_final: 0.5828 (tt) REVERT: F 293 MET cc_start: 0.9143 (mmm) cc_final: 0.8913 (pp-130) REVERT: F 414 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8639 (ttmm) REVERT: A 92 TYR cc_start: 0.7874 (m-80) cc_final: 0.7659 (m-80) REVERT: A 217 MET cc_start: 0.8104 (mmm) cc_final: 0.7860 (mmm) outliers start: 65 outliers final: 36 residues processed: 139 average time/residue: 0.5088 time to fit residues: 79.1451 Evaluate side-chains 119 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 77 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 268 TRP Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain F residue 492 GLU Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 450 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 17 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 160 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 29 optimal weight: 0.0670 overall best weight: 1.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.122707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.086536 restraints weight = 40275.803| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 4.34 r_work: 0.3147 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14333 Z= 0.184 Angle : 0.639 13.875 19424 Z= 0.315 Chirality : 0.045 0.171 2121 Planarity : 0.005 0.063 2514 Dihedral : 6.181 109.715 1952 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 3.99 % Allowed : 23.77 % Favored : 72.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.20), residues: 1757 helix: 3.91 (0.27), residues: 304 sheet: -0.39 (0.21), residues: 564 loop : -0.37 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 322 TYR 0.019 0.001 TYR A 387 PHE 0.018 0.001 PHE A 67 TRP 0.018 0.001 TRP F 332 HIS 0.004 0.001 HIS F 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (14323) covalent geometry : angle 0.63854 / 0.31 (19404) SS BOND : bond 0.00409 / 0.29 ( 10) SS BOND : angle 1.21371 / 0.71 ( 20) hydrogen bonds : bond 0.03430 / 2.36 ( 669) hydrogen bonds : angle 4.91220 / 3.43 ( 1827) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 82 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 58 MET cc_start: 0.9239 (ptp) cc_final: 0.8954 (ptp) REVERT: E 190 VAL cc_start: 0.9485 (OUTLIER) cc_final: 0.9205 (p) REVERT: E 246 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: B 70 GLN cc_start: 0.8835 (pt0) cc_final: 0.8544 (pt0) REVERT: B 105 ARG cc_start: 0.8847 (mtm-85) cc_final: 0.8631 (mtm-85) REVERT: B 279 LEU cc_start: 0.6777 (OUTLIER) cc_final: 0.6506 (tp) REVERT: B 282 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8229 (tp30) REVERT: B 319 ARG cc_start: 0.8923 (tmm160) cc_final: 0.8488 (ttp-110) REVERT: B 416 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8652 (pp) REVERT: F 43 MET cc_start: 0.8142 (mmm) cc_final: 0.7803 (mmm) REVERT: F 58 MET cc_start: 0.7020 (pp-130) cc_final: 0.6629 (pp-130) REVERT: F 259 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5761 (tt) REVERT: F 293 MET cc_start: 0.9116 (mmm) cc_final: 0.8914 (pp-130) REVERT: F 414 LYS cc_start: 0.9109 (OUTLIER) cc_final: 0.8644 (ttmm) REVERT: A 175 LEU cc_start: 0.9174 (pt) cc_final: 0.8960 (tm) REVERT: A 217 MET cc_start: 0.8119 (mmm) cc_final: 0.7875 (mmm) outliers start: 61 outliers final: 34 residues processed: 134 average time/residue: 0.5010 time to fit residues: 75.0534 Evaluate side-chains 115 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 74 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 116 VAL Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 246 GLN Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 268 TRP Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 9 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 44 optimal weight: 0.9990 chunk 158 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 169 optimal weight: 0.4980 chunk 153 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.124050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.089062 restraints weight = 40244.265| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 4.52 r_work: 0.3177 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14333 Z= 0.136 Angle : 0.637 12.896 19424 Z= 0.312 Chirality : 0.045 0.225 2121 Planarity : 0.005 0.069 2514 Dihedral : 5.952 98.853 1952 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 3.21 % Allowed : 25.34 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.20), residues: 1757 helix: 4.03 (0.26), residues: 298 sheet: -0.36 (0.20), residues: 572 loop : -0.31 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 322 TYR 0.020 0.001 TYR A 387 PHE 0.030 0.001 PHE F 281 TRP 0.026 0.001 TRP F 67 HIS 0.004 0.001 HIS B 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (14323) covalent geometry : angle 0.63629 / 0.31 (19404) SS BOND : bond 0.00330 / 0.23 ( 10) SS BOND : angle 1.15553 / 0.68 ( 20) hydrogen bonds : bond 0.03362 / 2.31 ( 669) hydrogen bonds : angle 4.80018 / 3.35 ( 1827) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 84 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 58 MET cc_start: 0.9169 (ptp) cc_final: 0.8849 (ptp) REVERT: E 190 VAL cc_start: 0.9513 (OUTLIER) cc_final: 0.9263 (p) REVERT: E 290 MET cc_start: 0.8194 (ppp) cc_final: 0.7822 (ppp) REVERT: E 293 MET cc_start: 0.9086 (ppp) cc_final: 0.8698 (ppp) REVERT: B 70 GLN cc_start: 0.8809 (pt0) cc_final: 0.8538 (pt0) REVERT: B 105 ARG cc_start: 0.8862 (mtm-85) cc_final: 0.8631 (mtm-85) REVERT: B 279 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6533 (tp) REVERT: B 282 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8233 (tp30) REVERT: B 319 ARG cc_start: 0.8944 (tmm160) cc_final: 0.8484 (ttp-110) REVERT: B 416 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8575 (pp) REVERT: F 43 MET cc_start: 0.8142 (mmm) cc_final: 0.7820 (mmm) REVERT: F 58 MET cc_start: 0.6897 (pp-130) cc_final: 0.6611 (pp-130) REVERT: F 67 TRP cc_start: 0.6297 (m100) cc_final: 0.5993 (m-10) REVERT: F 259 LEU cc_start: 0.6295 (OUTLIER) cc_final: 0.5859 (tt) REVERT: F 414 LYS cc_start: 0.9080 (OUTLIER) cc_final: 0.8641 (ttmm) REVERT: A 175 LEU cc_start: 0.9132 (pt) cc_final: 0.8921 (tm) REVERT: A 217 MET cc_start: 0.8084 (mmm) cc_final: 0.7829 (mmm) outliers start: 49 outliers final: 33 residues processed: 124 average time/residue: 0.4848 time to fit residues: 67.3120 Evaluate side-chains 120 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 81 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 182 TYR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 268 TRP Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 282 GLU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 309 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 203 VAL Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 450 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 139 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 162 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 170 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 167 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.121724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.086860 restraints weight = 40588.380| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 4.30 r_work: 0.3141 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 14333 Z= 0.249 Angle : 0.690 15.738 19424 Z= 0.339 Chirality : 0.046 0.201 2121 Planarity : 0.005 0.078 2514 Dihedral : 6.125 103.302 1952 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.53 % Favored : 96.41 % Rotamer: Outliers : 3.34 % Allowed : 25.28 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.20), residues: 1757 helix: 3.86 (0.26), residues: 304 sheet: -0.37 (0.21), residues: 565 loop : -0.39 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 322 TYR 0.025 0.002 TYR A 387 PHE 0.017 0.002 PHE A 67 TRP 0.018 0.002 TRP F 332 HIS 0.006 0.001 HIS F 481 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.25 (14323) covalent geometry : angle 0.68902 / 0.34 (19404) SS BOND : bond 0.00508 / 0.36 ( 10) SS BOND : angle 1.30400 / 0.75 ( 20) hydrogen bonds : bond 0.03580 / 2.48 ( 669) hydrogen bonds : angle 5.01656 / 3.50 ( 1827) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 72 time to evaluate : 0.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 190 VAL cc_start: 0.9510 (OUTLIER) cc_final: 0.9229 (p) REVERT: B 134 ASP cc_start: 0.8202 (t0) cc_final: 0.7904 (t0) REVERT: B 279 LEU cc_start: 0.6774 (OUTLIER) cc_final: 0.6503 (tp) REVERT: B 319 ARG cc_start: 0.8932 (tmm160) cc_final: 0.8508 (ttp-110) REVERT: B 416 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8658 (pp) REVERT: F 43 MET cc_start: 0.8161 (mmm) cc_final: 0.7827 (mmm) REVERT: F 67 TRP cc_start: 0.6343 (m100) cc_final: 0.6041 (m-10) REVERT: F 259 LEU cc_start: 0.6254 (OUTLIER) cc_final: 0.5971 (tp) REVERT: F 414 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8633 (ttmm) REVERT: A 217 MET cc_start: 0.8126 (mmm) cc_final: 0.7901 (mmm) outliers start: 51 outliers final: 34 residues processed: 118 average time/residue: 0.5056 time to fit residues: 67.0543 Evaluate side-chains 106 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 67 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 268 TRP Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 434 VAL Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 177 ILE Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 387 TYR Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 81 optimal weight: 9.9990 chunk 172 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 94 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 9.9990 chunk 114 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.8742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.121612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.086898 restraints weight = 40704.145| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 4.21 r_work: 0.3216 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14333 Z= 0.147 Angle : 0.656 12.305 19424 Z= 0.324 Chirality : 0.045 0.205 2121 Planarity : 0.005 0.081 2514 Dihedral : 5.970 96.646 1952 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.76 % Rotamer: Outliers : 2.82 % Allowed : 25.61 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.20), residues: 1757 helix: 3.98 (0.27), residues: 294 sheet: -0.38 (0.20), residues: 576 loop : -0.29 (0.21), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.000 ARG E 322 TYR 0.025 0.001 TYR A 387 PHE 0.032 0.001 PHE F 281 TRP 0.019 0.001 TRP F 332 HIS 0.008 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (14323) covalent geometry : angle 0.65488 / 0.32 (19404) SS BOND : bond 0.00386 / 0.28 ( 10) SS BOND : angle 1.10996 / 0.63 ( 20) hydrogen bonds : bond 0.03416 / 2.35 ( 669) hydrogen bonds : angle 4.89616 / 3.42 ( 1827) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3514 Ramachandran restraints generated. 1757 Oldfield, 0 Emsley, 1757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 77 time to evaluate : 0.533 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: E 58 MET cc_start: 0.9347 (ptp) cc_final: 0.8624 (pmm) REVERT: B 279 LEU cc_start: 0.6593 (OUTLIER) cc_final: 0.6319 (tp) REVERT: B 416 ILE cc_start: 0.8993 (OUTLIER) cc_final: 0.8628 (pp) REVERT: F 43 MET cc_start: 0.8229 (mmm) cc_final: 0.7943 (mmm) REVERT: F 58 MET cc_start: 0.6666 (pp-130) cc_final: 0.6401 (pp-130) REVERT: F 67 TRP cc_start: 0.6459 (m100) cc_final: 0.6189 (m-10) REVERT: F 259 LEU cc_start: 0.6539 (OUTLIER) cc_final: 0.6101 (tt) REVERT: F 414 LYS cc_start: 0.9020 (OUTLIER) cc_final: 0.8584 (ttmm) REVERT: A 217 MET cc_start: 0.8055 (mmm) cc_final: 0.7777 (mmm) outliers start: 43 outliers final: 30 residues processed: 116 average time/residue: 0.5210 time to fit residues: 67.7303 Evaluate side-chains 113 residues out of total 1529 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 132 ASP Chi-restraints excluded: chain E residue 180 SER Chi-restraints excluded: chain B residue 125 CYS Chi-restraints excluded: chain B residue 141 VAL Chi-restraints excluded: chain B residue 247 CYS Chi-restraints excluded: chain B residue 265 CYS Chi-restraints excluded: chain B residue 268 TRP Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 415 LEU Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 199 VAL Chi-restraints excluded: chain F residue 207 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 218 VAL Chi-restraints excluded: chain F residue 259 LEU Chi-restraints excluded: chain F residue 270 LEU Chi-restraints excluded: chain F residue 399 VAL Chi-restraints excluded: chain F residue 411 VAL Chi-restraints excluded: chain F residue 414 LYS Chi-restraints excluded: chain A residue 29 GLN Chi-restraints excluded: chain A residue 51 CYS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 139 HIS Chi-restraints excluded: chain A residue 152 SER Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 450 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 170 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 127 optimal weight: 0.0980 chunk 90 optimal weight: 0.9990 chunk 76 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 136 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 46 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN ** F 374 ASN ** 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 = 0.4122 r_free = 0.4122 target = 0.122199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.087595 restraints weight = 40346.497| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 4.30 r_work: 0.3159 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14333 Z= 0.130 Angle : 0.648 13.020 19424 Z= 0.320 Chirality : 0.046 0.446 2121 Planarity : 0.005 0.075 2514 Dihedral : 5.744 80.456 1952 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.85 % Favored : 97.10 % Rotamer: Outliers : 2.69 % Allowed : 25.67 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.25 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.20), residues: 1757 helix: 3.83 (0.27), residues: 300 sheet: -0.28 (0.20), residues: 582 loop : -0.31 (0.21), residues: 875 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.000 ARG E 322 TYR 0.024 0.001 TYR A 387 PHE 0.019 0.001 PHE B 381 TRP 0.019 0.001 TRP F 332 HIS 0.006 0.001 HIS A 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (14323) covalent geometry : angle 0.64697 / 0.32 (19404) SS BOND : bond 0.00396 / 0.30 ( 10) SS BOND : angle 1.04971 / 0.60 ( 20) hydrogen bonds : bond 0.03416 / 2.34 ( 669) hydrogen bonds : angle 4.75299 / 3.33 ( 1827) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5975.84 seconds wall clock time: 102 minutes 26.71 seconds (6146.71 seconds total)