Starting phenix.real_space_refine on Wed Mar 4 19:16:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6uzz_20965/03_2026/6uzz_20965.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uzz_20965/03_2026/6uzz_20965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uzz_20965/03_2026/6uzz_20965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uzz_20965/03_2026/6uzz_20965.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uzz_20965/03_2026/6uzz_20965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uzz_20965/03_2026/6uzz_20965.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 Ca 8 9.91 5 S 80 5.16 5 C 10196 2.51 5 N 2708 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15832 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2848 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 7, 'TRANS': 344} Chain breaks: 2 Chain: "B" Number of atoms: 1108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1108 Classifications: {'peptide': 144} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 2, 'TRANS': 141} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'ASP:plan': 5} Unresolved non-hydrogen planarities: 15 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, E, G, D, F, H Residues with excluded nonbonded symmetry interactions: 4 residue: pdb="CA CA B 202 " occ=0.83 residue: pdb="CA CA D 202 " occ=0.83 residue: pdb="CA CA F 202 " occ=0.83 residue: pdb="CA CA H 202 " occ=0.83 Time building chain proxies: 2.75, per 1000 atoms: 0.17 Number of scatterers: 15832 At special positions: 0 Unit cell: (112.27, 112.27, 125.66, 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) Ca 8 19.99 S 80 16.00 O 2840 8.00 N 2708 7.00 C 10196 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.14 Conformation dependent library (CDL) restraints added in 543.2 milliseconds 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3680 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 4 sheets defined 78.9% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 120 through 143 Processing helix chain 'A' and resid 150 through 155 Processing helix chain 'A' and resid 156 through 178 removed outlier: 3.548A pdb=" N ILE A 161 " --> pdb=" O PHE A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 181 No H-bonds generated for 'chain 'A' and resid 179 through 181' Processing helix chain 'A' and resid 186 through 194 Processing helix chain 'A' and resid 196 through 216 Processing helix chain 'A' and resid 224 through 237 removed outlier: 4.279A pdb=" N PHE A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 233 " --> pdb=" O GLY A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 241 removed outlier: 3.854A pdb=" N VAL A 241 " --> pdb=" O MET A 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 238 through 241' Processing helix chain 'A' and resid 245 through 258 Processing helix chain 'A' and resid 258 through 285 Processing helix chain 'A' and resid 298 through 311 removed outlier: 3.595A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR A 311 " --> pdb=" O VAL A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 336 Processing helix chain 'A' and resid 337 through 358 Proline residue: A 343 - end of helix Processing helix chain 'A' and resid 359 through 361 No H-bonds generated for 'chain 'A' and resid 359 through 361' Processing helix chain 'A' and resid 363 through 366 Processing helix chain 'A' and resid 367 through 384 Processing helix chain 'A' and resid 389 through 395 removed outlier: 4.016A pdb=" N TRP A 392 " --> pdb=" O SER A 389 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 393 " --> pdb=" O SER A 390 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE A 394 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 532 removed outlier: 3.638A pdb=" N THR A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 567 removed outlier: 3.713A pdb=" N VAL A 541 " --> pdb=" O ASP A 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 22 removed outlier: 3.675A pdb=" N LEU B 19 " --> pdb=" O GLU B 15 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 40 removed outlier: 4.393A pdb=" N VAL B 36 " --> pdb=" O GLU B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.677A pdb=" N GLU B 83 " --> pdb=" O ASP B 79 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG B 91 " --> pdb=" O ARG B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 103 through 113 removed outlier: 3.501A pdb=" N ASN B 112 " --> pdb=" O HIS B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 removed outlier: 3.656A pdb=" N ARG B 127 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 147 Processing helix chain 'C' and resid 105 through 115 Processing helix chain 'C' and resid 120 through 143 Processing helix chain 'C' and resid 150 through 155 Processing helix chain 'C' and resid 156 through 178 removed outlier: 3.548A pdb=" N ILE C 161 " --> pdb=" O PHE C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 181 No H-bonds generated for 'chain 'C' and resid 179 through 181' Processing helix chain 'C' and resid 186 through 194 Processing helix chain 'C' and resid 196 through 216 Processing helix chain 'C' and resid 224 through 237 removed outlier: 4.280A pdb=" N PHE C 232 " --> pdb=" O ARG C 228 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU C 233 " --> pdb=" O GLY C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 241 removed outlier: 3.853A pdb=" N VAL C 241 " --> pdb=" O MET C 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 238 through 241' Processing helix chain 'C' and resid 245 through 258 Processing helix chain 'C' and resid 258 through 285 Processing helix chain 'C' and resid 298 through 311 removed outlier: 3.594A pdb=" N ALA C 302 " --> pdb=" O SER C 298 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR C 311 " --> pdb=" O VAL C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 336 Processing helix chain 'C' and resid 337 through 358 Proline residue: C 343 - end of helix Processing helix chain 'C' and resid 359 through 361 No H-bonds generated for 'chain 'C' and resid 359 through 361' Processing helix chain 'C' and resid 363 through 366 Processing helix chain 'C' and resid 367 through 384 Processing helix chain 'C' and resid 389 through 395 removed outlier: 4.016A pdb=" N TRP C 392 " --> pdb=" O SER C 389 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS C 393 " --> pdb=" O SER C 390 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE C 394 " --> pdb=" O THR C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 532 removed outlier: 3.638A pdb=" N THR C 513 " --> pdb=" O HIS C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 537 through 567 removed outlier: 3.713A pdb=" N VAL C 541 " --> pdb=" O ASP C 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 22 removed outlier: 3.675A pdb=" N LEU D 19 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE D 20 " --> pdb=" O ALA D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 40 removed outlier: 4.394A pdb=" N VAL D 36 " --> pdb=" O GLU D 32 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 54 Processing helix chain 'D' and resid 65 through 75 Processing helix chain 'D' and resid 79 through 91 removed outlier: 3.679A pdb=" N GLU D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU D 84 " --> pdb=" O THR D 80 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG D 91 " --> pdb=" O ARG D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 103 through 113 removed outlier: 3.501A pdb=" N ASN D 112 " --> pdb=" O HIS D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 128 removed outlier: 3.657A pdb=" N ARG D 127 " --> pdb=" O ASP D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 147 Processing helix chain 'E' and resid 105 through 115 Processing helix chain 'E' and resid 120 through 143 Processing helix chain 'E' and resid 150 through 155 Processing helix chain 'E' and resid 156 through 178 removed outlier: 3.548A pdb=" N ILE E 161 " --> pdb=" O PHE E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 181 No H-bonds generated for 'chain 'E' and resid 179 through 181' Processing helix chain 'E' and resid 186 through 194 Processing helix chain 'E' and resid 196 through 216 Processing helix chain 'E' and resid 224 through 237 removed outlier: 4.279A pdb=" N PHE E 232 " --> pdb=" O ARG E 228 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU E 233 " --> pdb=" O GLY E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 241 removed outlier: 3.853A pdb=" N VAL E 241 " --> pdb=" O MET E 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 238 through 241' Processing helix chain 'E' and resid 245 through 258 Processing helix chain 'E' and resid 258 through 285 Processing helix chain 'E' and resid 298 through 311 removed outlier: 3.594A pdb=" N ALA E 302 " --> pdb=" O SER E 298 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N THR E 311 " --> pdb=" O VAL E 307 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 336 Processing helix chain 'E' and resid 337 through 358 Proline residue: E 343 - end of helix Processing helix chain 'E' and resid 359 through 361 No H-bonds generated for 'chain 'E' and resid 359 through 361' Processing helix chain 'E' and resid 363 through 366 Processing helix chain 'E' and resid 367 through 384 Processing helix chain 'E' and resid 389 through 395 removed outlier: 4.016A pdb=" N TRP E 392 " --> pdb=" O SER E 389 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS E 393 " --> pdb=" O SER E 390 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE E 394 " --> pdb=" O THR E 391 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 532 removed outlier: 3.638A pdb=" N THR E 513 " --> pdb=" O HIS E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 567 removed outlier: 3.713A pdb=" N VAL E 541 " --> pdb=" O ASP E 537 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 22 removed outlier: 3.675A pdb=" N LEU F 19 " --> pdb=" O GLU F 15 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N PHE F 20 " --> pdb=" O ALA F 16 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 40 removed outlier: 4.394A pdb=" N VAL F 36 " --> pdb=" O GLU F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 45 through 54 Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 79 through 91 removed outlier: 3.678A pdb=" N GLU F 83 " --> pdb=" O ASP F 79 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU F 84 " --> pdb=" O THR F 80 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG F 91 " --> pdb=" O ARG F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 103 through 113 removed outlier: 3.501A pdb=" N ASN F 112 " --> pdb=" O HIS F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 128 removed outlier: 3.657A pdb=" N ARG F 127 " --> pdb=" O ASP F 123 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 147 Processing helix chain 'G' and resid 105 through 115 Processing helix chain 'G' and resid 120 through 143 Processing helix chain 'G' and resid 150 through 155 Processing helix chain 'G' and resid 156 through 178 removed outlier: 3.548A pdb=" N ILE G 161 " --> pdb=" O PHE G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 181 No H-bonds generated for 'chain 'G' and resid 179 through 181' Processing helix chain 'G' and resid 186 through 194 Processing helix chain 'G' and resid 196 through 216 Processing helix chain 'G' and resid 224 through 237 removed outlier: 4.280A pdb=" N PHE G 232 " --> pdb=" O ARG G 228 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU G 233 " --> pdb=" O GLY G 229 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 241 removed outlier: 3.853A pdb=" N VAL G 241 " --> pdb=" O MET G 238 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 238 through 241' Processing helix chain 'G' and resid 245 through 258 Processing helix chain 'G' and resid 258 through 285 Processing helix chain 'G' and resid 298 through 311 removed outlier: 3.594A pdb=" N ALA G 302 " --> pdb=" O SER G 298 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR G 311 " --> pdb=" O VAL G 307 " (cutoff:3.500A) Processing helix chain 'G' and resid 322 through 336 Processing helix chain 'G' and resid 337 through 358 Proline residue: G 343 - end of helix Processing helix chain 'G' and resid 359 through 361 No H-bonds generated for 'chain 'G' and resid 359 through 361' Processing helix chain 'G' and resid 363 through 366 Processing helix chain 'G' and resid 367 through 384 Processing helix chain 'G' and resid 389 through 395 removed outlier: 4.016A pdb=" N TRP G 392 " --> pdb=" O SER G 389 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS G 393 " --> pdb=" O SER G 390 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE G 394 " --> pdb=" O THR G 391 " (cutoff:3.500A) Processing helix chain 'G' and resid 509 through 532 removed outlier: 3.638A pdb=" N THR G 513 " --> pdb=" O HIS G 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 567 removed outlier: 3.714A pdb=" N VAL G 541 " --> pdb=" O ASP G 537 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 22 removed outlier: 3.676A pdb=" N LEU H 19 " --> pdb=" O GLU H 15 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N PHE H 20 " --> pdb=" O ALA H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 40 removed outlier: 4.394A pdb=" N VAL H 36 " --> pdb=" O GLU H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 54 Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 79 through 91 removed outlier: 3.679A pdb=" N GLU H 83 " --> pdb=" O ASP H 79 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU H 84 " --> pdb=" O THR H 80 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG H 91 " --> pdb=" O ARG H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 94 No H-bonds generated for 'chain 'H' and resid 92 through 94' Processing helix chain 'H' and resid 103 through 113 removed outlier: 3.501A pdb=" N ASN H 112 " --> pdb=" O HIS H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 128 removed outlier: 3.657A pdb=" N ARG H 127 " --> pdb=" O ASP H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 147 Processing sheet with id=AA1, first strand: chain 'B' and resid 100 through 102 Processing sheet with id=AA2, first strand: chain 'D' and resid 100 through 102 Processing sheet with id=AA3, first strand: chain 'F' and resid 100 through 102 Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 102 1045 hydrogen bonds defined for protein. 3111 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: 1.89 Time building geometry restraints manager: 1.55 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: 5043 1.34 - 1.45: 2602 1.45 - 1.57: 8371 1.57 - 1.69: 0 1.69 - 1.80: 136 Bond restraints: 16152 Sorted by residual: bond pdb=" CG LEU H 117 " pdb=" CD1 LEU H 117 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.03e+00 bond pdb=" CG LEU B 117 " pdb=" CD1 LEU B 117 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.01e+00 bond pdb=" CG LEU D 117 " pdb=" CD1 LEU D 117 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.93e+00 bond pdb=" CG LEU F 117 " pdb=" CD1 LEU F 117 " ideal model delta sigma weight residual 1.521 1.456 0.065 3.30e-02 9.18e+02 3.91e+00 bond pdb=" CG LEU C 273 " pdb=" CD1 LEU C 273 " ideal model delta sigma weight residual 1.521 1.457 0.064 3.30e-02 9.18e+02 3.81e+00 ... (remaining 16147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 20754 1.91 - 3.81: 912 3.81 - 5.72: 114 5.72 - 7.63: 32 7.63 - 9.54: 12 Bond angle restraints: 21824 Sorted by residual: angle pdb=" C LYS B 95 " pdb=" N ASP B 96 " pdb=" CA ASP B 96 " ideal model delta sigma weight residual 121.54 131.08 -9.54 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C LYS H 95 " pdb=" N ASP H 96 " pdb=" CA ASP H 96 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.49e+01 angle pdb=" C LYS F 95 " pdb=" N ASP F 96 " pdb=" CA ASP F 96 " ideal model delta sigma weight residual 121.54 131.06 -9.52 1.91e+00 2.74e-01 2.48e+01 angle pdb=" C LYS D 95 " pdb=" N ASP D 96 " pdb=" CA ASP D 96 " ideal model delta sigma weight residual 121.54 131.05 -9.51 1.91e+00 2.74e-01 2.48e+01 angle pdb=" N LEU G 342 " pdb=" CA LEU G 342 " pdb=" C LEU G 342 " ideal model delta sigma weight residual 109.81 118.20 -8.39 2.21e+00 2.05e-01 1.44e+01 ... (remaining 21819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.17: 8814 14.17 - 28.33: 488 28.33 - 42.50: 158 42.50 - 56.67: 16 56.67 - 70.83: 16 Dihedral angle restraints: 9492 sinusoidal: 3776 harmonic: 5716 Sorted by residual: dihedral pdb=" CA ARG H 75 " pdb=" C ARG H 75 " pdb=" N LYS H 76 " pdb=" CA LYS H 76 " ideal model delta harmonic sigma weight residual -180.00 -155.68 -24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ARG B 75 " pdb=" C ARG B 75 " pdb=" N LYS B 76 " pdb=" CA LYS B 76 " ideal model delta harmonic sigma weight residual -180.00 -155.69 -24.31 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ARG D 75 " pdb=" C ARG D 75 " pdb=" N LYS D 76 " pdb=" CA LYS D 76 " ideal model delta harmonic sigma weight residual 180.00 -155.70 -24.30 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 9489 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1537 0.048 - 0.095: 672 0.095 - 0.143: 184 0.143 - 0.190: 39 0.190 - 0.238: 12 Chirality restraints: 2444 Sorted by residual: chirality pdb=" CB ILE C 337 " pdb=" CA ILE C 337 " pdb=" CG1 ILE C 337 " pdb=" CG2 ILE C 337 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB ILE G 337 " pdb=" CA ILE G 337 " pdb=" CG1 ILE G 337 " pdb=" CG2 ILE G 337 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CB ILE A 337 " pdb=" CA ILE A 337 " pdb=" CG1 ILE A 337 " pdb=" CG2 ILE A 337 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 2441 not shown) Planarity restraints: 2752 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE G 351 " -0.024 2.00e-02 2.50e+03 2.07e-02 7.48e+00 pdb=" CG PHE G 351 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE G 351 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE G 351 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE G 351 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE G 351 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE G 351 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 351 " -0.024 2.00e-02 2.50e+03 2.06e-02 7.40e+00 pdb=" CG PHE A 351 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 351 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 351 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 351 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE A 351 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 351 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 351 " 0.024 2.00e-02 2.50e+03 2.05e-02 7.38e+00 pdb=" CG PHE C 351 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE C 351 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 351 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE C 351 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE C 351 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE C 351 " 0.003 2.00e-02 2.50e+03 ... (remaining 2749 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 5249 2.84 - 3.36: 14813 3.36 - 3.87: 25316 3.87 - 4.39: 28496 4.39 - 4.90: 49558 Nonbonded interactions: 123432 Sorted by model distance: nonbonded pdb=" OH TYR A 522 " pdb=" OG SER B 82 " model vdw 2.325 3.040 nonbonded pdb=" OE2 GLU A 284 " pdb=" OG1 THR A 322 " model vdw 2.357 3.040 nonbonded pdb=" OE2 GLU G 284 " pdb=" OG1 THR G 322 " model vdw 2.357 3.040 nonbonded pdb=" OE2 GLU C 284 " pdb=" OG1 THR C 322 " model vdw 2.357 3.040 nonbonded pdb=" OE2 GLU E 284 " pdb=" OG1 THR E 322 " model vdw 2.357 3.040 ... (remaining 123427 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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=0.83 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: 1.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.590 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.009 0.069 16152 Z= 0.371 Angle : 0.922 9.536 21824 Z= 0.509 Chirality : 0.057 0.238 2444 Planarity : 0.006 0.050 2752 Dihedral : 10.608 70.833 5812 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.20 % Allowed : 1.84 % Favored : 97.95 % Rotamer: Outliers : 0.24 % Allowed : 2.17 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.22 (0.13), residues: 1952 helix: -2.92 (0.08), residues: 1504 sheet: None (None), residues: 0 loop : -1.30 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 360 TYR 0.025 0.003 TYR C 299 PHE 0.048 0.003 PHE G 351 TRP 0.032 0.003 TRP C 379 HIS 0.006 0.001 HIS E 105 Details of bonding type rmsd covalent geometry : bond 0.00929 (16152) covalent geometry : angle 0.92161 (21824) hydrogen bonds : bond 0.19452 ( 1045) hydrogen bonds : angle 6.76214 ( 3111) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 372 time to evaluate : 0.603 Fit side-chains revert: symmetry clash REVERT: A 147 GLN cc_start: 0.8310 (mt0) cc_final: 0.7897 (mt0) REVERT: A 195 ARG cc_start: 0.8408 (ttp-170) cc_final: 0.8143 (ttm170) REVERT: A 228 ARG cc_start: 0.8081 (mtt180) cc_final: 0.7659 (tmt170) REVERT: A 261 GLU cc_start: 0.8618 (mp0) cc_final: 0.8356 (mp0) REVERT: A 527 LYS cc_start: 0.7897 (tmmt) cc_final: 0.6965 (ttmt) REVERT: A 539 ARG cc_start: 0.8007 (ttt-90) cc_final: 0.7470 (ttm110) REVERT: A 543 GLU cc_start: 0.7840 (tt0) cc_final: 0.7623 (mt-10) REVERT: A 546 SER cc_start: 0.8755 (t) cc_final: 0.8340 (m) REVERT: A 562 ARG cc_start: 0.7329 (ttm170) cc_final: 0.7041 (tmt-80) REVERT: B 15 GLU cc_start: 0.8449 (tp30) cc_final: 0.8136 (tp30) REVERT: B 43 ASN cc_start: 0.8536 (t0) cc_final: 0.8322 (t0) REVERT: B 54 ASN cc_start: 0.8418 (m110) cc_final: 0.8049 (m110) REVERT: B 83 GLU cc_start: 0.7607 (tt0) cc_final: 0.7235 (mt-10) REVERT: B 117 LEU cc_start: 0.7281 (mp) cc_final: 0.6924 (mp) REVERT: C 147 GLN cc_start: 0.8305 (mt0) cc_final: 0.7891 (mt0) REVERT: C 195 ARG cc_start: 0.8403 (ttp-170) cc_final: 0.8137 (ttm170) REVERT: C 228 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7663 (tmt170) REVERT: C 261 GLU cc_start: 0.8611 (mp0) cc_final: 0.8344 (mp0) REVERT: C 527 LYS cc_start: 0.7907 (tmmt) cc_final: 0.6976 (ttmt) REVERT: C 539 ARG cc_start: 0.7999 (ttt-90) cc_final: 0.7477 (ttm110) REVERT: C 543 GLU cc_start: 0.7837 (tt0) cc_final: 0.7618 (mt-10) REVERT: C 546 SER cc_start: 0.8744 (t) cc_final: 0.8324 (m) REVERT: C 562 ARG cc_start: 0.7325 (ttm170) cc_final: 0.7039 (tmt-80) REVERT: D 15 GLU cc_start: 0.8439 (tp30) cc_final: 0.8138 (tp30) REVERT: D 54 ASN cc_start: 0.8480 (m110) cc_final: 0.8152 (m110) REVERT: D 83 GLU cc_start: 0.7600 (tt0) cc_final: 0.7220 (mt-10) REVERT: D 117 LEU cc_start: 0.7529 (mp) cc_final: 0.7029 (mp) REVERT: D 144 GLN cc_start: 0.8668 (mm110) cc_final: 0.8387 (mm-40) REVERT: E 147 GLN cc_start: 0.8313 (mt0) cc_final: 0.7896 (mt0) REVERT: E 195 ARG cc_start: 0.8404 (ttp-170) cc_final: 0.8139 (ttm170) REVERT: E 228 ARG cc_start: 0.8125 (mtt180) cc_final: 0.7668 (tmt170) REVERT: E 261 GLU cc_start: 0.8617 (mp0) cc_final: 0.8355 (mp0) REVERT: E 527 LYS cc_start: 0.7895 (tmmt) cc_final: 0.6963 (ttmt) REVERT: E 539 ARG cc_start: 0.8003 (ttt-90) cc_final: 0.7479 (ttm110) REVERT: E 543 GLU cc_start: 0.7857 (tt0) cc_final: 0.7635 (mt-10) REVERT: E 546 SER cc_start: 0.8747 (t) cc_final: 0.8327 (m) REVERT: E 562 ARG cc_start: 0.7349 (ttm170) cc_final: 0.7057 (tmt-80) REVERT: F 15 GLU cc_start: 0.8439 (tp30) cc_final: 0.8139 (tp30) REVERT: F 54 ASN cc_start: 0.8460 (m110) cc_final: 0.8126 (m110) REVERT: F 83 GLU cc_start: 0.7567 (tt0) cc_final: 0.7257 (mt-10) REVERT: F 117 LEU cc_start: 0.7536 (mp) cc_final: 0.7032 (mp) REVERT: F 144 GLN cc_start: 0.8663 (mm110) cc_final: 0.8402 (mm-40) REVERT: G 147 GLN cc_start: 0.8316 (mt0) cc_final: 0.7903 (mt0) REVERT: G 195 ARG cc_start: 0.8403 (ttp-170) cc_final: 0.8138 (ttm170) REVERT: G 228 ARG cc_start: 0.8122 (mtt180) cc_final: 0.7710 (tmt170) REVERT: G 260 GLN cc_start: 0.7655 (tp-100) cc_final: 0.7438 (tt0) REVERT: G 261 GLU cc_start: 0.8614 (mp0) cc_final: 0.8349 (mp0) REVERT: G 527 LYS cc_start: 0.7889 (tmmt) cc_final: 0.6958 (ttmt) REVERT: G 539 ARG cc_start: 0.7999 (ttt-90) cc_final: 0.7480 (ttm110) REVERT: G 543 GLU cc_start: 0.7840 (tt0) cc_final: 0.7622 (mt-10) REVERT: G 546 SER cc_start: 0.8748 (t) cc_final: 0.8330 (m) REVERT: G 562 ARG cc_start: 0.7334 (ttm170) cc_final: 0.7030 (tmt-80) REVERT: H 15 GLU cc_start: 0.8440 (tp30) cc_final: 0.8141 (tp30) REVERT: H 54 ASN cc_start: 0.8459 (m110) cc_final: 0.8120 (m110) REVERT: H 83 GLU cc_start: 0.7573 (tt0) cc_final: 0.7260 (mt-10) REVERT: H 117 LEU cc_start: 0.7537 (mp) cc_final: 0.7032 (mp) REVERT: H 144 GLN cc_start: 0.8671 (mm110) cc_final: 0.8415 (mm-40) outliers start: 4 outliers final: 0 residues processed: 376 average time/residue: 0.1732 time to fit residues: 88.2519 Evaluate side-chains 246 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 HIS A 357 GLN A 386 ASN A 560 GLN C 240 HIS C 357 GLN ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 386 ASN C 560 GLN E 240 HIS E 357 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 ASN E 560 GLN G 240 HIS G 357 GLN ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 386 ASN G 560 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102835 restraints weight = 20213.075| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.47 r_work: 0.3085 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3098 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3098 r_free = 0.3098 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3098 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16152 Z= 0.131 Angle : 0.519 5.680 21824 Z= 0.281 Chirality : 0.038 0.118 2444 Planarity : 0.004 0.026 2752 Dihedral : 4.142 18.363 2164 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.45 % Allowed : 7.65 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.17), residues: 1952 helix: -0.01 (0.12), residues: 1492 sheet: None (None), residues: 0 loop : -0.78 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 511 TYR 0.012 0.001 TYR A 545 PHE 0.019 0.001 PHE C 351 TRP 0.020 0.002 TRP A 379 HIS 0.003 0.001 HIS A 258 Details of bonding type rmsd covalent geometry : bond 0.00299 (16152) covalent geometry : angle 0.51893 (21824) hydrogen bonds : bond 0.04636 ( 1045) hydrogen bonds : angle 3.78125 ( 3111) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 309 time to evaluate : 0.440 Fit side-chains REVERT: A 147 GLN cc_start: 0.8042 (mt0) cc_final: 0.7796 (mt0) REVERT: A 195 ARG cc_start: 0.8546 (ttp-170) cc_final: 0.8320 (ttm170) REVERT: A 228 ARG cc_start: 0.8153 (mtt180) cc_final: 0.7448 (tmt170) REVERT: A 235 ILE cc_start: 0.8386 (mt) cc_final: 0.8036 (mm) REVERT: A 238 MET cc_start: 0.8626 (tpp) cc_final: 0.8151 (mmt) REVERT: A 527 LYS cc_start: 0.8016 (tmmt) cc_final: 0.7207 (ttmt) REVERT: A 539 ARG cc_start: 0.8152 (ttt-90) cc_final: 0.7736 (ttm110) REVERT: A 546 SER cc_start: 0.8761 (t) cc_final: 0.8288 (m) REVERT: A 560 GLN cc_start: 0.7799 (tp-100) cc_final: 0.7556 (tp-100) REVERT: A 562 ARG cc_start: 0.7364 (ttm170) cc_final: 0.7117 (tmt-80) REVERT: B 23 ASP cc_start: 0.4079 (OUTLIER) cc_final: 0.3699 (p0) REVERT: B 54 ASN cc_start: 0.8371 (m110) cc_final: 0.7886 (m110) REVERT: B 105 GLU cc_start: 0.7669 (tp30) cc_final: 0.7242 (tt0) REVERT: B 117 LEU cc_start: 0.7782 (mp) cc_final: 0.7416 (mp) REVERT: B 118 THR cc_start: 0.8068 (m) cc_final: 0.7720 (p) REVERT: C 147 GLN cc_start: 0.8039 (mt0) cc_final: 0.7794 (mt0) REVERT: C 195 ARG cc_start: 0.8559 (ttp-170) cc_final: 0.8337 (ttm170) REVERT: C 228 ARG cc_start: 0.8145 (mtt180) cc_final: 0.7447 (tmt170) REVERT: C 235 ILE cc_start: 0.8415 (mt) cc_final: 0.8064 (mm) REVERT: C 527 LYS cc_start: 0.8034 (tmmt) cc_final: 0.7213 (ttmt) REVERT: C 539 ARG cc_start: 0.8149 (ttt-90) cc_final: 0.7737 (ttm110) REVERT: C 546 SER cc_start: 0.8764 (t) cc_final: 0.8295 (m) REVERT: C 560 GLN cc_start: 0.7792 (tp-100) cc_final: 0.7402 (tp40) REVERT: C 562 ARG cc_start: 0.7358 (ttm170) cc_final: 0.7110 (tmt-80) REVERT: D 54 ASN cc_start: 0.8381 (m110) cc_final: 0.7892 (m110) REVERT: D 117 LEU cc_start: 0.7919 (mp) cc_final: 0.7489 (mp) REVERT: D 118 THR cc_start: 0.7941 (m) cc_final: 0.7574 (p) REVERT: D 141 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7682 (tp30) REVERT: E 147 GLN cc_start: 0.8041 (mt0) cc_final: 0.7797 (mt0) REVERT: E 195 ARG cc_start: 0.8558 (ttp-170) cc_final: 0.8335 (ttm170) REVERT: E 228 ARG cc_start: 0.8146 (mtt180) cc_final: 0.7447 (tmt170) REVERT: E 235 ILE cc_start: 0.8407 (mt) cc_final: 0.8061 (mm) REVERT: E 527 LYS cc_start: 0.8043 (tmmt) cc_final: 0.7216 (ttmt) REVERT: E 539 ARG cc_start: 0.8148 (ttt-90) cc_final: 0.7739 (ttm110) REVERT: E 546 SER cc_start: 0.8765 (t) cc_final: 0.8296 (m) REVERT: E 560 GLN cc_start: 0.7789 (tp-100) cc_final: 0.7403 (tp40) REVERT: E 562 ARG cc_start: 0.7359 (ttm170) cc_final: 0.7113 (tmt-80) REVERT: F 54 ASN cc_start: 0.8389 (m110) cc_final: 0.7893 (m110) REVERT: F 117 LEU cc_start: 0.7928 (mp) cc_final: 0.7499 (mp) REVERT: F 118 THR cc_start: 0.7941 (m) cc_final: 0.7569 (p) REVERT: G 147 GLN cc_start: 0.8049 (mt0) cc_final: 0.7803 (mt0) REVERT: G 195 ARG cc_start: 0.8549 (ttp-170) cc_final: 0.8324 (ttm170) REVERT: G 228 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7449 (tmt170) REVERT: G 235 ILE cc_start: 0.8410 (mt) cc_final: 0.8063 (mm) REVERT: G 260 GLN cc_start: 0.7872 (tp-100) cc_final: 0.7597 (tt0) REVERT: G 527 LYS cc_start: 0.8039 (tmmt) cc_final: 0.7213 (ttmt) REVERT: G 539 ARG cc_start: 0.8143 (ttt-90) cc_final: 0.7739 (ttm110) REVERT: G 546 SER cc_start: 0.8766 (t) cc_final: 0.8300 (m) REVERT: G 560 GLN cc_start: 0.7790 (tp-100) cc_final: 0.7407 (tp40) REVERT: G 562 ARG cc_start: 0.7358 (ttm170) cc_final: 0.7098 (tmt-80) REVERT: H 54 ASN cc_start: 0.8390 (m110) cc_final: 0.7895 (m110) REVERT: H 117 LEU cc_start: 0.7918 (mp) cc_final: 0.7478 (mp) REVERT: H 118 THR cc_start: 0.7935 (m) cc_final: 0.7567 (p) outliers start: 24 outliers final: 17 residues processed: 326 average time/residue: 0.1549 time to fit residues: 69.6618 Evaluate side-chains 272 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 254 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 509 HIS Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 39 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 177 optimal weight: 0.0970 chunk 87 optimal weight: 2.9990 chunk 120 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 113 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 83 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 357 GLN A 549 HIS C 112 ASN C 357 GLN C 549 HIS E 112 ASN E 357 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 549 HIS G 112 ASN G 357 GLN ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 549 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.145101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.104467 restraints weight = 20239.906| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.47 r_work: 0.3095 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3106 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3106 r_free = 0.3106 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3106 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16152 Z= 0.110 Angle : 0.466 5.743 21824 Z= 0.246 Chirality : 0.037 0.117 2444 Planarity : 0.003 0.022 2752 Dihedral : 3.738 16.971 2164 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.87 % Allowed : 10.30 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.19), residues: 1952 helix: 1.18 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -0.41 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 75 TYR 0.011 0.001 TYR G 545 PHE 0.013 0.001 PHE E 351 TRP 0.014 0.001 TRP G 379 HIS 0.002 0.000 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00243 (16152) covalent geometry : angle 0.46642 (21824) hydrogen bonds : bond 0.04084 ( 1045) hydrogen bonds : angle 3.45544 ( 3111) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 258 time to evaluate : 0.609 Fit side-chains REVERT: A 147 GLN cc_start: 0.8021 (mt0) cc_final: 0.7776 (mt0) REVERT: A 157 PHE cc_start: 0.7499 (t80) cc_final: 0.6935 (t80) REVERT: A 195 ARG cc_start: 0.8544 (ttp-170) cc_final: 0.8293 (ttm170) REVERT: A 228 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7459 (tmt170) REVERT: A 235 ILE cc_start: 0.8445 (mt) cc_final: 0.8080 (mm) REVERT: A 357 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7606 (tp40) REVERT: A 527 LYS cc_start: 0.7927 (tmmt) cc_final: 0.7160 (ttmt) REVERT: A 539 ARG cc_start: 0.8005 (ttt-90) cc_final: 0.7601 (ttm-80) REVERT: A 546 SER cc_start: 0.8803 (t) cc_final: 0.8339 (m) REVERT: A 560 GLN cc_start: 0.7571 (tp-100) cc_final: 0.7224 (tp-100) REVERT: B 23 ASP cc_start: 0.4044 (OUTLIER) cc_final: 0.3669 (p0) REVERT: B 54 ASN cc_start: 0.8328 (m110) cc_final: 0.7861 (m110) REVERT: B 105 GLU cc_start: 0.7509 (tp30) cc_final: 0.7092 (tt0) REVERT: B 117 LEU cc_start: 0.7899 (mp) cc_final: 0.7471 (mp) REVERT: B 144 GLN cc_start: 0.8503 (mm-40) cc_final: 0.8171 (mm110) REVERT: C 147 GLN cc_start: 0.7976 (mt0) cc_final: 0.7742 (mt0) REVERT: C 195 ARG cc_start: 0.8547 (ttp-170) cc_final: 0.8294 (ttm170) REVERT: C 228 ARG cc_start: 0.8161 (mtt180) cc_final: 0.7466 (tmt170) REVERT: C 235 ILE cc_start: 0.8483 (mt) cc_final: 0.8118 (mm) REVERT: C 357 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7611 (tp40) REVERT: C 527 LYS cc_start: 0.7924 (tmmt) cc_final: 0.7157 (ttmt) REVERT: C 539 ARG cc_start: 0.8004 (ttt-90) cc_final: 0.7604 (ttm-80) REVERT: C 546 SER cc_start: 0.8814 (t) cc_final: 0.8346 (m) REVERT: C 560 GLN cc_start: 0.7607 (tp-100) cc_final: 0.7190 (tp40) REVERT: D 42 GLN cc_start: 0.8738 (mm-40) cc_final: 0.8438 (mm110) REVERT: D 54 ASN cc_start: 0.8351 (m110) cc_final: 0.7806 (m110) REVERT: D 117 LEU cc_start: 0.7993 (mp) cc_final: 0.7558 (mp) REVERT: D 118 THR cc_start: 0.8006 (m) cc_final: 0.7604 (p) REVERT: E 147 GLN cc_start: 0.7954 (mt0) cc_final: 0.7718 (mt0) REVERT: E 195 ARG cc_start: 0.8532 (ttp-170) cc_final: 0.8277 (ttm170) REVERT: E 228 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7468 (tmt170) REVERT: E 235 ILE cc_start: 0.8477 (mt) cc_final: 0.8107 (mm) REVERT: E 357 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7612 (tp40) REVERT: E 527 LYS cc_start: 0.7921 (tmmt) cc_final: 0.7152 (ttmt) REVERT: E 539 ARG cc_start: 0.8007 (ttt-90) cc_final: 0.7598 (ttm-80) REVERT: E 546 SER cc_start: 0.8804 (t) cc_final: 0.8337 (m) REVERT: E 560 GLN cc_start: 0.7601 (tp-100) cc_final: 0.7189 (tp40) REVERT: F 42 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8427 (mm110) REVERT: F 54 ASN cc_start: 0.8353 (m110) cc_final: 0.7806 (m110) REVERT: F 117 LEU cc_start: 0.7996 (mp) cc_final: 0.7545 (mp) REVERT: F 118 THR cc_start: 0.7991 (m) cc_final: 0.7588 (p) REVERT: G 147 GLN cc_start: 0.8000 (mt0) cc_final: 0.7733 (mt0) REVERT: G 195 ARG cc_start: 0.8541 (ttp-170) cc_final: 0.8291 (ttm170) REVERT: G 228 ARG cc_start: 0.8153 (mtt180) cc_final: 0.7437 (tmt170) REVERT: G 235 ILE cc_start: 0.8473 (mt) cc_final: 0.8102 (mm) REVERT: G 260 GLN cc_start: 0.7780 (tp-100) cc_final: 0.7529 (tt0) REVERT: G 357 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7608 (tp40) REVERT: G 527 LYS cc_start: 0.7931 (tmmt) cc_final: 0.7172 (ttmt) REVERT: G 539 ARG cc_start: 0.8001 (ttt-90) cc_final: 0.7599 (ttm-80) REVERT: G 546 SER cc_start: 0.8796 (t) cc_final: 0.8340 (m) REVERT: G 560 GLN cc_start: 0.7617 (tp-100) cc_final: 0.7207 (tp40) REVERT: H 42 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8430 (mm110) REVERT: H 54 ASN cc_start: 0.8355 (m110) cc_final: 0.7809 (m110) REVERT: H 117 LEU cc_start: 0.7991 (mp) cc_final: 0.7548 (mp) REVERT: H 118 THR cc_start: 0.7995 (m) cc_final: 0.7590 (p) outliers start: 31 outliers final: 13 residues processed: 271 average time/residue: 0.1679 time to fit residues: 61.9633 Evaluate side-chains 261 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 243 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 119 ASP Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 39 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 155 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 83 optimal weight: 2.9990 chunk 156 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 180 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 134 optimal weight: 0.0970 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 560 GLN C 357 GLN C 560 GLN E 357 GLN ** E 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 357 GLN G 560 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.145331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.104468 restraints weight = 20174.108| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.48 r_work: 0.3107 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.73 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16152 Z= 0.103 Angle : 0.442 6.405 21824 Z= 0.232 Chirality : 0.037 0.116 2444 Planarity : 0.002 0.020 2752 Dihedral : 3.542 14.759 2164 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.81 % Allowed : 11.45 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.19), residues: 1952 helix: 1.80 (0.13), residues: 1516 sheet: None (None), residues: 0 loop : -0.19 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 293 TYR 0.011 0.001 TYR A 545 PHE 0.011 0.001 PHE E 351 TRP 0.012 0.001 TRP A 379 HIS 0.002 0.000 HIS G 258 Details of bonding type rmsd covalent geometry : bond 0.00228 (16152) covalent geometry : angle 0.44173 (21824) hydrogen bonds : bond 0.03784 ( 1045) hydrogen bonds : angle 3.32027 ( 3111) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 252 time to evaluate : 0.451 Fit side-chains REVERT: A 147 GLN cc_start: 0.7983 (mt0) cc_final: 0.7782 (mt0) REVERT: A 228 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7400 (tmt170) REVERT: A 235 ILE cc_start: 0.8479 (mt) cc_final: 0.8107 (mm) REVERT: A 357 GLN cc_start: 0.8011 (OUTLIER) cc_final: 0.7547 (tp40) REVERT: A 527 LYS cc_start: 0.7937 (tmmt) cc_final: 0.7180 (ttmt) REVERT: A 539 ARG cc_start: 0.8046 (ttt-90) cc_final: 0.7718 (ttm110) REVERT: A 546 SER cc_start: 0.8812 (t) cc_final: 0.8317 (m) REVERT: A 560 GLN cc_start: 0.7787 (tp40) cc_final: 0.7209 (tp40) REVERT: B 23 ASP cc_start: 0.3982 (OUTLIER) cc_final: 0.3474 (p0) REVERT: B 42 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8330 (mm110) REVERT: B 43 ASN cc_start: 0.8630 (t0) cc_final: 0.8388 (t0) REVERT: B 54 ASN cc_start: 0.8297 (m110) cc_final: 0.7702 (m110) REVERT: B 105 GLU cc_start: 0.7481 (tp30) cc_final: 0.7080 (tt0) REVERT: B 117 LEU cc_start: 0.7981 (mp) cc_final: 0.7561 (mp) REVERT: B 144 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8078 (mm110) REVERT: C 136 CYS cc_start: 0.8253 (OUTLIER) cc_final: 0.8028 (m) REVERT: C 147 GLN cc_start: 0.7981 (mt0) cc_final: 0.7755 (mt0) REVERT: C 228 ARG cc_start: 0.8073 (mtt180) cc_final: 0.7403 (tmt170) REVERT: C 235 ILE cc_start: 0.8503 (mt) cc_final: 0.8115 (mm) REVERT: C 357 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7548 (tp40) REVERT: C 527 LYS cc_start: 0.7931 (tmmt) cc_final: 0.7171 (ttmt) REVERT: C 539 ARG cc_start: 0.8038 (ttt-90) cc_final: 0.7711 (ttm110) REVERT: C 546 SER cc_start: 0.8834 (t) cc_final: 0.8343 (m) REVERT: C 560 GLN cc_start: 0.7777 (tp40) cc_final: 0.7197 (tp40) REVERT: D 23 ASP cc_start: 0.3954 (OUTLIER) cc_final: 0.3503 (p0) REVERT: D 42 GLN cc_start: 0.8622 (mm-40) cc_final: 0.8305 (mm110) REVERT: D 54 ASN cc_start: 0.8304 (m110) cc_final: 0.8036 (m110) REVERT: D 105 GLU cc_start: 0.7655 (tp30) cc_final: 0.7223 (tt0) REVERT: D 117 LEU cc_start: 0.8023 (mp) cc_final: 0.7788 (mt) REVERT: D 118 THR cc_start: 0.7980 (m) cc_final: 0.7563 (p) REVERT: E 136 CYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8037 (m) REVERT: E 147 GLN cc_start: 0.7969 (mt0) cc_final: 0.7744 (mt0) REVERT: E 228 ARG cc_start: 0.8076 (mtt180) cc_final: 0.7405 (tmt170) REVERT: E 235 ILE cc_start: 0.8499 (mt) cc_final: 0.8111 (mm) REVERT: E 357 GLN cc_start: 0.8014 (OUTLIER) cc_final: 0.7539 (tp40) REVERT: E 527 LYS cc_start: 0.7929 (tmmt) cc_final: 0.7170 (ttmt) REVERT: E 539 ARG cc_start: 0.8044 (ttt-90) cc_final: 0.7714 (ttm110) REVERT: E 546 SER cc_start: 0.8839 (t) cc_final: 0.8347 (m) REVERT: E 560 GLN cc_start: 0.7679 (tp-100) cc_final: 0.7155 (tp40) REVERT: F 42 GLN cc_start: 0.8604 (mm-40) cc_final: 0.8288 (mm110) REVERT: F 54 ASN cc_start: 0.8303 (m110) cc_final: 0.8031 (m110) REVERT: F 105 GLU cc_start: 0.7652 (tp30) cc_final: 0.7221 (tt0) REVERT: F 117 LEU cc_start: 0.8035 (mp) cc_final: 0.7801 (mt) REVERT: F 118 THR cc_start: 0.7978 (m) cc_final: 0.7559 (p) REVERT: G 136 CYS cc_start: 0.8264 (OUTLIER) cc_final: 0.8047 (m) REVERT: G 147 GLN cc_start: 0.7961 (mt0) cc_final: 0.7755 (mt0) REVERT: G 228 ARG cc_start: 0.8016 (mtt180) cc_final: 0.7336 (tmt170) REVERT: G 235 ILE cc_start: 0.8494 (mt) cc_final: 0.8105 (mm) REVERT: G 260 GLN cc_start: 0.7834 (tp-100) cc_final: 0.7567 (tt0) REVERT: G 284 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8350 (mm-30) REVERT: G 357 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.7550 (tp40) REVERT: G 527 LYS cc_start: 0.7947 (tmmt) cc_final: 0.7180 (ttmt) REVERT: G 539 ARG cc_start: 0.8044 (ttt-90) cc_final: 0.7682 (ttm-80) REVERT: G 546 SER cc_start: 0.8831 (t) cc_final: 0.8344 (m) REVERT: G 560 GLN cc_start: 0.7786 (tp40) cc_final: 0.7206 (tp40) REVERT: H 42 GLN cc_start: 0.8613 (mm-40) cc_final: 0.8296 (mm110) REVERT: H 54 ASN cc_start: 0.8307 (m110) cc_final: 0.8036 (m110) REVERT: H 105 GLU cc_start: 0.7664 (tp30) cc_final: 0.7227 (tt0) REVERT: H 117 LEU cc_start: 0.8019 (mp) cc_final: 0.7768 (mt) REVERT: H 118 THR cc_start: 0.7973 (m) cc_final: 0.7553 (p) outliers start: 30 outliers final: 12 residues processed: 274 average time/residue: 0.1533 time to fit residues: 58.0771 Evaluate side-chains 259 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 238 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 136 CYS Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 136 CYS Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 136 CYS Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 39 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 91 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 173 optimal weight: 0.6980 chunk 70 optimal weight: 0.0030 chunk 11 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 176 optimal weight: 0.9990 overall best weight: 1.3396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN C 357 GLN E 357 GLN G 357 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.140887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.103163 restraints weight = 21137.672| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 1.93 r_work: 0.3076 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.72 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 16152 Z= 0.148 Angle : 0.482 6.565 21824 Z= 0.255 Chirality : 0.039 0.132 2444 Planarity : 0.003 0.021 2752 Dihedral : 3.585 14.834 2164 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.93 % Allowed : 13.13 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.19), residues: 1952 helix: 1.97 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.19 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 360 TYR 0.014 0.001 TYR G 545 PHE 0.011 0.001 PHE G 351 TRP 0.013 0.001 TRP G 379 HIS 0.002 0.001 HIS C 126 Details of bonding type rmsd covalent geometry : bond 0.00355 (16152) covalent geometry : angle 0.48243 (21824) hydrogen bonds : bond 0.04327 ( 1045) hydrogen bonds : angle 3.38619 ( 3111) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 0.618 Fit side-chains REVERT: A 147 GLN cc_start: 0.8179 (mt0) cc_final: 0.7932 (mt0) REVERT: A 228 ARG cc_start: 0.8144 (mtt180) cc_final: 0.7651 (tmt170) REVERT: A 235 ILE cc_start: 0.8936 (mt) cc_final: 0.8503 (mm) REVERT: A 357 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8145 (tp40) REVERT: A 527 LYS cc_start: 0.8655 (tmmt) cc_final: 0.7900 (ttmt) REVERT: A 539 ARG cc_start: 0.8558 (ttt-90) cc_final: 0.8354 (ttm-80) REVERT: A 546 SER cc_start: 0.9081 (t) cc_final: 0.8645 (m) REVERT: A 560 GLN cc_start: 0.8078 (tp40) cc_final: 0.7599 (tp40) REVERT: B 23 ASP cc_start: 0.5205 (OUTLIER) cc_final: 0.4251 (p0) REVERT: B 42 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8565 (mm110) REVERT: B 45 THR cc_start: 0.8106 (OUTLIER) cc_final: 0.7824 (t) REVERT: B 54 ASN cc_start: 0.8702 (m110) cc_final: 0.8408 (m110) REVERT: B 105 GLU cc_start: 0.7937 (tp30) cc_final: 0.7633 (tt0) REVERT: B 117 LEU cc_start: 0.8812 (mp) cc_final: 0.8430 (mt) REVERT: C 147 GLN cc_start: 0.8182 (mt0) cc_final: 0.7931 (mt0) REVERT: C 228 ARG cc_start: 0.8094 (mtt180) cc_final: 0.7605 (tmt170) REVERT: C 235 ILE cc_start: 0.8916 (mt) cc_final: 0.8471 (mm) REVERT: C 284 GLU cc_start: 0.8752 (mm-30) cc_final: 0.8440 (mm-30) REVERT: C 357 GLN cc_start: 0.8409 (OUTLIER) cc_final: 0.8151 (tp40) REVERT: C 527 LYS cc_start: 0.8649 (tmmt) cc_final: 0.7895 (ttmt) REVERT: C 539 ARG cc_start: 0.8547 (ttt-90) cc_final: 0.8341 (ttm-80) REVERT: C 546 SER cc_start: 0.9071 (t) cc_final: 0.8630 (m) REVERT: C 560 GLN cc_start: 0.8072 (tp40) cc_final: 0.7588 (tp40) REVERT: D 23 ASP cc_start: 0.5077 (OUTLIER) cc_final: 0.4178 (p0) REVERT: D 42 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8551 (mm110) REVERT: D 43 ASN cc_start: 0.8529 (t0) cc_final: 0.8252 (t0) REVERT: D 45 THR cc_start: 0.8080 (OUTLIER) cc_final: 0.7808 (t) REVERT: D 54 ASN cc_start: 0.8766 (m110) cc_final: 0.8478 (m110) REVERT: D 117 LEU cc_start: 0.8793 (mp) cc_final: 0.8403 (mt) REVERT: E 147 GLN cc_start: 0.8183 (mt0) cc_final: 0.7936 (mt0) REVERT: E 228 ARG cc_start: 0.8099 (mtt180) cc_final: 0.7602 (tmt170) REVERT: E 235 ILE cc_start: 0.8956 (mt) cc_final: 0.8520 (mm) REVERT: E 284 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8398 (mm-30) REVERT: E 357 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8156 (tp40) REVERT: E 527 LYS cc_start: 0.8654 (tmmt) cc_final: 0.7907 (ttmt) REVERT: E 539 ARG cc_start: 0.8569 (ttt-90) cc_final: 0.8350 (ttm-80) REVERT: E 546 SER cc_start: 0.9081 (t) cc_final: 0.8647 (m) REVERT: E 560 GLN cc_start: 0.7991 (tp-100) cc_final: 0.7554 (tp40) REVERT: F 42 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8531 (mm110) REVERT: F 45 THR cc_start: 0.8084 (OUTLIER) cc_final: 0.7816 (t) REVERT: F 54 ASN cc_start: 0.8771 (m110) cc_final: 0.8484 (m110) REVERT: F 117 LEU cc_start: 0.8815 (mp) cc_final: 0.8415 (mt) REVERT: G 147 GLN cc_start: 0.8166 (mt0) cc_final: 0.7921 (mt0) REVERT: G 228 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7608 (tmt170) REVERT: G 235 ILE cc_start: 0.8952 (mt) cc_final: 0.8510 (mm) REVERT: G 357 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8158 (tp40) REVERT: G 363 HIS cc_start: 0.8116 (t70) cc_final: 0.7859 (t70) REVERT: G 527 LYS cc_start: 0.8628 (tmmt) cc_final: 0.7883 (ttmt) REVERT: G 539 ARG cc_start: 0.8543 (ttt-90) cc_final: 0.8339 (ttm-80) REVERT: G 546 SER cc_start: 0.9087 (t) cc_final: 0.8652 (m) REVERT: G 560 GLN cc_start: 0.8077 (tp40) cc_final: 0.7597 (tp40) REVERT: H 42 GLN cc_start: 0.8796 (mm-40) cc_final: 0.8533 (mm110) REVERT: H 45 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7804 (t) REVERT: H 54 ASN cc_start: 0.8762 (m110) cc_final: 0.8472 (m110) REVERT: H 117 LEU cc_start: 0.8818 (mp) cc_final: 0.8444 (mt) outliers start: 32 outliers final: 17 residues processed: 269 average time/residue: 0.1540 time to fit residues: 57.5688 Evaluate side-chains 271 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 244 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 550 LEU Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 45 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 9 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 chunk 164 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 194 optimal weight: 8.9990 chunk 32 optimal weight: 0.6980 chunk 171 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 101 optimal weight: 0.7980 chunk 162 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN C 357 GLN E 357 GLN G 357 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.143001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.105680 restraints weight = 20996.143| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.90 r_work: 0.3103 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2996 r_free = 0.2996 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16152 Z= 0.111 Angle : 0.445 6.987 21824 Z= 0.235 Chirality : 0.038 0.121 2444 Planarity : 0.002 0.021 2752 Dihedral : 3.492 14.478 2164 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.63 % Allowed : 13.43 % Favored : 84.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.19), residues: 1952 helix: 2.13 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.12 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 293 TYR 0.011 0.001 TYR A 545 PHE 0.010 0.001 PHE C 351 TRP 0.012 0.001 TRP A 379 HIS 0.002 0.001 HIS A 258 Details of bonding type rmsd covalent geometry : bond 0.00252 (16152) covalent geometry : angle 0.44529 (21824) hydrogen bonds : bond 0.03911 ( 1045) hydrogen bonds : angle 3.25292 ( 3111) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 245 time to evaluate : 0.599 Fit side-chains REVERT: A 147 GLN cc_start: 0.8173 (mt0) cc_final: 0.7933 (mt0) REVERT: A 228 ARG cc_start: 0.8091 (mtt180) cc_final: 0.7622 (tmt170) REVERT: A 235 ILE cc_start: 0.8944 (mt) cc_final: 0.8500 (mm) REVERT: A 295 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7739 (mt-10) REVERT: A 357 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8137 (tp40) REVERT: A 527 LYS cc_start: 0.8628 (tmmt) cc_final: 0.7891 (ttmt) REVERT: A 546 SER cc_start: 0.9067 (t) cc_final: 0.8692 (m) REVERT: A 560 GLN cc_start: 0.8054 (tp40) cc_final: 0.7574 (tp40) REVERT: B 23 ASP cc_start: 0.4993 (OUTLIER) cc_final: 0.4185 (p0) REVERT: B 42 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8561 (mm110) REVERT: B 45 THR cc_start: 0.8077 (OUTLIER) cc_final: 0.7811 (t) REVERT: B 54 ASN cc_start: 0.8655 (m110) cc_final: 0.8379 (m110) REVERT: B 105 GLU cc_start: 0.7920 (tp30) cc_final: 0.7590 (tt0) REVERT: B 117 LEU cc_start: 0.8822 (mp) cc_final: 0.8494 (mt) REVERT: C 147 GLN cc_start: 0.8199 (mt0) cc_final: 0.7932 (mt0) REVERT: C 228 ARG cc_start: 0.8061 (mtt180) cc_final: 0.7616 (tmt170) REVERT: C 235 ILE cc_start: 0.8934 (mt) cc_final: 0.8488 (mm) REVERT: C 284 GLU cc_start: 0.8658 (mm-30) cc_final: 0.8419 (mm-30) REVERT: C 357 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8133 (tp40) REVERT: C 527 LYS cc_start: 0.8639 (tmmt) cc_final: 0.7895 (ttmt) REVERT: C 546 SER cc_start: 0.9058 (t) cc_final: 0.8688 (m) REVERT: C 560 GLN cc_start: 0.8051 (tp40) cc_final: 0.7567 (tp40) REVERT: D 23 ASP cc_start: 0.4904 (OUTLIER) cc_final: 0.4184 (p0) REVERT: D 42 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8561 (mm110) REVERT: D 43 ASN cc_start: 0.8528 (t0) cc_final: 0.8233 (t0) REVERT: D 45 THR cc_start: 0.8071 (OUTLIER) cc_final: 0.7817 (t) REVERT: D 54 ASN cc_start: 0.8745 (m110) cc_final: 0.8471 (m110) REVERT: D 70 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8219 (mp) REVERT: D 105 GLU cc_start: 0.8045 (tp30) cc_final: 0.7706 (tt0) REVERT: D 117 LEU cc_start: 0.8799 (mp) cc_final: 0.8453 (mt) REVERT: E 147 GLN cc_start: 0.8185 (mt0) cc_final: 0.7921 (mt0) REVERT: E 228 ARG cc_start: 0.8065 (mtt180) cc_final: 0.7604 (tmt170) REVERT: E 235 ILE cc_start: 0.8959 (mt) cc_final: 0.8520 (mm) REVERT: E 284 GLU cc_start: 0.8625 (mm-30) cc_final: 0.8389 (mm-30) REVERT: E 357 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8133 (tp40) REVERT: E 527 LYS cc_start: 0.8644 (tmmt) cc_final: 0.7900 (ttmt) REVERT: E 546 SER cc_start: 0.9069 (t) cc_final: 0.8700 (m) REVERT: E 560 GLN cc_start: 0.7971 (tp-100) cc_final: 0.7538 (tp40) REVERT: F 42 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8550 (mm110) REVERT: F 43 ASN cc_start: 0.8480 (t0) cc_final: 0.8177 (t0) REVERT: F 45 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7832 (t) REVERT: F 54 ASN cc_start: 0.8760 (m110) cc_final: 0.8487 (m110) REVERT: F 70 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8219 (mp) REVERT: F 117 LEU cc_start: 0.8815 (mp) cc_final: 0.8459 (mt) REVERT: G 147 GLN cc_start: 0.8177 (mt0) cc_final: 0.7912 (mt0) REVERT: G 228 ARG cc_start: 0.8075 (mtt180) cc_final: 0.7617 (tmt170) REVERT: G 235 ILE cc_start: 0.8949 (mt) cc_final: 0.8490 (mm) REVERT: G 357 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8139 (tp40) REVERT: G 527 LYS cc_start: 0.8619 (tmmt) cc_final: 0.7886 (ttmt) REVERT: G 546 SER cc_start: 0.9069 (t) cc_final: 0.8700 (m) REVERT: G 560 GLN cc_start: 0.8057 (tp40) cc_final: 0.7583 (tp40) REVERT: H 42 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8551 (mm110) REVERT: H 43 ASN cc_start: 0.8524 (t0) cc_final: 0.8230 (t0) REVERT: H 45 THR cc_start: 0.8051 (OUTLIER) cc_final: 0.7810 (t) REVERT: H 54 ASN cc_start: 0.8757 (m110) cc_final: 0.8485 (m110) REVERT: H 70 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8212 (mp) REVERT: H 105 GLU cc_start: 0.8067 (tp30) cc_final: 0.7723 (tt0) REVERT: H 117 LEU cc_start: 0.8818 (mp) cc_final: 0.8464 (mt) outliers start: 27 outliers final: 14 residues processed: 263 average time/residue: 0.1490 time to fit residues: 54.3867 Evaluate side-chains 265 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 213 LEU Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 70 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 24 optimal weight: 0.9980 chunk 177 optimal weight: 0.5980 chunk 138 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 168 optimal weight: 0.5980 chunk 170 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN C 357 GLN E 357 GLN G 357 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.140401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.102757 restraints weight = 20878.356| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 1.92 r_work: 0.3070 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16152 Z= 0.153 Angle : 0.476 7.210 21824 Z= 0.253 Chirality : 0.039 0.132 2444 Planarity : 0.003 0.037 2752 Dihedral : 3.584 15.480 2164 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.17 % Allowed : 13.19 % Favored : 84.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.40 (0.19), residues: 1952 helix: 2.09 (0.13), residues: 1524 sheet: None (None), residues: 0 loop : -0.18 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 366 TYR 0.014 0.001 TYR G 545 PHE 0.012 0.001 PHE G 351 TRP 0.012 0.001 TRP A 379 HIS 0.002 0.001 HIS A 258 Details of bonding type rmsd covalent geometry : bond 0.00372 (16152) covalent geometry : angle 0.47625 (21824) hydrogen bonds : bond 0.04345 ( 1045) hydrogen bonds : angle 3.35425 ( 3111) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 237 time to evaluate : 0.553 Fit side-chains REVERT: A 147 GLN cc_start: 0.8204 (mt0) cc_final: 0.7926 (mt0) REVERT: A 228 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7619 (tmt170) REVERT: A 235 ILE cc_start: 0.8935 (mt) cc_final: 0.8492 (mm) REVERT: A 295 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7712 (mt-10) REVERT: A 357 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8105 (tp40) REVERT: A 527 LYS cc_start: 0.8612 (tmmt) cc_final: 0.7843 (ttmt) REVERT: A 546 SER cc_start: 0.9082 (t) cc_final: 0.8622 (m) REVERT: A 560 GLN cc_start: 0.8057 (tp40) cc_final: 0.7564 (tp40) REVERT: B 23 ASP cc_start: 0.5243 (OUTLIER) cc_final: 0.4205 (p0) REVERT: B 42 GLN cc_start: 0.8790 (mm-40) cc_final: 0.8523 (mm110) REVERT: B 45 THR cc_start: 0.8019 (OUTLIER) cc_final: 0.7722 (t) REVERT: B 54 ASN cc_start: 0.8668 (m110) cc_final: 0.8343 (m110) REVERT: B 105 GLU cc_start: 0.8031 (tp30) cc_final: 0.7665 (tt0) REVERT: C 228 ARG cc_start: 0.8162 (mtt180) cc_final: 0.7638 (tmt170) REVERT: C 235 ILE cc_start: 0.8991 (mt) cc_final: 0.8565 (mm) REVERT: C 284 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8544 (mm-30) REVERT: C 357 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8107 (tp40) REVERT: C 363 HIS cc_start: 0.8005 (t70) cc_final: 0.7744 (t70) REVERT: C 527 LYS cc_start: 0.8614 (tmmt) cc_final: 0.7841 (ttmt) REVERT: C 546 SER cc_start: 0.9080 (t) cc_final: 0.8612 (m) REVERT: C 560 GLN cc_start: 0.8049 (tp40) cc_final: 0.7560 (tp40) REVERT: D 23 ASP cc_start: 0.5085 (OUTLIER) cc_final: 0.4157 (p0) REVERT: D 42 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8532 (mm110) REVERT: D 43 ASN cc_start: 0.8498 (t0) cc_final: 0.8209 (t0) REVERT: D 45 THR cc_start: 0.7986 (OUTLIER) cc_final: 0.7697 (t) REVERT: D 54 ASN cc_start: 0.8736 (m110) cc_final: 0.8429 (m110) REVERT: D 70 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8198 (mp) REVERT: E 228 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7627 (tmt170) REVERT: E 235 ILE cc_start: 0.9004 (mt) cc_final: 0.8578 (mm) REVERT: E 284 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8505 (mm-30) REVERT: E 357 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8107 (tp40) REVERT: E 363 HIS cc_start: 0.8081 (t70) cc_final: 0.7824 (t70) REVERT: E 527 LYS cc_start: 0.8614 (tmmt) cc_final: 0.7843 (ttmt) REVERT: E 546 SER cc_start: 0.9083 (t) cc_final: 0.8618 (m) REVERT: E 560 GLN cc_start: 0.7960 (tp-100) cc_final: 0.7515 (tp40) REVERT: F 42 GLN cc_start: 0.8791 (mm-40) cc_final: 0.8509 (mm110) REVERT: F 43 ASN cc_start: 0.8482 (t0) cc_final: 0.8179 (t0) REVERT: F 45 THR cc_start: 0.7998 (OUTLIER) cc_final: 0.7722 (t) REVERT: F 54 ASN cc_start: 0.8748 (m110) cc_final: 0.8446 (m110) REVERT: F 70 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8197 (mp) REVERT: G 147 GLN cc_start: 0.8169 (mt0) cc_final: 0.7964 (mt0) REVERT: G 228 ARG cc_start: 0.8202 (mtt180) cc_final: 0.7646 (tmt170) REVERT: G 235 ILE cc_start: 0.9007 (mt) cc_final: 0.8576 (mm) REVERT: G 357 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.8114 (tp40) REVERT: G 363 HIS cc_start: 0.8106 (t70) cc_final: 0.7844 (t70) REVERT: G 527 LYS cc_start: 0.8598 (tmmt) cc_final: 0.7824 (ttmt) REVERT: G 546 SER cc_start: 0.9083 (t) cc_final: 0.8621 (m) REVERT: G 560 GLN cc_start: 0.8051 (tp40) cc_final: 0.7562 (tp40) REVERT: H 42 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8518 (mm110) REVERT: H 43 ASN cc_start: 0.8493 (t0) cc_final: 0.8206 (t0) REVERT: H 45 THR cc_start: 0.8005 (OUTLIER) cc_final: 0.7722 (t) REVERT: H 54 ASN cc_start: 0.8742 (m110) cc_final: 0.8440 (m110) REVERT: H 70 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8201 (mp) outliers start: 36 outliers final: 18 residues processed: 259 average time/residue: 0.1629 time to fit residues: 58.0921 Evaluate side-chains 265 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 234 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 357 GLN Chi-restraints excluded: chain C residue 550 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 357 GLN Chi-restraints excluded: chain E residue 550 LEU Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 357 GLN Chi-restraints excluded: chain G residue 550 LEU Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 70 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 92 optimal weight: 1.9990 chunk 145 optimal weight: 6.9990 chunk 93 optimal weight: 0.5980 chunk 176 optimal weight: 0.8980 chunk 99 optimal weight: 4.9990 chunk 8 optimal weight: 0.0010 chunk 139 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 182 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 177 optimal weight: 0.6980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN C 357 GLN ** C 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 357 GLN G 357 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.144607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.111155 restraints weight = 20942.509| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.15 r_work: 0.3087 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2950 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16152 Z= 0.099 Angle : 0.445 7.629 21824 Z= 0.231 Chirality : 0.037 0.116 2444 Planarity : 0.002 0.035 2752 Dihedral : 3.431 14.517 2164 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.81 % Allowed : 13.80 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.19), residues: 1952 helix: 2.33 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.04 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 366 TYR 0.010 0.001 TYR C 545 PHE 0.011 0.001 PHE G 351 TRP 0.012 0.001 TRP G 379 HIS 0.002 0.000 HIS G 258 Details of bonding type rmsd covalent geometry : bond 0.00213 (16152) covalent geometry : angle 0.44459 (21824) hydrogen bonds : bond 0.03646 ( 1045) hydrogen bonds : angle 3.18842 ( 3111) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.640 Fit side-chains REVERT: A 228 ARG cc_start: 0.8129 (mtt180) cc_final: 0.7619 (tmt170) REVERT: A 235 ILE cc_start: 0.8950 (mt) cc_final: 0.8503 (mm) REVERT: A 295 GLU cc_start: 0.8109 (mm-30) cc_final: 0.7801 (mt-10) REVERT: A 366 ARG cc_start: 0.8288 (ttm-80) cc_final: 0.8066 (ttm110) REVERT: A 527 LYS cc_start: 0.8676 (tmmt) cc_final: 0.7966 (ttmt) REVERT: A 546 SER cc_start: 0.9081 (t) cc_final: 0.8726 (m) REVERT: A 560 GLN cc_start: 0.8073 (tp40) cc_final: 0.7604 (tp40) REVERT: B 23 ASP cc_start: 0.5130 (OUTLIER) cc_final: 0.4122 (p0) REVERT: B 42 GLN cc_start: 0.8774 (mm-40) cc_final: 0.8305 (mm110) REVERT: B 45 THR cc_start: 0.8189 (OUTLIER) cc_final: 0.7932 (t) REVERT: B 54 ASN cc_start: 0.8706 (m110) cc_final: 0.8423 (m110) REVERT: B 105 GLU cc_start: 0.8075 (tp30) cc_final: 0.7696 (tt0) REVERT: C 228 ARG cc_start: 0.8103 (mtt180) cc_final: 0.7654 (tmt170) REVERT: C 235 ILE cc_start: 0.8994 (mt) cc_final: 0.8567 (mm) REVERT: C 363 HIS cc_start: 0.8045 (t70) cc_final: 0.7826 (t70) REVERT: C 527 LYS cc_start: 0.8658 (tmmt) cc_final: 0.7945 (ttmt) REVERT: C 546 SER cc_start: 0.9075 (t) cc_final: 0.8719 (m) REVERT: C 560 GLN cc_start: 0.8071 (tp40) cc_final: 0.7597 (tp40) REVERT: D 23 ASP cc_start: 0.4911 (OUTLIER) cc_final: 0.4115 (p0) REVERT: D 42 GLN cc_start: 0.8827 (mm-40) cc_final: 0.8599 (mm110) REVERT: D 43 ASN cc_start: 0.8449 (t0) cc_final: 0.8178 (t0) REVERT: D 45 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7851 (t) REVERT: D 54 ASN cc_start: 0.8769 (m110) cc_final: 0.8320 (m110) REVERT: D 70 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8268 (mp) REVERT: D 105 GLU cc_start: 0.8107 (tp30) cc_final: 0.7778 (tt0) REVERT: D 117 LEU cc_start: 0.8901 (mp) cc_final: 0.8629 (mt) REVERT: E 228 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7632 (tmt170) REVERT: E 235 ILE cc_start: 0.9002 (mt) cc_final: 0.8569 (mm) REVERT: E 363 HIS cc_start: 0.8115 (t70) cc_final: 0.7842 (t70) REVERT: E 366 ARG cc_start: 0.8295 (ttm-80) cc_final: 0.8072 (ttm110) REVERT: E 527 LYS cc_start: 0.8695 (tmmt) cc_final: 0.7964 (ttmt) REVERT: E 546 SER cc_start: 0.9083 (t) cc_final: 0.8729 (m) REVERT: E 560 GLN cc_start: 0.7985 (tp-100) cc_final: 0.7568 (tp40) REVERT: F 42 GLN cc_start: 0.8803 (mm-40) cc_final: 0.8569 (mm110) REVERT: F 43 ASN cc_start: 0.8397 (t0) cc_final: 0.8121 (t0) REVERT: F 45 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7869 (t) REVERT: F 54 ASN cc_start: 0.8789 (m110) cc_final: 0.8347 (m110) REVERT: F 70 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8276 (mp) REVERT: F 117 LEU cc_start: 0.8911 (mp) cc_final: 0.8631 (mt) REVERT: G 228 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7652 (tmt170) REVERT: G 235 ILE cc_start: 0.9005 (mt) cc_final: 0.8577 (mm) REVERT: G 527 LYS cc_start: 0.8680 (tmmt) cc_final: 0.7952 (ttmt) REVERT: G 546 SER cc_start: 0.9087 (t) cc_final: 0.8732 (m) REVERT: G 560 GLN cc_start: 0.8061 (tp40) cc_final: 0.7594 (tp40) REVERT: H 42 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8578 (mm110) REVERT: H 43 ASN cc_start: 0.8466 (t0) cc_final: 0.8202 (t0) REVERT: H 45 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7857 (t) REVERT: H 54 ASN cc_start: 0.8771 (m110) cc_final: 0.8325 (m110) REVERT: H 70 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8267 (mp) REVERT: H 105 GLU cc_start: 0.8136 (tp30) cc_final: 0.7672 (mm-30) REVERT: H 117 LEU cc_start: 0.8921 (mp) cc_final: 0.8635 (mt) outliers start: 30 outliers final: 15 residues processed: 261 average time/residue: 0.1538 time to fit residues: 55.2048 Evaluate side-chains 257 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 233 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 358 LYS Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 70 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 55 optimal weight: 2.9990 chunk 70 optimal weight: 0.0000 chunk 109 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 89 optimal weight: 0.0170 chunk 32 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 overall best weight: 1.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.142273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.104836 restraints weight = 20978.991| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 1.91 r_work: 0.3091 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2952 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.74 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2987 r_free = 0.2987 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 16152 Z= 0.121 Angle : 0.465 7.765 21824 Z= 0.242 Chirality : 0.038 0.133 2444 Planarity : 0.003 0.033 2752 Dihedral : 3.450 15.045 2164 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.81 % Allowed : 13.73 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.74 (0.19), residues: 1952 helix: 2.32 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : 0.01 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 366 TYR 0.012 0.001 TYR G 545 PHE 0.011 0.001 PHE G 351 TRP 0.011 0.001 TRP G 379 HIS 0.002 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00283 (16152) covalent geometry : angle 0.46549 (21824) hydrogen bonds : bond 0.03967 ( 1045) hydrogen bonds : angle 3.23327 ( 3111) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 233 time to evaluate : 0.589 Fit side-chains REVERT: A 228 ARG cc_start: 0.8105 (mtt180) cc_final: 0.7621 (tmt170) REVERT: A 235 ILE cc_start: 0.9003 (mt) cc_final: 0.8581 (mm) REVERT: A 295 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7754 (mt-10) REVERT: A 366 ARG cc_start: 0.8322 (ttm-80) cc_final: 0.8065 (ttm110) REVERT: A 527 LYS cc_start: 0.8650 (tmmt) cc_final: 0.7905 (ttmt) REVERT: A 546 SER cc_start: 0.9091 (t) cc_final: 0.8680 (m) REVERT: A 560 GLN cc_start: 0.8074 (tp40) cc_final: 0.7594 (tp40) REVERT: B 23 ASP cc_start: 0.5196 (OUTLIER) cc_final: 0.4197 (p0) REVERT: B 42 GLN cc_start: 0.8649 (mm-40) cc_final: 0.8413 (mm110) REVERT: B 45 THR cc_start: 0.8178 (OUTLIER) cc_final: 0.7948 (t) REVERT: B 54 ASN cc_start: 0.8688 (m110) cc_final: 0.8391 (m110) REVERT: B 105 GLU cc_start: 0.8075 (tp30) cc_final: 0.7681 (tt0) REVERT: C 228 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7636 (tmt170) REVERT: C 235 ILE cc_start: 0.8981 (mt) cc_final: 0.8550 (mm) REVERT: C 363 HIS cc_start: 0.7998 (t70) cc_final: 0.7785 (t70) REVERT: C 527 LYS cc_start: 0.8663 (tmmt) cc_final: 0.7890 (ttmt) REVERT: C 546 SER cc_start: 0.9090 (t) cc_final: 0.8675 (m) REVERT: C 560 GLN cc_start: 0.8061 (tp40) cc_final: 0.7582 (tp40) REVERT: D 23 ASP cc_start: 0.5075 (OUTLIER) cc_final: 0.4154 (p0) REVERT: D 42 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8577 (mm110) REVERT: D 43 ASN cc_start: 0.8404 (t0) cc_final: 0.8152 (t0) REVERT: D 45 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7796 (t) REVERT: D 54 ASN cc_start: 0.8745 (m110) cc_final: 0.8463 (m110) REVERT: D 70 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8218 (mp) REVERT: D 105 GLU cc_start: 0.8038 (tp30) cc_final: 0.7706 (tt0) REVERT: E 228 ARG cc_start: 0.8134 (mtt180) cc_final: 0.7591 (tmt170) REVERT: E 235 ILE cc_start: 0.8979 (mt) cc_final: 0.8552 (mm) REVERT: E 363 HIS cc_start: 0.8084 (t70) cc_final: 0.7816 (t70) REVERT: E 366 ARG cc_start: 0.8293 (ttm-80) cc_final: 0.8054 (ttm110) REVERT: E 527 LYS cc_start: 0.8661 (tmmt) cc_final: 0.7896 (ttmt) REVERT: E 546 SER cc_start: 0.9098 (t) cc_final: 0.8686 (m) REVERT: E 560 GLN cc_start: 0.7847 (tp-100) cc_final: 0.7429 (tp40) REVERT: F 42 GLN cc_start: 0.8794 (mm-40) cc_final: 0.8552 (mm110) REVERT: F 43 ASN cc_start: 0.8455 (t0) cc_final: 0.8183 (t0) REVERT: F 45 THR cc_start: 0.8089 (OUTLIER) cc_final: 0.7847 (t) REVERT: F 54 ASN cc_start: 0.8733 (m110) cc_final: 0.8452 (m110) REVERT: F 70 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8222 (mp) REVERT: F 105 GLU cc_start: 0.8037 (tp30) cc_final: 0.7583 (mm-30) REVERT: G 228 ARG cc_start: 0.8113 (mtt180) cc_final: 0.7638 (tmt170) REVERT: G 235 ILE cc_start: 0.8988 (mt) cc_final: 0.8554 (mm) REVERT: G 363 HIS cc_start: 0.8098 (t70) cc_final: 0.7812 (t70) REVERT: G 366 ARG cc_start: 0.8293 (ttm-80) cc_final: 0.8082 (ttm110) REVERT: G 527 LYS cc_start: 0.8651 (tmmt) cc_final: 0.7888 (ttmt) REVERT: G 546 SER cc_start: 0.9095 (t) cc_final: 0.8684 (m) REVERT: G 560 GLN cc_start: 0.8063 (tp40) cc_final: 0.7587 (tp40) REVERT: H 42 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8563 (mm110) REVERT: H 43 ASN cc_start: 0.8414 (t0) cc_final: 0.8160 (t0) REVERT: H 45 THR cc_start: 0.8054 (OUTLIER) cc_final: 0.7821 (t) REVERT: H 54 ASN cc_start: 0.8730 (m110) cc_final: 0.8449 (m110) REVERT: H 70 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8236 (mp) REVERT: H 105 GLU cc_start: 0.8048 (tp30) cc_final: 0.7571 (mm-30) outliers start: 30 outliers final: 17 residues processed: 253 average time/residue: 0.1536 time to fit residues: 53.4930 Evaluate side-chains 252 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 28 optimal weight: 2.9990 chunk 121 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 179 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 187 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.144097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.106854 restraints weight = 20828.673| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.91 r_work: 0.3114 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2973 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 16152 Z= 0.111 Angle : 0.454 7.855 21824 Z= 0.235 Chirality : 0.038 0.130 2444 Planarity : 0.003 0.032 2752 Dihedral : 3.404 14.958 2164 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.69 % Allowed : 13.92 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.83 (0.19), residues: 1952 helix: 2.38 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : 0.07 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 366 TYR 0.011 0.001 TYR A 545 PHE 0.011 0.001 PHE G 351 TRP 0.011 0.001 TRP G 379 HIS 0.002 0.001 HIS G 258 Details of bonding type rmsd covalent geometry : bond 0.00255 (16152) covalent geometry : angle 0.45430 (21824) hydrogen bonds : bond 0.03748 ( 1045) hydrogen bonds : angle 3.17859 ( 3111) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3904 Ramachandran restraints generated. 1952 Oldfield, 0 Emsley, 1952 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 231 time to evaluate : 0.545 Fit side-chains REVERT: A 228 ARG cc_start: 0.8078 (mtt180) cc_final: 0.7565 (tmt170) REVERT: A 235 ILE cc_start: 0.8975 (mt) cc_final: 0.8550 (mm) REVERT: A 295 GLU cc_start: 0.8119 (mm-30) cc_final: 0.7753 (mt-10) REVERT: A 366 ARG cc_start: 0.8299 (ttm-80) cc_final: 0.8052 (ttm110) REVERT: A 527 LYS cc_start: 0.8646 (tmmt) cc_final: 0.7884 (ttmt) REVERT: A 546 SER cc_start: 0.9065 (t) cc_final: 0.8683 (m) REVERT: A 560 GLN cc_start: 0.8054 (tp40) cc_final: 0.7576 (tp40) REVERT: B 23 ASP cc_start: 0.5139 (OUTLIER) cc_final: 0.4112 (p0) REVERT: B 38 ARG cc_start: 0.8864 (mtm-85) cc_final: 0.8510 (mtt90) REVERT: B 54 ASN cc_start: 0.8667 (m110) cc_final: 0.8463 (m110) REVERT: B 105 GLU cc_start: 0.8058 (tp30) cc_final: 0.7673 (tt0) REVERT: C 228 ARG cc_start: 0.8068 (mtt180) cc_final: 0.7570 (tmt170) REVERT: C 235 ILE cc_start: 0.8959 (mt) cc_final: 0.8525 (mm) REVERT: C 363 HIS cc_start: 0.8071 (t70) cc_final: 0.7844 (t70) REVERT: C 527 LYS cc_start: 0.8635 (tmmt) cc_final: 0.7865 (ttmt) REVERT: C 546 SER cc_start: 0.9063 (t) cc_final: 0.8682 (m) REVERT: C 560 GLN cc_start: 0.8043 (tp40) cc_final: 0.7562 (tp40) REVERT: D 23 ASP cc_start: 0.4953 (OUTLIER) cc_final: 0.4058 (p0) REVERT: D 42 GLN cc_start: 0.8831 (mm-40) cc_final: 0.8586 (mm110) REVERT: D 43 ASN cc_start: 0.8185 (t0) cc_final: 0.7920 (t0) REVERT: D 45 THR cc_start: 0.8030 (OUTLIER) cc_final: 0.7809 (t) REVERT: D 54 ASN cc_start: 0.8738 (m110) cc_final: 0.8267 (m110) REVERT: D 70 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8158 (mp) REVERT: D 105 GLU cc_start: 0.8018 (tp30) cc_final: 0.7686 (tt0) REVERT: E 228 ARG cc_start: 0.8062 (mtt180) cc_final: 0.7542 (tmt170) REVERT: E 235 ILE cc_start: 0.8961 (mt) cc_final: 0.8528 (mm) REVERT: E 363 HIS cc_start: 0.8064 (t70) cc_final: 0.7794 (t70) REVERT: E 366 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.8019 (ttm110) REVERT: E 527 LYS cc_start: 0.8650 (tmmt) cc_final: 0.7881 (ttmt) REVERT: E 546 SER cc_start: 0.9073 (t) cc_final: 0.8694 (m) REVERT: E 560 GLN cc_start: 0.7948 (tp-100) cc_final: 0.7512 (tp40) REVERT: F 42 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8561 (mm110) REVERT: F 43 ASN cc_start: 0.8392 (t0) cc_final: 0.8144 (t0) REVERT: F 45 THR cc_start: 0.8062 (OUTLIER) cc_final: 0.7855 (t) REVERT: F 54 ASN cc_start: 0.8746 (m110) cc_final: 0.8284 (m110) REVERT: F 70 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8161 (mp) REVERT: F 105 GLU cc_start: 0.8029 (tp30) cc_final: 0.7690 (tt0) REVERT: G 228 ARG cc_start: 0.8080 (mtt180) cc_final: 0.7570 (tmt170) REVERT: G 235 ILE cc_start: 0.8964 (mt) cc_final: 0.8549 (mm) REVERT: G 363 HIS cc_start: 0.8131 (t70) cc_final: 0.7854 (t70) REVERT: G 366 ARG cc_start: 0.8260 (ttm-80) cc_final: 0.8046 (ttm110) REVERT: G 527 LYS cc_start: 0.8635 (tmmt) cc_final: 0.7874 (ttmt) REVERT: G 546 SER cc_start: 0.9073 (t) cc_final: 0.8692 (m) REVERT: G 560 GLN cc_start: 0.8040 (tp40) cc_final: 0.7562 (tp40) REVERT: H 42 GLN cc_start: 0.8820 (mm-40) cc_final: 0.8575 (mm110) REVERT: H 43 ASN cc_start: 0.8251 (t0) cc_final: 0.8002 (t0) REVERT: H 45 THR cc_start: 0.8043 (OUTLIER) cc_final: 0.7827 (t) REVERT: H 54 ASN cc_start: 0.8744 (m110) cc_final: 0.8284 (m110) REVERT: H 70 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8163 (mp) REVERT: H 105 GLU cc_start: 0.8021 (tp30) cc_final: 0.7688 (tt0) outliers start: 28 outliers final: 18 residues processed: 250 average time/residue: 0.1630 time to fit residues: 56.2530 Evaluate side-chains 253 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 227 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain B residue 23 ASP Chi-restraints excluded: chain B residue 39 SER Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 554 VAL Chi-restraints excluded: chain D residue 23 ASP Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 70 LEU Chi-restraints excluded: chain E residue 131 LEU Chi-restraints excluded: chain E residue 210 MET Chi-restraints excluded: chain E residue 307 VAL Chi-restraints excluded: chain E residue 554 VAL Chi-restraints excluded: chain F residue 39 SER Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 70 LEU Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 210 MET Chi-restraints excluded: chain G residue 307 VAL Chi-restraints excluded: chain G residue 554 VAL Chi-restraints excluded: chain H residue 39 SER Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 70 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 22 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 178 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 167 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 180 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 60 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.144386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.111020 restraints weight = 20785.847| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.18 r_work: 0.3077 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3083 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3083 r_free = 0.3083 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3083 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 16152 Z= 0.110 Angle : 0.456 8.022 21824 Z= 0.236 Chirality : 0.038 0.123 2444 Planarity : 0.003 0.030 2752 Dihedral : 3.389 14.453 2164 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.93 % Allowed : 13.80 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.87 (0.19), residues: 1952 helix: 2.40 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : 0.09 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 366 TYR 0.011 0.001 TYR G 545 PHE 0.011 0.001 PHE G 351 TRP 0.011 0.001 TRP G 379 HIS 0.002 0.001 HIS C 258 Details of bonding type rmsd covalent geometry : bond 0.00252 (16152) covalent geometry : angle 0.45596 (21824) hydrogen bonds : bond 0.03744 ( 1045) hydrogen bonds : angle 3.17714 ( 3111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4182.62 seconds wall clock time: 71 minutes 57.04 seconds (4317.04 seconds total)