Starting phenix.real_space_refine on Wed Sep 17 22:44:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vc2_43130/09_2025/8vc2_43130.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vc2_43130/09_2025/8vc2_43130.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8vc2_43130/09_2025/8vc2_43130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vc2_43130/09_2025/8vc2_43130.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vc2_43130/09_2025/8vc2_43130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vc2_43130/09_2025/8vc2_43130.map" } resolution = 3.98 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= 0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 120 5.16 5 C 7720 2.51 5 N 1932 2.21 5 O 2020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11796 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2918 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 11, 'TRANS': 367} Chain breaks: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 71 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 4, 'GLU:plan': 2, 'HIS:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 45 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'PSC': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'PSC:plan-3': 1, 'PSC:plan-4': 1} Unresolved non-hydrogen planarities: 6 Restraints were copied for chains: B, C, D Time building chain proxies: 2.62, per 1000 atoms: 0.22 Number of scatterers: 11796 At special positions: 0 Unit cell: (103.75, 103.75, 96.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 120 16.00 P 4 15.00 O 2020 8.00 N 1932 7.00 C 7720 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: 1.34 Conformation dependent library (CDL) restraints added in 615.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 85.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 Processing helix chain 'A' and resid 51 through 79 Processing helix chain 'A' and resid 89 through 112 removed outlier: 3.669A pdb=" N VAL A 102 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 135 removed outlier: 4.555A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 175 removed outlier: 4.070A pdb=" N GLU A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 230 removed outlier: 3.533A pdb=" N TYR A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 340 removed outlier: 5.042A pdb=" N GLY A 292 " --> pdb=" O CYS A 288 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Proline residue: A 315 - end of helix removed outlier: 3.635A pdb=" N LEU A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 344 through 390 removed outlier: 4.128A pdb=" N MET A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 3.724A pdb=" N GLU A 375 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.983A pdb=" N MET A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 424 through 446 removed outlier: 3.650A pdb=" N VAL A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 51 through 79 Processing helix chain 'B' and resid 89 through 112 removed outlier: 3.669A pdb=" N VAL B 102 " --> pdb=" O CYS B 98 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 135 removed outlier: 4.555A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 175 removed outlier: 4.070A pdb=" N GLU B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 230 removed outlier: 3.533A pdb=" N TYR B 186 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLY B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 340 removed outlier: 5.042A pdb=" N GLY B 292 " --> pdb=" O CYS B 288 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Proline residue: B 315 - end of helix removed outlier: 3.633A pdb=" N LEU B 320 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Proline residue: B 331 - end of helix Processing helix chain 'B' and resid 344 through 390 removed outlier: 4.129A pdb=" N MET B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) Proline residue: B 368 - end of helix removed outlier: 3.724A pdb=" N GLU B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 410 removed outlier: 3.982A pdb=" N MET B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 424 through 446 removed outlier: 3.650A pdb=" N VAL B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 32 Processing helix chain 'C' and resid 51 through 79 Processing helix chain 'C' and resid 89 through 112 removed outlier: 3.668A pdb=" N VAL C 102 " --> pdb=" O CYS C 98 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 135 removed outlier: 4.555A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU C 134 " --> pdb=" O ALA C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 175 removed outlier: 4.069A pdb=" N GLU C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 230 removed outlier: 3.533A pdb=" N TYR C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 340 removed outlier: 5.042A pdb=" N GLY C 292 " --> pdb=" O CYS C 288 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS C 302 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) Proline residue: C 315 - end of helix removed outlier: 3.634A pdb=" N LEU C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Proline residue: C 331 - end of helix Processing helix chain 'C' and resid 344 through 390 removed outlier: 4.128A pdb=" N MET C 362 " --> pdb=" O HIS C 358 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.724A pdb=" N GLU C 375 " --> pdb=" O TYR C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 410 removed outlier: 3.983A pdb=" N MET C 408 " --> pdb=" O SER C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 424 through 446 removed outlier: 3.650A pdb=" N VAL C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR C 436 " --> pdb=" O GLY C 432 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL C 439 " --> pdb=" O THR C 435 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 444 " --> pdb=" O ILE C 440 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 32 Processing helix chain 'D' and resid 51 through 79 Processing helix chain 'D' and resid 89 through 112 removed outlier: 3.668A pdb=" N VAL D 102 " --> pdb=" O CYS D 98 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 135 removed outlier: 4.556A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU D 134 " --> pdb=" O ALA D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 175 removed outlier: 4.070A pdb=" N GLU D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 155 " --> pdb=" O LEU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 230 removed outlier: 3.533A pdb=" N TYR D 186 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLY D 188 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE D 189 " --> pdb=" O ASN D 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER D 226 " --> pdb=" O ASN D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 340 removed outlier: 5.042A pdb=" N GLY D 292 " --> pdb=" O CYS D 288 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS D 302 " --> pdb=" O ARG D 298 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) Proline residue: D 315 - end of helix removed outlier: 3.633A pdb=" N LEU D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Proline residue: D 331 - end of helix Processing helix chain 'D' and resid 344 through 390 removed outlier: 4.129A pdb=" N MET D 362 " --> pdb=" O HIS D 358 " (cutoff:3.500A) Proline residue: D 368 - end of helix removed outlier: 3.725A pdb=" N GLU D 375 " --> pdb=" O TYR D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 410 removed outlier: 3.983A pdb=" N MET D 408 " --> pdb=" O SER D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 424 through 446 removed outlier: 3.651A pdb=" N VAL D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR D 436 " --> pdb=" O GLY D 432 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL D 439 " --> pdb=" O THR D 435 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE D 444 " --> pdb=" O ILE D 440 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 19 Processing sheet with id=AA4, first strand: chain 'D' and resid 17 through 19 988 hydrogen bonds defined for protein. 2940 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: 1.99 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1752 1.30 - 1.43: 3008 1.43 - 1.56: 7016 1.56 - 1.69: 56 1.69 - 1.81: 180 Bond restraints: 12012 Sorted by residual: bond pdb=" C1 PSC C 501 " pdb=" O01 PSC C 501 " ideal model delta sigma weight residual 1.331 1.443 -0.112 2.00e-02 2.50e+03 3.14e+01 bond pdb=" C1 PSC B 501 " pdb=" O01 PSC B 501 " ideal model delta sigma weight residual 1.331 1.443 -0.112 2.00e-02 2.50e+03 3.11e+01 bond pdb=" C1 PSC D 501 " pdb=" O01 PSC D 501 " ideal model delta sigma weight residual 1.331 1.442 -0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" C1 PSC A 501 " pdb=" O01 PSC A 501 " ideal model delta sigma weight residual 1.331 1.441 -0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" C19 PSC B 501 " pdb=" O03 PSC B 501 " ideal model delta sigma weight residual 1.326 1.426 -0.100 2.00e-02 2.50e+03 2.51e+01 ... (remaining 12007 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.36: 16188 3.36 - 6.71: 92 6.71 - 10.07: 4 10.07 - 13.43: 8 13.43 - 16.78: 4 Bond angle restraints: 16296 Sorted by residual: angle pdb=" O11 PSC B 501 " pdb=" P PSC B 501 " pdb=" O12 PSC B 501 " ideal model delta sigma weight residual 93.08 109.86 -16.78 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O11 PSC D 501 " pdb=" P PSC D 501 " pdb=" O12 PSC D 501 " ideal model delta sigma weight residual 93.08 109.86 -16.78 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O11 PSC C 501 " pdb=" P PSC C 501 " pdb=" O12 PSC C 501 " ideal model delta sigma weight residual 93.08 109.85 -16.77 3.00e+00 1.11e-01 3.13e+01 angle pdb=" O11 PSC A 501 " pdb=" P PSC A 501 " pdb=" O12 PSC A 501 " ideal model delta sigma weight residual 93.08 109.85 -16.77 3.00e+00 1.11e-01 3.12e+01 angle pdb=" C2 PSC A 501 " pdb=" C1 PSC A 501 " pdb=" O01 PSC A 501 " ideal model delta sigma weight residual 111.06 121.59 -10.53 3.00e+00 1.11e-01 1.23e+01 ... (remaining 16291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.84: 6877 23.84 - 47.68: 223 47.68 - 71.53: 76 71.53 - 95.37: 8 95.37 - 119.21: 4 Dihedral angle restraints: 7188 sinusoidal: 2764 harmonic: 4424 Sorted by residual: dihedral pdb=" CA LEU C 135 " pdb=" C LEU C 135 " pdb=" N GLY C 136 " pdb=" CA GLY C 136 " ideal model delta harmonic sigma weight residual 180.00 157.00 23.00 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA LEU A 135 " pdb=" C LEU A 135 " pdb=" N GLY A 136 " pdb=" CA GLY A 136 " ideal model delta harmonic sigma weight residual 180.00 157.01 22.99 0 5.00e+00 4.00e-02 2.11e+01 dihedral pdb=" CA LEU B 135 " pdb=" C LEU B 135 " pdb=" N GLY B 136 " pdb=" CA GLY B 136 " ideal model delta harmonic sigma weight residual 180.00 157.02 22.98 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 7185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1294 0.029 - 0.058: 527 0.058 - 0.087: 133 0.087 - 0.116: 46 0.116 - 0.144: 16 Chirality restraints: 2016 Sorted by residual: chirality pdb=" C02 PSC A 501 " pdb=" C01 PSC A 501 " pdb=" C03 PSC A 501 " pdb=" O01 PSC A 501 " both_signs ideal model delta sigma weight residual False 2.37 2.51 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA TYR C 124 " pdb=" N TYR C 124 " pdb=" C TYR C 124 " pdb=" CB TYR C 124 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.21e-01 chirality pdb=" CA TYR B 124 " pdb=" N TYR B 124 " pdb=" C TYR B 124 " pdb=" CB TYR B 124 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 ... (remaining 2013 not shown) Planarity restraints: 1956 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 309 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C ALA B 309 " 0.058 2.00e-02 2.50e+03 pdb=" O ALA B 309 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP B 310 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 309 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.11e+01 pdb=" C ALA C 309 " 0.058 2.00e-02 2.50e+03 pdb=" O ALA C 309 " -0.021 2.00e-02 2.50e+03 pdb=" N ASP C 310 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 309 " 0.017 2.00e-02 2.50e+03 3.33e-02 1.11e+01 pdb=" C ALA D 309 " -0.058 2.00e-02 2.50e+03 pdb=" O ALA D 309 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP D 310 " 0.020 2.00e-02 2.50e+03 ... (remaining 1953 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3829 2.86 - 3.37: 12927 3.37 - 3.88: 19578 3.88 - 4.39: 21966 4.39 - 4.90: 36502 Nonbonded interactions: 94802 Sorted by model distance: nonbonded pdb=" OD2 ASP A 165 " pdb=" NE1 TRP A 354 " model vdw 2.353 3.120 nonbonded pdb=" OD2 ASP B 165 " pdb=" NE1 TRP B 354 " model vdw 2.353 3.120 nonbonded pdb=" OD2 ASP D 165 " pdb=" NE1 TRP D 354 " model vdw 2.353 3.120 nonbonded pdb=" OD2 ASP C 165 " pdb=" NE1 TRP C 354 " model vdw 2.354 3.120 nonbonded pdb=" OE2 GLU A 76 " pdb=" ND2 ASN A 185 " model vdw 2.363 3.120 ... (remaining 94797 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.660 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.570 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 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 : 0.006 0.112 12012 Z= 0.295 Angle : 0.843 16.784 16296 Z= 0.468 Chirality : 0.036 0.144 2016 Planarity : 0.010 0.087 1956 Dihedral : 14.087 119.212 4332 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.31 % Allowed : 1.18 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.98 (0.20), residues: 1500 helix: -0.33 (0.14), residues: 1232 sheet: 0.54 (0.71), residues: 48 loop : -1.91 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.003 ARG D 117 TYR 0.037 0.006 TYR B 124 PHE 0.010 0.002 PHE C 203 TRP 0.029 0.007 TRP D 354 HIS 0.008 0.003 HIS D 358 Details of bonding type rmsd covalent geometry : bond 0.00558 (12012) covalent geometry : angle 0.84302 (16296) hydrogen bonds : bond 0.09684 ( 988) hydrogen bonds : angle 5.48264 ( 2940) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 449 time to evaluate : 0.505 Fit side-chains revert: symmetry clash REVERT: A 197 MET cc_start: 0.7610 (mmm) cc_final: 0.7153 (tmm) REVERT: A 401 GLU cc_start: 0.7893 (tt0) cc_final: 0.7298 (tt0) REVERT: A 404 SER cc_start: 0.8411 (p) cc_final: 0.8001 (t) REVERT: B 167 CYS cc_start: 0.7256 (m) cc_final: 0.6814 (t) REVERT: B 197 MET cc_start: 0.7666 (mmm) cc_final: 0.7313 (tmm) REVERT: B 384 CYS cc_start: 0.5109 (m) cc_final: 0.4103 (m) REVERT: B 401 GLU cc_start: 0.7990 (tt0) cc_final: 0.7257 (tt0) REVERT: B 404 SER cc_start: 0.8480 (p) cc_final: 0.8125 (t) REVERT: C 167 CYS cc_start: 0.7238 (m) cc_final: 0.6838 (t) REVERT: C 197 MET cc_start: 0.7604 (mmm) cc_final: 0.7260 (tmm) REVERT: C 384 CYS cc_start: 0.5188 (m) cc_final: 0.4765 (m) REVERT: C 401 GLU cc_start: 0.7925 (tt0) cc_final: 0.7317 (tt0) REVERT: C 404 SER cc_start: 0.8485 (p) cc_final: 0.8157 (t) REVERT: D 167 CYS cc_start: 0.7256 (m) cc_final: 0.6819 (t) REVERT: D 197 MET cc_start: 0.7618 (mmm) cc_final: 0.7282 (tmm) REVERT: D 384 CYS cc_start: 0.5078 (m) cc_final: 0.4742 (m) REVERT: D 401 GLU cc_start: 0.7859 (tt0) cc_final: 0.7290 (tt0) REVERT: D 404 SER cc_start: 0.8483 (p) cc_final: 0.8120 (t) outliers start: 4 outliers final: 1 residues processed: 453 average time/residue: 0.1086 time to fit residues: 71.0397 Evaluate side-chains 298 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 297 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.2980 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4522 r_free = 0.4522 target = 0.227426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.193014 restraints weight = 12789.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.198227 restraints weight = 8002.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.202605 restraints weight = 5773.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.204856 restraints weight = 4467.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.207107 restraints weight = 3762.894| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 12012 Z= 0.150 Angle : 0.646 10.294 16296 Z= 0.329 Chirality : 0.037 0.134 2016 Planarity : 0.004 0.044 1956 Dihedral : 8.592 65.893 1750 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 4.64 % Allowed : 14.70 % Favored : 80.66 % 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 aren not related in a simple way. whole: 1.61 (0.22), residues: 1500 helix: 1.42 (0.14), residues: 1264 sheet: 0.12 (0.71), residues: 48 loop : -0.81 (0.49), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 344 TYR 0.018 0.002 TYR D 124 PHE 0.017 0.002 PHE C 203 TRP 0.006 0.001 TRP C 193 HIS 0.003 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00319 (12012) covalent geometry : angle 0.64618 (16296) hydrogen bonds : bond 0.04608 ( 988) hydrogen bonds : angle 3.90342 ( 2940) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 322 time to evaluate : 0.452 Fit side-chains REVERT: A 26 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7647 (mp) REVERT: B 26 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7605 (mp) REVERT: B 125 MET cc_start: 0.6804 (mmt) cc_final: 0.6543 (tpt) REVERT: B 346 HIS cc_start: 0.7673 (OUTLIER) cc_final: 0.6954 (t-90) REVERT: C 26 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7608 (mp) REVERT: C 179 GLN cc_start: 0.7370 (tm-30) cc_final: 0.6908 (pm20) REVERT: C 297 MET cc_start: 0.7263 (mpp) cc_final: 0.6880 (mpp) REVERT: C 346 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.6941 (t-90) REVERT: C 401 GLU cc_start: 0.8240 (tt0) cc_final: 0.7683 (tt0) REVERT: D 26 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7625 (mp) REVERT: D 125 MET cc_start: 0.6764 (mmt) cc_final: 0.6549 (tpt) REVERT: D 179 GLN cc_start: 0.7400 (tm-30) cc_final: 0.6953 (pm20) REVERT: D 346 HIS cc_start: 0.7690 (OUTLIER) cc_final: 0.6942 (t-90) REVERT: D 401 GLU cc_start: 0.8217 (tt0) cc_final: 0.7594 (tt0) outliers start: 59 outliers final: 28 residues processed: 360 average time/residue: 0.1011 time to fit residues: 53.2632 Evaluate side-chains 286 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 251 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 395 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 134 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 112 optimal weight: 0.0770 chunk 52 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 119 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS B 358 HIS C 358 HIS D 358 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.229679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.194868 restraints weight = 12994.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.200092 restraints weight = 8343.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.203936 restraints weight = 6079.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.205994 restraints weight = 4803.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.208187 restraints weight = 4121.571| |-----------------------------------------------------------------------------| r_work (final): 0.4334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.3660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12012 Z= 0.138 Angle : 0.649 11.606 16296 Z= 0.318 Chirality : 0.038 0.194 2016 Planarity : 0.004 0.054 1956 Dihedral : 7.670 56.569 1748 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 3.93 % Allowed : 18.55 % Favored : 77.52 % 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 aren not related in a simple way. whole: 2.11 (0.22), residues: 1500 helix: 1.78 (0.14), residues: 1268 sheet: 0.31 (0.77), residues: 48 loop : -0.83 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 117 TYR 0.016 0.001 TYR C 124 PHE 0.014 0.001 PHE C 203 TRP 0.006 0.001 TRP A 180 HIS 0.002 0.001 HIS B 326 Details of bonding type rmsd covalent geometry : bond 0.00302 (12012) covalent geometry : angle 0.64894 (16296) hydrogen bonds : bond 0.04239 ( 988) hydrogen bonds : angle 3.80147 ( 2940) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 275 time to evaluate : 0.514 Fit side-chains REVERT: A 26 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7586 (mp) REVERT: A 27 LYS cc_start: 0.7409 (tttt) cc_final: 0.7085 (tmtt) REVERT: A 121 MET cc_start: 0.7898 (tmm) cc_final: 0.7665 (tmm) REVERT: A 197 MET cc_start: 0.7586 (tpt) cc_final: 0.7285 (tmm) REVERT: A 297 MET cc_start: 0.7110 (mpp) cc_final: 0.6588 (mpp) REVERT: B 26 LEU cc_start: 0.7974 (OUTLIER) cc_final: 0.7631 (mp) REVERT: B 297 MET cc_start: 0.7134 (mpp) cc_final: 0.6712 (mpp) REVERT: B 346 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.6934 (t-90) REVERT: B 443 GLN cc_start: 0.7827 (tt0) cc_final: 0.7289 (tt0) REVERT: C 26 LEU cc_start: 0.8025 (tp) cc_final: 0.7625 (mp) REVERT: C 27 LYS cc_start: 0.7461 (tttt) cc_final: 0.7154 (tttm) REVERT: C 67 ILE cc_start: 0.8830 (tp) cc_final: 0.8484 (tt) REVERT: C 171 MET cc_start: 0.7803 (tmm) cc_final: 0.7594 (tmm) REVERT: C 179 GLN cc_start: 0.7377 (tm-30) cc_final: 0.6904 (pm20) REVERT: C 346 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.6936 (t-90) REVERT: D 26 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7647 (mp) REVERT: D 67 ILE cc_start: 0.8820 (tp) cc_final: 0.8517 (tt) REVERT: D 179 GLN cc_start: 0.7363 (tm-30) cc_final: 0.6862 (pm20) REVERT: D 297 MET cc_start: 0.7180 (mpp) cc_final: 0.6787 (mpp) REVERT: D 346 HIS cc_start: 0.7632 (OUTLIER) cc_final: 0.6935 (t-90) REVERT: D 443 GLN cc_start: 0.7905 (tt0) cc_final: 0.7496 (tt0) outliers start: 50 outliers final: 38 residues processed: 304 average time/residue: 0.0977 time to fit residues: 44.1813 Evaluate side-chains 284 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 240 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 5 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 110 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 95 optimal weight: 0.2980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4512 r_free = 0.4512 target = 0.225821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.188517 restraints weight = 13043.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.193654 restraints weight = 8392.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.197494 restraints weight = 6165.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.199713 restraints weight = 4931.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.201845 restraints weight = 4241.925| |-----------------------------------------------------------------------------| r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6907 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12012 Z= 0.134 Angle : 0.626 11.882 16296 Z= 0.310 Chirality : 0.038 0.164 2016 Planarity : 0.004 0.056 1956 Dihedral : 7.251 51.828 1748 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.03 % Allowed : 19.65 % Favored : 75.31 % 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 aren not related in a simple way. whole: 2.43 (0.22), residues: 1500 helix: 2.02 (0.14), residues: 1268 sheet: -0.00 (0.75), residues: 48 loop : -0.79 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 117 TYR 0.018 0.001 TYR B 124 PHE 0.011 0.001 PHE A 39 TRP 0.006 0.001 TRP A 193 HIS 0.002 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00305 (12012) covalent geometry : angle 0.62644 (16296) hydrogen bonds : bond 0.04223 ( 988) hydrogen bonds : angle 3.77212 ( 2940) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 287 time to evaluate : 0.406 Fit side-chains REVERT: A 26 LEU cc_start: 0.7872 (OUTLIER) cc_final: 0.7604 (mp) REVERT: A 121 MET cc_start: 0.7815 (tmm) cc_final: 0.7503 (tmm) REVERT: A 297 MET cc_start: 0.7228 (mpp) cc_final: 0.6761 (mpp) REVERT: A 332 TYR cc_start: 0.7391 (t80) cc_final: 0.7143 (t80) REVERT: B 26 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7737 (mp) REVERT: B 67 ILE cc_start: 0.8849 (tp) cc_final: 0.8535 (tt) REVERT: B 121 MET cc_start: 0.7869 (tmm) cc_final: 0.7607 (tmm) REVERT: B 297 MET cc_start: 0.7230 (mpp) cc_final: 0.6834 (mpp) REVERT: B 346 HIS cc_start: 0.7592 (OUTLIER) cc_final: 0.6934 (t-90) REVERT: C 26 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7657 (mp) REVERT: C 67 ILE cc_start: 0.8851 (tp) cc_final: 0.8575 (tt) REVERT: C 179 GLN cc_start: 0.7357 (tm-30) cc_final: 0.7135 (pm20) REVERT: C 346 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.6967 (t-90) REVERT: D 24 PHE cc_start: 0.7794 (t80) cc_final: 0.7473 (t80) REVERT: D 26 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7668 (mp) REVERT: D 67 ILE cc_start: 0.8842 (tp) cc_final: 0.8597 (tt) REVERT: D 179 GLN cc_start: 0.7526 (tm-30) cc_final: 0.7204 (pm20) REVERT: D 297 MET cc_start: 0.7219 (mpp) cc_final: 0.6909 (mpp) REVERT: D 346 HIS cc_start: 0.7614 (OUTLIER) cc_final: 0.6941 (t-90) REVERT: D 443 GLN cc_start: 0.8016 (tt0) cc_final: 0.7757 (tt0) outliers start: 64 outliers final: 42 residues processed: 329 average time/residue: 0.1000 time to fit residues: 48.8748 Evaluate side-chains 301 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 51 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 104 optimal weight: 0.0770 chunk 1 optimal weight: 0.5980 chunk 3 optimal weight: 7.9990 chunk 121 optimal weight: 0.9980 chunk 95 optimal weight: 20.0000 chunk 28 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.226941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.190586 restraints weight = 12956.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.195443 restraints weight = 8546.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.198566 restraints weight = 6327.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.201475 restraints weight = 5146.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.202860 restraints weight = 4419.918| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.4481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12012 Z= 0.130 Angle : 0.640 11.770 16296 Z= 0.310 Chirality : 0.037 0.162 2016 Planarity : 0.004 0.056 1956 Dihedral : 6.997 51.454 1748 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 5.66 % Allowed : 20.52 % Favored : 73.82 % 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 aren not related in a simple way. whole: 2.74 (0.22), residues: 1500 helix: 2.33 (0.14), residues: 1256 sheet: -0.15 (0.73), residues: 48 loop : -1.20 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 117 TYR 0.018 0.001 TYR D 124 PHE 0.010 0.001 PHE A 39 TRP 0.006 0.001 TRP A 193 HIS 0.002 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00293 (12012) covalent geometry : angle 0.64050 (16296) hydrogen bonds : bond 0.03972 ( 988) hydrogen bonds : angle 3.69065 ( 2940) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 261 time to evaluate : 0.455 Fit side-chains REVERT: A 26 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7553 (mp) REVERT: A 67 ILE cc_start: 0.8849 (tp) cc_final: 0.8575 (tt) REVERT: A 121 MET cc_start: 0.7687 (tmm) cc_final: 0.7393 (tmm) REVERT: A 197 MET cc_start: 0.7604 (tpt) cc_final: 0.7394 (tmm) REVERT: A 362 MET cc_start: 0.7090 (tmm) cc_final: 0.6783 (tmm) REVERT: B 26 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7754 (mp) REVERT: B 67 ILE cc_start: 0.8881 (tp) cc_final: 0.8546 (tt) REVERT: B 297 MET cc_start: 0.7172 (mpp) cc_final: 0.6917 (mpp) REVERT: B 346 HIS cc_start: 0.7615 (OUTLIER) cc_final: 0.6950 (t-90) REVERT: C 26 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7748 (mp) REVERT: C 67 ILE cc_start: 0.8967 (tp) cc_final: 0.8575 (tt) REVERT: C 178 ARG cc_start: 0.7604 (ttp-170) cc_final: 0.7396 (ptt180) REVERT: C 297 MET cc_start: 0.7111 (mpp) cc_final: 0.6847 (mpp) REVERT: C 301 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7649 (mp) REVERT: C 346 HIS cc_start: 0.7657 (OUTLIER) cc_final: 0.7008 (t-90) REVERT: D 26 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7803 (mp) REVERT: D 67 ILE cc_start: 0.8934 (tp) cc_final: 0.8564 (tt) REVERT: D 297 MET cc_start: 0.7270 (mpp) cc_final: 0.7056 (mpp) REVERT: D 346 HIS cc_start: 0.7636 (OUTLIER) cc_final: 0.6943 (t-90) REVERT: D 443 GLN cc_start: 0.7976 (tt0) cc_final: 0.7751 (tt0) outliers start: 72 outliers final: 52 residues processed: 309 average time/residue: 0.0951 time to fit residues: 43.4248 Evaluate side-chains 307 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 247 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 68 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 5.9990 chunk 130 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 117 optimal weight: 9.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 HIS A 443 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.225766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.190013 restraints weight = 13026.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.193412 restraints weight = 8877.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.195673 restraints weight = 6726.915| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.198189 restraints weight = 5360.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.199259 restraints weight = 4526.971| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12012 Z= 0.135 Angle : 0.649 11.550 16296 Z= 0.312 Chirality : 0.037 0.165 2016 Planarity : 0.004 0.055 1956 Dihedral : 6.810 52.066 1748 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.58 % Allowed : 20.36 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.86 (0.22), residues: 1500 helix: 2.42 (0.14), residues: 1256 sheet: -0.13 (0.74), residues: 48 loop : -1.21 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 117 TYR 0.016 0.001 TYR D 124 PHE 0.009 0.001 PHE A 39 TRP 0.008 0.001 TRP C 180 HIS 0.002 0.001 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00313 (12012) covalent geometry : angle 0.64947 (16296) hydrogen bonds : bond 0.04000 ( 988) hydrogen bonds : angle 3.69819 ( 2940) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 249 time to evaluate : 0.343 Fit side-chains REVERT: A 26 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7575 (mp) REVERT: A 27 LYS cc_start: 0.7253 (tttt) cc_final: 0.6931 (tmtt) REVERT: A 67 ILE cc_start: 0.8943 (tp) cc_final: 0.8562 (tt) REVERT: A 362 MET cc_start: 0.7216 (tmm) cc_final: 0.6918 (tmm) REVERT: B 26 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7674 (mp) REVERT: B 117 ARG cc_start: 0.6960 (ttp-110) cc_final: 0.6540 (mtm110) REVERT: B 121 MET cc_start: 0.7623 (tmm) cc_final: 0.7340 (tmm) REVERT: B 297 MET cc_start: 0.7289 (mpp) cc_final: 0.7027 (mpp) REVERT: B 346 HIS cc_start: 0.7675 (OUTLIER) cc_final: 0.6941 (t-90) REVERT: C 26 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7590 (mp) REVERT: C 297 MET cc_start: 0.7271 (mpp) cc_final: 0.6980 (mpp) REVERT: C 301 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7657 (mp) REVERT: C 346 HIS cc_start: 0.7725 (OUTLIER) cc_final: 0.6994 (t-90) REVERT: D 26 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7666 (mp) REVERT: D 346 HIS cc_start: 0.7686 (OUTLIER) cc_final: 0.6906 (t-90) REVERT: D 401 GLU cc_start: 0.8467 (tt0) cc_final: 0.8242 (tt0) REVERT: D 443 GLN cc_start: 0.8009 (tt0) cc_final: 0.7467 (tt0) outliers start: 71 outliers final: 54 residues processed: 297 average time/residue: 0.1018 time to fit residues: 44.7017 Evaluate side-chains 296 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 234 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 104 optimal weight: 2.9990 chunk 139 optimal weight: 0.7980 chunk 57 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 82 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS B 443 GLN ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.226339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.188618 restraints weight = 12954.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.193517 restraints weight = 8484.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.197368 restraints weight = 6268.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.199567 restraints weight = 5044.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.201016 restraints weight = 4358.363| |-----------------------------------------------------------------------------| r_work (final): 0.4277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12012 Z= 0.133 Angle : 0.674 13.633 16296 Z= 0.318 Chirality : 0.037 0.177 2016 Planarity : 0.004 0.055 1956 Dihedral : 6.722 53.325 1748 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 5.27 % Allowed : 21.54 % Favored : 73.19 % 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 aren not related in a simple way. whole: 2.93 (0.22), residues: 1500 helix: 2.49 (0.14), residues: 1256 sheet: -0.35 (0.73), residues: 48 loop : -1.28 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 178 TYR 0.016 0.001 TYR D 124 PHE 0.013 0.001 PHE D 31 TRP 0.006 0.001 TRP A 193 HIS 0.002 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00307 (12012) covalent geometry : angle 0.67394 (16296) hydrogen bonds : bond 0.03918 ( 988) hydrogen bonds : angle 3.67487 ( 2940) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 243 time to evaluate : 0.510 Fit side-chains REVERT: A 26 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7545 (mp) REVERT: A 27 LYS cc_start: 0.7199 (tttt) cc_final: 0.6851 (tmtt) REVERT: A 67 ILE cc_start: 0.8934 (tp) cc_final: 0.8530 (tt) REVERT: B 26 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7667 (mp) REVERT: B 27 LYS cc_start: 0.7428 (tttt) cc_final: 0.7049 (tptt) REVERT: B 121 MET cc_start: 0.7601 (tmm) cc_final: 0.7333 (tmm) REVERT: B 346 HIS cc_start: 0.7580 (OUTLIER) cc_final: 0.6920 (t-90) REVERT: C 26 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7575 (mp) REVERT: C 27 LYS cc_start: 0.7360 (tttt) cc_final: 0.7078 (tptm) REVERT: C 301 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7607 (mp) REVERT: C 346 HIS cc_start: 0.7676 (OUTLIER) cc_final: 0.6944 (t-90) REVERT: D 26 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7689 (mp) REVERT: D 27 LYS cc_start: 0.7490 (tttt) cc_final: 0.7149 (tptt) REVERT: D 346 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.6932 (t-90) REVERT: D 401 GLU cc_start: 0.8456 (tt0) cc_final: 0.8189 (tt0) REVERT: D 443 GLN cc_start: 0.7934 (tt0) cc_final: 0.7377 (mt0) outliers start: 67 outliers final: 52 residues processed: 291 average time/residue: 0.1010 time to fit residues: 43.0125 Evaluate side-chains 295 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 235 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 427 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 83 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 139 optimal weight: 0.8980 chunk 68 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 44 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 138 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.225589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.188950 restraints weight = 12966.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.193518 restraints weight = 8629.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.196957 restraints weight = 6442.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.198991 restraints weight = 5258.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.200673 restraints weight = 4575.948| |-----------------------------------------------------------------------------| r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12012 Z= 0.139 Angle : 0.700 13.804 16296 Z= 0.329 Chirality : 0.038 0.175 2016 Planarity : 0.004 0.056 1956 Dihedral : 6.633 53.688 1748 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 5.19 % Allowed : 22.72 % Favored : 72.09 % 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 aren not related in a simple way. whole: 2.93 (0.22), residues: 1500 helix: 2.51 (0.14), residues: 1256 sheet: -0.48 (0.71), residues: 48 loop : -1.38 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 117 TYR 0.015 0.001 TYR D 124 PHE 0.012 0.001 PHE D 31 TRP 0.006 0.001 TRP A 193 HIS 0.002 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00324 (12012) covalent geometry : angle 0.70002 (16296) hydrogen bonds : bond 0.03948 ( 988) hydrogen bonds : angle 3.69834 ( 2940) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 239 time to evaluate : 0.433 Fit side-chains REVERT: A 26 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7450 (mp) REVERT: A 27 LYS cc_start: 0.7155 (tttt) cc_final: 0.6809 (tmtt) REVERT: A 117 ARG cc_start: 0.7120 (ttm110) cc_final: 0.6843 (ttp-110) REVERT: A 216 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7722 (tt) REVERT: A 362 MET cc_start: 0.7114 (tmm) cc_final: 0.6877 (tmm) REVERT: B 26 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7601 (mp) REVERT: B 117 ARG cc_start: 0.7195 (ttp-110) cc_final: 0.6757 (mtm110) REVERT: B 121 MET cc_start: 0.7689 (tmm) cc_final: 0.7397 (tmm) REVERT: B 346 HIS cc_start: 0.7563 (OUTLIER) cc_final: 0.6909 (t-90) REVERT: C 26 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7469 (mp) REVERT: C 117 ARG cc_start: 0.7137 (ttp-110) cc_final: 0.6674 (mtm110) REVERT: C 297 MET cc_start: 0.7111 (mpp) cc_final: 0.6696 (mpp) REVERT: C 301 LEU cc_start: 0.7842 (OUTLIER) cc_final: 0.7598 (mp) REVERT: C 346 HIS cc_start: 0.7630 (OUTLIER) cc_final: 0.6926 (t-90) REVERT: D 26 LEU cc_start: 0.7821 (OUTLIER) cc_final: 0.7554 (mp) REVERT: D 117 ARG cc_start: 0.7107 (ttp-110) cc_final: 0.6654 (mtm110) REVERT: D 346 HIS cc_start: 0.7598 (OUTLIER) cc_final: 0.6934 (t-90) outliers start: 66 outliers final: 51 residues processed: 288 average time/residue: 0.0971 time to fit residues: 41.1128 Evaluate side-chains 294 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 234 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 19 optimal weight: 0.8980 chunk 50 optimal weight: 0.0040 chunk 120 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 114 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.227734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.191302 restraints weight = 12835.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.195357 restraints weight = 8494.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.199122 restraints weight = 6429.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.201140 restraints weight = 5222.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.202945 restraints weight = 4542.492| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.5248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12012 Z= 0.129 Angle : 0.705 14.268 16296 Z= 0.325 Chirality : 0.038 0.180 2016 Planarity : 0.004 0.057 1956 Dihedral : 6.584 55.197 1748 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.80 % Allowed : 22.88 % Favored : 72.33 % 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 aren not related in a simple way. whole: 3.00 (0.22), residues: 1500 helix: 2.57 (0.14), residues: 1256 sheet: -0.59 (0.70), residues: 48 loop : -1.45 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 117 TYR 0.017 0.001 TYR D 124 PHE 0.009 0.001 PHE A 39 TRP 0.006 0.001 TRP A 193 HIS 0.002 0.001 HIS A 326 Details of bonding type rmsd covalent geometry : bond 0.00292 (12012) covalent geometry : angle 0.70450 (16296) hydrogen bonds : bond 0.03771 ( 988) hydrogen bonds : angle 3.64832 ( 2940) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 237 time to evaluate : 0.509 Fit side-chains REVERT: A 24 PHE cc_start: 0.7739 (t80) cc_final: 0.7235 (t80) REVERT: A 27 LYS cc_start: 0.7068 (tttt) cc_final: 0.6710 (tmtt) REVERT: A 216 LEU cc_start: 0.8034 (OUTLIER) cc_final: 0.7706 (tt) REVERT: A 332 TYR cc_start: 0.7826 (t80) cc_final: 0.7345 (t80) REVERT: B 27 LYS cc_start: 0.7284 (tttt) cc_final: 0.6987 (tptm) REVERT: B 117 ARG cc_start: 0.7179 (ttp-110) cc_final: 0.6793 (mtm110) REVERT: B 121 MET cc_start: 0.7591 (tmm) cc_final: 0.7322 (tmm) REVERT: B 297 MET cc_start: 0.7169 (mpp) cc_final: 0.6839 (mpp) REVERT: B 332 TYR cc_start: 0.7745 (t80) cc_final: 0.7379 (t80) REVERT: B 346 HIS cc_start: 0.7555 (OUTLIER) cc_final: 0.6934 (t-90) REVERT: C 26 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7422 (mp) REVERT: C 27 LYS cc_start: 0.7174 (tttt) cc_final: 0.6883 (tmtt) REVERT: C 117 ARG cc_start: 0.7145 (ttp-110) cc_final: 0.6682 (mtm110) REVERT: C 227 GLN cc_start: 0.8174 (tp-100) cc_final: 0.7602 (tm-30) REVERT: C 297 MET cc_start: 0.7057 (mpp) cc_final: 0.6631 (mpp) REVERT: C 301 LEU cc_start: 0.7697 (OUTLIER) cc_final: 0.7456 (mp) REVERT: C 332 TYR cc_start: 0.7756 (t80) cc_final: 0.7267 (t80) REVERT: C 346 HIS cc_start: 0.7679 (OUTLIER) cc_final: 0.6829 (t-90) REVERT: D 27 LYS cc_start: 0.7302 (tttt) cc_final: 0.7041 (tptm) REVERT: D 117 ARG cc_start: 0.7128 (ttp-110) cc_final: 0.6696 (mtm110) REVERT: D 332 TYR cc_start: 0.7734 (t80) cc_final: 0.7229 (t80) REVERT: D 346 HIS cc_start: 0.7615 (OUTLIER) cc_final: 0.6969 (t-90) REVERT: D 401 GLU cc_start: 0.8408 (tt0) cc_final: 0.8159 (tt0) outliers start: 61 outliers final: 45 residues processed: 280 average time/residue: 0.1009 time to fit residues: 42.3680 Evaluate side-chains 278 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 227 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 111 optimal weight: 9.9990 chunk 125 optimal weight: 1.9990 chunk 44 optimal weight: 0.0670 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 137 optimal weight: 0.5980 chunk 140 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 108 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 HIS ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS D 22 HIS ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.226673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.189918 restraints weight = 12993.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.194526 restraints weight = 8735.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.197550 restraints weight = 6554.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.200232 restraints weight = 5390.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.201493 restraints weight = 4659.572| |-----------------------------------------------------------------------------| r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.5383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12012 Z= 0.132 Angle : 0.704 14.560 16296 Z= 0.327 Chirality : 0.039 0.267 2016 Planarity : 0.004 0.056 1956 Dihedral : 6.540 55.052 1748 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.25 % Allowed : 23.74 % Favored : 72.01 % 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 aren not related in a simple way. whole: 3.02 (0.22), residues: 1500 helix: 2.59 (0.15), residues: 1256 sheet: -0.62 (0.69), residues: 48 loop : -1.49 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 117 TYR 0.015 0.001 TYR D 124 PHE 0.009 0.001 PHE A 39 TRP 0.006 0.001 TRP A 193 HIS 0.008 0.001 HIS A 22 Details of bonding type rmsd covalent geometry : bond 0.00303 (12012) covalent geometry : angle 0.70435 (16296) hydrogen bonds : bond 0.03851 ( 988) hydrogen bonds : angle 3.68046 ( 2940) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 233 time to evaluate : 0.565 Fit side-chains REVERT: A 24 PHE cc_start: 0.7859 (t80) cc_final: 0.7406 (t80) REVERT: A 27 LYS cc_start: 0.7030 (tttt) cc_final: 0.6743 (tmtt) REVERT: A 117 ARG cc_start: 0.7200 (ttp-110) cc_final: 0.6840 (mtm110) REVERT: A 125 MET cc_start: 0.7418 (tpt) cc_final: 0.7007 (tpt) REVERT: A 216 LEU cc_start: 0.8019 (OUTLIER) cc_final: 0.7707 (tt) REVERT: A 332 TYR cc_start: 0.7792 (t80) cc_final: 0.7416 (t80) REVERT: B 27 LYS cc_start: 0.7255 (tttt) cc_final: 0.6920 (tptt) REVERT: B 117 ARG cc_start: 0.7083 (ttp-110) cc_final: 0.6702 (mtm110) REVERT: B 121 MET cc_start: 0.7622 (tmm) cc_final: 0.7290 (tmm) REVERT: B 227 GLN cc_start: 0.8220 (tp-100) cc_final: 0.7665 (tm-30) REVERT: B 297 MET cc_start: 0.7202 (mpp) cc_final: 0.6879 (mpp) REVERT: B 332 TYR cc_start: 0.7711 (t80) cc_final: 0.7349 (t80) REVERT: B 346 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.7043 (t-90) REVERT: C 26 LEU cc_start: 0.7642 (OUTLIER) cc_final: 0.7345 (mp) REVERT: C 27 LYS cc_start: 0.7118 (tttt) cc_final: 0.6856 (tmtt) REVERT: C 117 ARG cc_start: 0.7173 (ttp-110) cc_final: 0.6762 (mtm110) REVERT: C 227 GLN cc_start: 0.8181 (tp-100) cc_final: 0.7643 (tm-30) REVERT: C 297 MET cc_start: 0.7068 (mpp) cc_final: 0.6671 (mpp) REVERT: C 301 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7564 (mp) REVERT: C 332 TYR cc_start: 0.7757 (t80) cc_final: 0.7379 (t80) REVERT: C 346 HIS cc_start: 0.7602 (OUTLIER) cc_final: 0.6901 (t-90) REVERT: D 27 LYS cc_start: 0.7262 (tttt) cc_final: 0.6930 (tptt) REVERT: D 117 ARG cc_start: 0.7166 (ttp-110) cc_final: 0.6721 (mtm110) REVERT: D 125 MET cc_start: 0.7265 (tpt) cc_final: 0.6996 (tpt) REVERT: D 227 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7622 (tm-30) REVERT: D 332 TYR cc_start: 0.7744 (t80) cc_final: 0.7353 (t80) REVERT: D 346 HIS cc_start: 0.7589 (OUTLIER) cc_final: 0.6997 (t-90) outliers start: 54 outliers final: 48 residues processed: 269 average time/residue: 0.0964 time to fit residues: 39.4432 Evaluate side-chains 280 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 226 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 129 VAL Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain C residue 26 LEU Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 91 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 64 optimal weight: 20.0000 chunk 104 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 137 optimal weight: 0.6980 chunk 99 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.226776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.189599 restraints weight = 13000.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.194194 restraints weight = 8703.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.197115 restraints weight = 6550.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.199908 restraints weight = 5400.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.201249 restraints weight = 4678.339| |-----------------------------------------------------------------------------| r_work (final): 0.4288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12012 Z= 0.132 Angle : 0.697 14.460 16296 Z= 0.324 Chirality : 0.039 0.281 2016 Planarity : 0.004 0.056 1956 Dihedral : 6.517 55.259 1748 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.64 % Allowed : 23.35 % Favored : 72.01 % 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 aren not related in a simple way. whole: 3.04 (0.22), residues: 1500 helix: 2.62 (0.15), residues: 1252 sheet: -0.66 (0.68), residues: 48 loop : -1.47 (0.46), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 117 TYR 0.014 0.001 TYR D 124 PHE 0.009 0.001 PHE A 39 TRP 0.005 0.001 TRP A 193 HIS 0.005 0.001 HIS D 22 Details of bonding type rmsd covalent geometry : bond 0.00309 (12012) covalent geometry : angle 0.69664 (16296) hydrogen bonds : bond 0.03835 ( 988) hydrogen bonds : angle 3.67556 ( 2940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1898.43 seconds wall clock time: 33 minutes 49.83 seconds (2029.83 seconds total)