Starting phenix.real_space_refine on Wed May 14 15:24:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vc2_43130/05_2025/8vc2_43130.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vc2_43130/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8vc2_43130/05_2025/8vc2_43130.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vc2_43130/05_2025/8vc2_43130.map" model { file = "/net/cci-nas-00/data/ceres_data/8vc2_43130/05_2025/8vc2_43130.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vc2_43130/05_2025/8vc2_43130.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 2, 'HIS:plan': 2, 'ARG:plan': 4, 'ASP:plan': 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-4': 1, 'PSC:plan-3': 1} Unresolved non-hydrogen planarities: 6 Restraints were copied for chains: C, B, D Time building chain proxies: 6.06, per 1000 atoms: 0.51 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: 3.08 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.00 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: 3.44 Time building geometry restraints manager: 3.53 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 1.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 26.940 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.750 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.029 0.007 TRP D 354 HIS 0.008 0.003 HIS D 358 PHE 0.010 0.002 PHE C 203 TYR 0.037 0.006 TYR B 124 ARG 0.019 0.003 ARG D 117 Details of bonding type rmsd hydrogen bonds : bond 0.09684 ( 988) hydrogen bonds : angle 5.48264 ( 2940) covalent geometry : bond 0.00558 (12012) covalent geometry : angle 0.84302 (16296) *********************** 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 : 1.295 Fit side-chains revert: symmetry clash REVERT: A 125 MET cc_start: 0.7062 (mmm) cc_final: 0.6758 (mmt) REVERT: A 197 MET cc_start: 0.7610 (mmm) cc_final: 0.7155 (tmm) REVERT: A 401 GLU cc_start: 0.7893 (tt0) cc_final: 0.7297 (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: 0.7256 (tt0) REVERT: B 404 SER cc_start: 0.8480 (p) cc_final: 0.8124 (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: 0.7259 (tmm) REVERT: C 384 CYS cc_start: 0.5188 (m) cc_final: 0.4764 (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: 0.8156 (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: 0.7283 (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: 0.8119 (t) outliers start: 4 outliers final: 1 residues processed: 453 average time/residue: 0.2243 time to fit residues: 145.3593 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 : 1.275 ------------------------------------------------------------------------------- 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 124 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 86 optimal weight: 40.0000 chunk 134 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 443 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.226188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.190635 restraints weight = 12779.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.196410 restraints weight = 7911.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.200686 restraints weight = 5616.078| |-----------------------------------------------------------------------------| r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6911 moved from start: 0.2870 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= 0.150 Angle : 0.649 10.264 16296 Z= 0.330 Chirality : 0.037 0.126 2016 Planarity : 0.004 0.043 1956 Dihedral : 8.704 67.786 1750 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.95 % Allowed : 14.31 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1500 helix: 1.38 (0.14), residues: 1264 sheet: 0.05 (0.70), residues: 48 loop : -0.82 (0.50), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.003 0.001 HIS B 326 PHE 0.016 0.002 PHE C 203 TYR 0.018 0.002 TYR D 124 ARG 0.003 0.000 ARG A 344 Details of bonding type rmsd hydrogen bonds : bond 0.04692 ( 988) hydrogen bonds : angle 3.95718 ( 2940) covalent geometry : bond 0.00330 (12012) covalent geometry : angle 0.64935 (16296) *********************** 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 384 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 321 time to evaluate : 1.257 Fit side-chains REVERT: A 26 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7568 (mp) REVERT: A 179 GLN cc_start: 0.7663 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: A 197 MET cc_start: 0.7784 (mmm) cc_final: 0.7436 (tmm) REVERT: B 26 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7589 (mp) REVERT: B 125 MET cc_start: 0.6802 (mmt) cc_final: 0.6518 (tpt) REVERT: B 346 HIS cc_start: 0.7753 (OUTLIER) cc_final: 0.7008 (t-90) REVERT: C 26 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7556 (mp) REVERT: C 179 GLN cc_start: 0.7540 (tm-30) cc_final: 0.7011 (pm20) REVERT: C 297 MET cc_start: 0.7327 (mpp) cc_final: 0.6935 (mpp) REVERT: C 346 HIS cc_start: 0.7779 (OUTLIER) cc_final: 0.7014 (t-90) REVERT: C 401 GLU cc_start: 0.8274 (tt0) cc_final: 0.7718 (tt0) REVERT: D 26 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7576 (mp) REVERT: D 179 GLN cc_start: 0.7569 (tm-30) cc_final: 0.7066 (pm20) REVERT: D 346 HIS cc_start: 0.7762 (OUTLIER) cc_final: 0.7010 (t-90) REVERT: D 401 GLU cc_start: 0.8262 (tt0) cc_final: 0.7627 (tt0) outliers start: 63 outliers final: 30 residues processed: 362 average time/residue: 0.2089 time to fit residues: 109.8005 Evaluate side-chains 288 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 179 GLN 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 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 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 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 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 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 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 46 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 144 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- 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 = 0.4512 r_free = 0.4512 target = 0.226815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.190609 restraints weight = 13047.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.196066 restraints weight = 8301.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.199981 restraints weight = 5998.385| |-----------------------------------------------------------------------------| r_work (final): 0.4273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.3620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 12012 Z= 0.147 Angle : 0.659 12.188 16296 Z= 0.325 Chirality : 0.038 0.185 2016 Planarity : 0.004 0.053 1956 Dihedral : 7.766 55.102 1748 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 4.56 % Allowed : 19.03 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.22), residues: 1500 helix: 1.72 (0.14), residues: 1268 sheet: 0.24 (0.75), residues: 48 loop : -0.81 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 193 HIS 0.003 0.001 HIS A 358 PHE 0.011 0.001 PHE C 203 TYR 0.015 0.001 TYR A 124 ARG 0.005 0.000 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.04391 ( 988) hydrogen bonds : angle 3.87883 ( 2940) covalent geometry : bond 0.00335 (12012) covalent geometry : angle 0.65935 (16296) *********************** 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 332 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 274 time to evaluate : 1.546 Fit side-chains REVERT: A 26 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7617 (mp) REVERT: A 27 LYS cc_start: 0.7545 (tttt) cc_final: 0.7159 (tmtt) REVERT: A 171 MET cc_start: 0.7930 (tmm) cc_final: 0.7696 (tmm) REVERT: A 179 GLN cc_start: 0.7470 (tm-30) cc_final: 0.7247 (pp30) REVERT: A 197 MET cc_start: 0.7771 (mmm) cc_final: 0.7479 (tmm) REVERT: A 297 MET cc_start: 0.7187 (mpp) cc_final: 0.6744 (mpp) REVERT: B 26 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7611 (mp) REVERT: B 171 MET cc_start: 0.7879 (tmm) cc_final: 0.7666 (tmm) REVERT: B 297 MET cc_start: 0.7146 (mpp) cc_final: 0.6642 (mpp) REVERT: B 346 HIS cc_start: 0.7702 (OUTLIER) cc_final: 0.7010 (t-90) REVERT: B 443 GLN cc_start: 0.7853 (tt0) cc_final: 0.7379 (tt0) REVERT: C 26 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7617 (mp) REVERT: C 27 LYS cc_start: 0.7557 (tttt) cc_final: 0.7244 (tttm) REVERT: C 67 ILE cc_start: 0.8864 (tp) cc_final: 0.8537 (tt) REVERT: C 121 MET cc_start: 0.7898 (tmm) cc_final: 0.7623 (tmm) REVERT: C 179 GLN cc_start: 0.7552 (tm-30) cc_final: 0.6987 (pm20) REVERT: C 346 HIS cc_start: 0.7728 (OUTLIER) cc_final: 0.7002 (t-90) REVERT: D 26 LEU cc_start: 0.7964 (OUTLIER) cc_final: 0.7618 (mp) REVERT: D 27 LYS cc_start: 0.7643 (tttt) cc_final: 0.7324 (tttm) REVERT: D 179 GLN cc_start: 0.7479 (tm-30) cc_final: 0.6883 (pm20) REVERT: D 346 HIS cc_start: 0.7710 (OUTLIER) cc_final: 0.7010 (t-90) outliers start: 58 outliers final: 39 residues processed: 312 average time/residue: 0.2160 time to fit residues: 97.9772 Evaluate side-chains 289 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 243 time to evaluate : 1.164 ------------------------------------------------------------------------------- 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 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 357 THR Chi-restraints excluded: chain B residue 379 THR 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 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 98 CYS Chi-restraints excluded: chain D residue 122 LEU 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 379 THR 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 0 optimal weight: 10.0000 chunk 94 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 147 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 133 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.225456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.190568 restraints weight = 12999.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.195484 restraints weight = 8508.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.199003 restraints weight = 6254.345| |-----------------------------------------------------------------------------| r_work (final): 0.4262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6973 moved from start: 0.4096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12012 Z= 0.133 Angle : 0.622 12.487 16296 Z= 0.306 Chirality : 0.037 0.160 2016 Planarity : 0.004 0.056 1956 Dihedral : 7.396 50.850 1748 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 5.66 % Allowed : 18.71 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.35 (0.22), residues: 1500 helix: 1.94 (0.14), residues: 1268 sheet: 0.11 (0.76), residues: 48 loop : -0.63 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 193 HIS 0.002 0.001 HIS B 326 PHE 0.011 0.001 PHE A 39 TYR 0.016 0.001 TYR A 124 ARG 0.005 0.000 ARG D 178 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 988) hydrogen bonds : angle 3.78683 ( 2940) covalent geometry : bond 0.00301 (12012) covalent geometry : angle 0.62158 (16296) *********************** 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 355 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 283 time to evaluate : 1.185 Fit side-chains REVERT: A 26 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7593 (mp) REVERT: A 121 MET cc_start: 0.7619 (tmm) cc_final: 0.7311 (tmm) REVERT: A 197 MET cc_start: 0.7682 (mmm) cc_final: 0.7474 (tpt) REVERT: A 297 MET cc_start: 0.7193 (mpp) cc_final: 0.6752 (mpp) REVERT: A 332 TYR cc_start: 0.7415 (t80) cc_final: 0.7186 (t80) REVERT: B 26 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7724 (mp) REVERT: B 67 ILE cc_start: 0.8861 (tp) cc_final: 0.8542 (tt) REVERT: B 121 MET cc_start: 0.7833 (tmm) cc_final: 0.7632 (tmm) REVERT: B 346 HIS cc_start: 0.7611 (OUTLIER) cc_final: 0.6963 (t-90) REVERT: C 26 LEU cc_start: 0.8006 (OUTLIER) cc_final: 0.7675 (mp) REVERT: C 67 ILE cc_start: 0.8870 (tp) cc_final: 0.8574 (tt) REVERT: C 121 MET cc_start: 0.7824 (tmm) cc_final: 0.7596 (tmm) REVERT: C 179 GLN cc_start: 0.7376 (tm-30) cc_final: 0.7166 (pm20) REVERT: C 301 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7808 (mp) REVERT: C 346 HIS cc_start: 0.7639 (OUTLIER) cc_final: 0.6967 (t-90) REVERT: C 443 GLN cc_start: 0.8019 (tt0) cc_final: 0.7383 (tt0) REVERT: D 26 LEU cc_start: 0.8014 (OUTLIER) cc_final: 0.7684 (mp) REVERT: D 67 ILE cc_start: 0.8908 (tp) cc_final: 0.8588 (tt) REVERT: D 179 GLN cc_start: 0.7533 (tm-30) cc_final: 0.7165 (pm20) REVERT: D 346 HIS cc_start: 0.7646 (OUTLIER) cc_final: 0.6997 (t-90) REVERT: D 419 MET cc_start: 0.7769 (mtp) cc_final: 0.7457 (ttm) outliers start: 72 outliers final: 47 residues processed: 331 average time/residue: 0.2017 time to fit residues: 98.1222 Evaluate side-chains 307 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 252 time to evaluate : 1.188 ------------------------------------------------------------------------------- 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 400 LEU 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 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 379 THR Chi-restraints excluded: chain B residue 427 ILE 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 427 ILE 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 379 THR 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 90 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 122 optimal weight: 8.9990 chunk 128 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 95 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 137 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.221409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.184566 restraints weight = 13031.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.189179 restraints weight = 8551.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.192649 restraints weight = 6380.815| |-----------------------------------------------------------------------------| r_work (final): 0.4206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 12012 Z= 0.163 Angle : 0.679 12.409 16296 Z= 0.326 Chirality : 0.039 0.159 2016 Planarity : 0.005 0.055 1956 Dihedral : 7.236 51.135 1748 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.74 % Allowed : 21.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.22), residues: 1500 helix: 2.10 (0.14), residues: 1256 sheet: -0.13 (0.74), residues: 48 loop : -1.22 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 193 HIS 0.002 0.001 HIS B 326 PHE 0.011 0.001 PHE A 39 TYR 0.015 0.001 TYR B 124 ARG 0.005 0.000 ARG D 117 Details of bonding type rmsd hydrogen bonds : bond 0.04408 ( 988) hydrogen bonds : angle 3.89109 ( 2940) covalent geometry : bond 0.00401 (12012) covalent geometry : angle 0.67900 (16296) *********************** 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 347 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 274 time to evaluate : 1.175 Fit side-chains REVERT: A 26 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7639 (mp) REVERT: A 362 MET cc_start: 0.7058 (tmm) cc_final: 0.6804 (tmm) REVERT: B 26 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7759 (mp) REVERT: B 67 ILE cc_start: 0.8912 (tp) cc_final: 0.8583 (tt) REVERT: B 346 HIS cc_start: 0.7686 (OUTLIER) cc_final: 0.7003 (t-90) REVERT: C 26 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7836 (mp) REVERT: C 346 HIS cc_start: 0.7662 (OUTLIER) cc_final: 0.6993 (t-90) REVERT: C 443 GLN cc_start: 0.8114 (tt0) cc_final: 0.7115 (tt0) REVERT: D 26 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7869 (mp) REVERT: D 67 ILE cc_start: 0.8902 (tp) cc_final: 0.8562 (tt) REVERT: D 121 MET cc_start: 0.7957 (tmm) cc_final: 0.7723 (tmm) REVERT: D 346 HIS cc_start: 0.7676 (OUTLIER) cc_final: 0.6972 (t-90) outliers start: 73 outliers final: 60 residues processed: 324 average time/residue: 0.2112 time to fit residues: 99.1695 Evaluate side-chains 315 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 248 time to evaluate : 1.200 ------------------------------------------------------------------------------- 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 363 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 LEU 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 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 364 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 408 MET 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 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 363 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 427 ILE 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 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 364 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 50 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 142 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 80 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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** B 370 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.223942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.187226 restraints weight = 13137.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.191693 restraints weight = 8665.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.195506 restraints weight = 6436.045| |-----------------------------------------------------------------------------| r_work (final): 0.4232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.4787 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= 0.144 Angle : 0.671 12.113 16296 Z= 0.325 Chirality : 0.038 0.173 2016 Planarity : 0.005 0.055 1956 Dihedral : 7.129 53.113 1748 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 6.13 % Allowed : 20.60 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.22), residues: 1500 helix: 2.28 (0.14), residues: 1256 sheet: -0.03 (0.75), residues: 48 loop : -1.24 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 180 HIS 0.002 0.001 HIS D 326 PHE 0.009 0.001 PHE B 39 TYR 0.018 0.001 TYR D 124 ARG 0.007 0.001 ARG C 117 Details of bonding type rmsd hydrogen bonds : bond 0.04160 ( 988) hydrogen bonds : angle 3.79314 ( 2940) covalent geometry : bond 0.00340 (12012) covalent geometry : angle 0.67058 (16296) *********************** 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 333 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 255 time to evaluate : 1.368 Fit side-chains REVERT: A 26 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7633 (mp) REVERT: A 27 LYS cc_start: 0.7348 (tttt) cc_final: 0.7009 (tmtt) REVERT: A 66 VAL cc_start: 0.7258 (t) cc_final: 0.7050 (t) REVERT: A 121 MET cc_start: 0.7642 (tmm) cc_final: 0.7430 (tmm) REVERT: B 26 LEU cc_start: 0.7986 (OUTLIER) cc_final: 0.7731 (mp) REVERT: B 117 ARG cc_start: 0.7069 (ttm110) cc_final: 0.6377 (mtm110) REVERT: B 121 MET cc_start: 0.7563 (tmm) cc_final: 0.7316 (tmm) REVERT: B 346 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.6867 (t-90) REVERT: C 26 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7724 (mp) REVERT: C 27 LYS cc_start: 0.7491 (tttt) cc_final: 0.7050 (tptm) REVERT: C 121 MET cc_start: 0.7624 (tmm) cc_final: 0.7389 (tmm) REVERT: C 301 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7785 (mp) REVERT: C 346 HIS cc_start: 0.7698 (OUTLIER) cc_final: 0.6834 (t-90) REVERT: D 26 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7791 (mp) REVERT: D 346 HIS cc_start: 0.7654 (OUTLIER) cc_final: 0.6862 (t-90) REVERT: D 419 MET cc_start: 0.7780 (mtp) cc_final: 0.7491 (ttm) outliers start: 78 outliers final: 58 residues processed: 306 average time/residue: 0.2202 time to fit residues: 97.1542 Evaluate side-chains 306 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 240 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 363 LEU Chi-restraints excluded: chain A residue 364 VAL 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 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 364 VAL Chi-restraints excluded: chain B residue 379 THR 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 123 SER 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 363 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 427 ILE 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 123 SER 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 364 VAL Chi-restraints excluded: chain D residue 379 THR 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 32 optimal weight: 0.4980 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 109 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 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 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 443 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.225188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.188583 restraints weight = 13103.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.193238 restraints weight = 8671.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.196281 restraints weight = 6451.893| |-----------------------------------------------------------------------------| r_work (final): 0.4238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.5047 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= 0.136 Angle : 0.690 12.731 16296 Z= 0.321 Chirality : 0.038 0.174 2016 Planarity : 0.004 0.057 1956 Dihedral : 6.938 53.749 1748 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 5.97 % Allowed : 21.46 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.75 (0.22), residues: 1500 helix: 2.38 (0.14), residues: 1256 sheet: -0.56 (0.70), residues: 48 loop : -1.40 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 193 HIS 0.003 0.001 HIS A 392 PHE 0.009 0.001 PHE B 39 TYR 0.016 0.001 TYR D 124 ARG 0.007 0.001 ARG A 117 Details of bonding type rmsd hydrogen bonds : bond 0.04023 ( 988) hydrogen bonds : angle 3.73143 ( 2940) covalent geometry : bond 0.00317 (12012) covalent geometry : angle 0.69020 (16296) *********************** 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 317 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 241 time to evaluate : 1.333 Fit side-chains REVERT: A 26 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7538 (mp) REVERT: A 27 LYS cc_start: 0.7318 (tttt) cc_final: 0.6957 (tmtt) REVERT: A 121 MET cc_start: 0.7600 (tmm) cc_final: 0.7395 (tmm) REVERT: A 216 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7693 (tt) REVERT: B 26 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7666 (mp) REVERT: B 27 LYS cc_start: 0.7354 (tttt) cc_final: 0.6969 (tptt) REVERT: B 346 HIS cc_start: 0.7604 (OUTLIER) cc_final: 0.6922 (t-90) REVERT: C 26 LEU cc_start: 0.7857 (OUTLIER) cc_final: 0.7564 (mp) REVERT: C 121 MET cc_start: 0.7582 (tmm) cc_final: 0.7345 (tmm) REVERT: C 179 GLN cc_start: 0.7699 (pp30) cc_final: 0.7439 (pp30) REVERT: C 301 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7687 (mp) REVERT: C 346 HIS cc_start: 0.7664 (OUTLIER) cc_final: 0.6931 (t-90) REVERT: C 401 GLU cc_start: 0.8372 (tt0) cc_final: 0.8114 (tt0) REVERT: D 26 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7656 (mp) REVERT: D 27 LYS cc_start: 0.7438 (tttt) cc_final: 0.7083 (tmtt) REVERT: D 121 MET cc_start: 0.7543 (tmm) cc_final: 0.7340 (tmm) REVERT: D 346 HIS cc_start: 0.7606 (OUTLIER) cc_final: 0.6918 (t-90) REVERT: D 401 GLU cc_start: 0.8435 (tt0) cc_final: 0.8222 (tt0) outliers start: 76 outliers final: 56 residues processed: 298 average time/residue: 0.2061 time to fit residues: 91.1002 Evaluate side-chains 302 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 237 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 216 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 364 VAL 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 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS 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 363 LEU Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 395 VAL 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 363 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 427 ILE 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 364 VAL Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 428 VAL Chi-restraints excluded: chain D residue 443 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 29 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 132 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 139 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 108 optimal weight: 0.3980 chunk 144 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 147 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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** ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS C 443 GLN ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.226330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.191066 restraints weight = 13066.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4217 r_free = 0.4217 target = 0.194236 restraints weight = 9129.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.196097 restraints weight = 6872.655| |-----------------------------------------------------------------------------| r_work (final): 0.4243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.5211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12012 Z= 0.134 Angle : 0.692 13.625 16296 Z= 0.323 Chirality : 0.038 0.172 2016 Planarity : 0.004 0.058 1956 Dihedral : 6.785 54.670 1748 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.50 % Allowed : 22.25 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.22), residues: 1500 helix: 2.45 (0.15), residues: 1256 sheet: -0.66 (0.68), residues: 48 loop : -1.45 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 193 HIS 0.002 0.001 HIS D 392 PHE 0.017 0.001 PHE D 444 TYR 0.016 0.001 TYR D 124 ARG 0.007 0.000 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.03938 ( 988) hydrogen bonds : angle 3.69792 ( 2940) covalent geometry : bond 0.00310 (12012) covalent geometry : angle 0.69234 (16296) *********************** 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 308 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 238 time to evaluate : 1.410 Fit side-chains revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7456 (mp) REVERT: A 27 LYS cc_start: 0.7155 (tttt) cc_final: 0.6828 (tmtt) REVERT: A 117 ARG cc_start: 0.6947 (ttp-110) cc_final: 0.6570 (mtm110) REVERT: A 121 MET cc_start: 0.7571 (tmm) cc_final: 0.7310 (tmm) REVERT: A 216 LEU cc_start: 0.7980 (OUTLIER) cc_final: 0.7651 (tt) REVERT: B 26 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7556 (mp) REVERT: B 332 TYR cc_start: 0.7881 (t80) cc_final: 0.7307 (t80) REVERT: B 346 HIS cc_start: 0.7650 (OUTLIER) cc_final: 0.6972 (t-90) REVERT: C 26 LEU cc_start: 0.7758 (OUTLIER) cc_final: 0.7523 (mp) REVERT: C 27 LYS cc_start: 0.7302 (tttt) cc_final: 0.6959 (tptt) REVERT: C 117 ARG cc_start: 0.7057 (ttp-110) cc_final: 0.6601 (mtm110) REVERT: C 121 MET cc_start: 0.7532 (tmm) cc_final: 0.7282 (tmm) REVERT: C 301 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7679 (mp) REVERT: C 346 HIS cc_start: 0.7651 (OUTLIER) cc_final: 0.6952 (t-90) REVERT: C 401 GLU cc_start: 0.8266 (tt0) cc_final: 0.7938 (tt0) REVERT: D 26 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7503 (mp) REVERT: D 117 ARG cc_start: 0.7030 (ttp-110) cc_final: 0.6631 (mtm110) REVERT: D 121 MET cc_start: 0.7519 (tmm) cc_final: 0.7312 (tmm) REVERT: D 346 HIS cc_start: 0.7659 (OUTLIER) cc_final: 0.6969 (t-90) REVERT: D 401 GLU cc_start: 0.8284 (tt0) cc_final: 0.8079 (tt0) outliers start: 70 outliers final: 56 residues processed: 293 average time/residue: 0.2077 time to fit residues: 89.2516 Evaluate side-chains 297 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 232 time to evaluate : 1.182 ------------------------------------------------------------------------------- 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 216 LEU Chi-restraints excluded: chain A residue 289 GLU 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 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 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 364 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 395 VAL 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 123 SER 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 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 363 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 427 ILE 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 123 SER 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 364 VAL 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 428 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 30 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 134 optimal weight: 4.9990 chunk 76 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 129 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 147 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.225380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.188298 restraints weight = 13091.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.192856 restraints weight = 8713.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.195594 restraints weight = 6505.818| |-----------------------------------------------------------------------------| r_work (final): 0.4233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7008 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12012 Z= 0.137 Angle : 0.703 14.128 16296 Z= 0.325 Chirality : 0.038 0.180 2016 Planarity : 0.004 0.057 1956 Dihedral : 6.642 54.219 1748 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 5.66 % Allowed : 22.72 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.22), residues: 1500 helix: 2.50 (0.14), residues: 1252 sheet: -0.71 (0.67), residues: 48 loop : -1.44 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 193 HIS 0.002 0.001 HIS B 326 PHE 0.008 0.001 PHE B 39 TYR 0.015 0.001 TYR B 124 ARG 0.007 0.000 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 988) hydrogen bonds : angle 3.73322 ( 2940) covalent geometry : bond 0.00324 (12012) covalent geometry : angle 0.70339 (16296) *********************** 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 315 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 243 time to evaluate : 1.284 Fit side-chains REVERT: A 27 LYS cc_start: 0.7085 (tttt) cc_final: 0.6764 (tmtt) REVERT: A 117 ARG cc_start: 0.6989 (ttp-110) cc_final: 0.6602 (mtm110) REVERT: A 121 MET cc_start: 0.7550 (tmm) cc_final: 0.7250 (tmm) REVERT: A 216 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7655 (tt) REVERT: A 401 GLU cc_start: 0.8395 (tt0) cc_final: 0.8070 (tt0) REVERT: A 419 MET cc_start: 0.7723 (mtp) cc_final: 0.7498 (ttm) REVERT: B 27 LYS cc_start: 0.7258 (tttt) cc_final: 0.6963 (tptm) REVERT: B 117 ARG cc_start: 0.7107 (ttp-110) cc_final: 0.6639 (mtm110) REVERT: B 332 TYR cc_start: 0.7797 (t80) cc_final: 0.7377 (t80) REVERT: B 346 HIS cc_start: 0.7667 (OUTLIER) cc_final: 0.7010 (t-90) REVERT: C 24 PHE cc_start: 0.7735 (t80) cc_final: 0.7034 (t80) REVERT: C 26 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7540 (mp) REVERT: C 117 ARG cc_start: 0.7043 (ttp-110) cc_final: 0.6721 (mtm110) REVERT: C 121 MET cc_start: 0.7565 (tmm) cc_final: 0.7255 (tmm) REVERT: C 297 MET cc_start: 0.7006 (mpp) cc_final: 0.6794 (mpp) REVERT: C 301 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7678 (mp) REVERT: C 332 TYR cc_start: 0.7816 (t80) cc_final: 0.7340 (t80) REVERT: C 346 HIS cc_start: 0.7691 (OUTLIER) cc_final: 0.7035 (t-90) REVERT: C 401 GLU cc_start: 0.8349 (tt0) cc_final: 0.8100 (tt0) REVERT: D 26 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7518 (mp) REVERT: D 27 LYS cc_start: 0.7237 (tttt) cc_final: 0.6928 (tmtt) REVERT: D 117 ARG cc_start: 0.7139 (ttp-110) cc_final: 0.6786 (mtm110) REVERT: D 121 MET cc_start: 0.7508 (tmm) cc_final: 0.7308 (tmm) REVERT: D 332 TYR cc_start: 0.7780 (t80) cc_final: 0.7251 (t80) REVERT: D 346 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.7021 (t-90) REVERT: D 401 GLU cc_start: 0.8447 (tt0) cc_final: 0.8174 (tt0) REVERT: D 443 GLN cc_start: 0.7637 (tt0) cc_final: 0.7108 (tt0) outliers start: 72 outliers final: 62 residues processed: 295 average time/residue: 0.2152 time to fit residues: 91.8621 Evaluate side-chains 304 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 235 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 A residue 400 LEU Chi-restraints excluded: chain A residue 443 GLN 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 395 VAL 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 123 SER 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 363 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 39 PHE 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 123 SER Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 338 ILE 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 364 VAL 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 428 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 3 optimal weight: 20.0000 chunk 123 optimal weight: 40.0000 chunk 131 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 126 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 105 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 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 22 HIS ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 HIS ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.226112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.189910 restraints weight = 12879.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.193783 restraints weight = 8598.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.197366 restraints weight = 6519.496| |-----------------------------------------------------------------------------| r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6968 moved from start: 0.5421 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= 0.136 Angle : 0.711 14.277 16296 Z= 0.328 Chirality : 0.038 0.183 2016 Planarity : 0.004 0.057 1956 Dihedral : 6.582 55.266 1748 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 5.58 % Allowed : 22.96 % Favored : 71.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.22), residues: 1500 helix: 2.50 (0.14), residues: 1256 sheet: -0.72 (0.67), residues: 48 loop : -1.42 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 193 HIS 0.009 0.001 HIS B 22 PHE 0.013 0.001 PHE C 31 TYR 0.014 0.001 TYR D 124 ARG 0.007 0.000 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.03933 ( 988) hydrogen bonds : angle 3.71985 ( 2940) covalent geometry : bond 0.00318 (12012) covalent geometry : angle 0.71113 (16296) ********************** 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 308 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 237 time to evaluate : 1.288 Fit side-chains REVERT: A 27 LYS cc_start: 0.7024 (tttt) cc_final: 0.6740 (tmtt) REVERT: A 117 ARG cc_start: 0.6975 (ttp-110) cc_final: 0.6561 (mtm110) REVERT: A 121 MET cc_start: 0.7586 (tmm) cc_final: 0.7248 (tmm) REVERT: A 216 LEU cc_start: 0.7985 (OUTLIER) cc_final: 0.7670 (tt) REVERT: A 332 TYR cc_start: 0.7847 (t80) cc_final: 0.7334 (t80) REVERT: A 401 GLU cc_start: 0.8399 (tt0) cc_final: 0.8095 (tt0) REVERT: B 24 PHE cc_start: 0.7838 (t80) cc_final: 0.7191 (t80) REVERT: B 27 LYS cc_start: 0.7177 (tttt) cc_final: 0.6853 (tptt) REVERT: B 117 ARG cc_start: 0.7140 (ttp-110) cc_final: 0.6704 (mtm110) REVERT: B 125 MET cc_start: 0.7404 (tpt) cc_final: 0.7036 (tpt) REVERT: B 332 TYR cc_start: 0.7717 (t80) cc_final: 0.7297 (t80) REVERT: B 346 HIS cc_start: 0.7550 (OUTLIER) cc_final: 0.7025 (t-90) REVERT: C 24 PHE cc_start: 0.7703 (t80) cc_final: 0.7016 (t80) REVERT: C 27 LYS cc_start: 0.7165 (tttt) cc_final: 0.6901 (tptm) REVERT: C 117 ARG cc_start: 0.7050 (ttp-110) cc_final: 0.6682 (mtm110) REVERT: C 121 MET cc_start: 0.7533 (tmm) cc_final: 0.7209 (tmm) REVERT: C 301 LEU cc_start: 0.7828 (OUTLIER) cc_final: 0.7586 (mp) REVERT: C 332 TYR cc_start: 0.7815 (t80) cc_final: 0.7336 (t80) REVERT: C 346 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.7020 (t-90) REVERT: C 401 GLU cc_start: 0.8351 (tt0) cc_final: 0.7681 (tt0) REVERT: D 27 LYS cc_start: 0.7192 (tttt) cc_final: 0.6906 (tmtt) REVERT: D 117 ARG cc_start: 0.7068 (ttp-110) cc_final: 0.6769 (mtm110) REVERT: D 121 MET cc_start: 0.7572 (tmm) cc_final: 0.7315 (tmm) REVERT: D 332 TYR cc_start: 0.7737 (t80) cc_final: 0.7353 (t80) REVERT: D 346 HIS cc_start: 0.7570 (OUTLIER) cc_final: 0.7028 (t-90) REVERT: D 401 GLU cc_start: 0.8430 (tt0) cc_final: 0.8041 (tt0) outliers start: 71 outliers final: 62 residues processed: 286 average time/residue: 0.2055 time to fit residues: 86.0706 Evaluate side-chains 297 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 230 time to evaluate : 1.180 ------------------------------------------------------------------------------- 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 345 LEU 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 400 LEU Chi-restraints excluded: chain A residue 443 GLN 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 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 395 VAL Chi-restraints excluded: chain B residue 408 MET 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 123 SER 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 363 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain D residue 39 PHE 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 123 SER Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 338 ILE 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 364 VAL 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 428 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 99 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 97 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 96 optimal weight: 0.6980 chunk 108 optimal weight: 0.0470 chunk 145 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- 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 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 HIS ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN D 22 HIS ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.227283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.191108 restraints weight = 13011.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.195685 restraints weight = 8577.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.199104 restraints weight = 6426.480| |-----------------------------------------------------------------------------| r_work (final): 0.4266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12012 Z= 0.130 Angle : 0.706 14.327 16296 Z= 0.324 Chirality : 0.038 0.181 2016 Planarity : 0.004 0.058 1956 Dihedral : 6.547 56.444 1748 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 5.35 % Allowed : 23.74 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.22), residues: 1500 helix: 2.58 (0.15), residues: 1252 sheet: -0.76 (0.67), residues: 48 loop : -1.37 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 180 HIS 0.009 0.001 HIS C 22 PHE 0.012 0.001 PHE C 31 TYR 0.016 0.001 TYR D 124 ARG 0.007 0.000 ARG B 117 Details of bonding type rmsd hydrogen bonds : bond 0.03809 ( 988) hydrogen bonds : angle 3.67387 ( 2940) covalent geometry : bond 0.00298 (12012) covalent geometry : angle 0.70601 (16296) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3485.75 seconds wall clock time: 62 minutes 1.19 seconds (3721.19 seconds total)