Starting phenix.real_space_refine on Sat Oct 12 08:51:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc2_43130/10_2024/8vc2_43130.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc2_43130/10_2024/8vc2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc2_43130/10_2024/8vc2_43130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc2_43130/10_2024/8vc2_43130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc2_43130/10_2024/8vc2_43130.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc2_43130/10_2024/8vc2_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-5477/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: 6.30, per 1000 atoms: 0.53 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: 2.99 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: 0.87 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: 3.58 Time building geometry restraints manager: 3.41 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.730 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.040 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.310 ------------------------------------------------------------------------------- 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= 0.360 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 *********************** 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 fitting. rotamer outliers: 4 poor density : 449 time to evaluate : 1.373 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: 0.2311 time to fit residues: 149.4338 Evaluate side-chains 298 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 297 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 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= 0.214 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 *********************** 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 fitting. rotamer outliers: 63 poor density : 321 time to evaluate : 1.360 Fit side-chains REVERT: A 26 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7636 (mp) REVERT: A 39 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6754 (p90) REVERT: A 197 MET cc_start: 0.7544 (mmm) cc_final: 0.7285 (tmm) REVERT: B 26 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7633 (mp) REVERT: B 125 MET cc_start: 0.7028 (mmt) cc_final: 0.6740 (tpt) REVERT: B 346 HIS cc_start: 0.7596 (OUTLIER) cc_final: 0.6877 (t-90) REVERT: C 179 GLN cc_start: 0.7211 (tm-30) cc_final: 0.6795 (pm20) REVERT: C 346 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.6873 (t-90) REVERT: C 401 GLU cc_start: 0.7933 (tt0) cc_final: 0.7478 (tt0) REVERT: D 26 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7617 (mp) REVERT: D 179 GLN cc_start: 0.7207 (tm-30) cc_final: 0.6822 (pm20) REVERT: D 346 HIS cc_start: 0.7594 (OUTLIER) cc_final: 0.6858 (t-90) REVERT: D 401 GLU cc_start: 0.7908 (tt0) cc_final: 0.7314 (tt0) outliers start: 63 outliers final: 30 residues processed: 362 average time/residue: 0.2291 time to fit residues: 120.7875 Evaluate side-chains 286 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 249 time to evaluate : 1.345 ------------------------------------------------------------------------------- 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 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 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 74 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 chunk 133 optimal weight: 0.8980 chunk 45 optimal weight: 0.2980 chunk 108 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12012 Z= 0.227 Angle : 0.670 12.157 16296 Z= 0.329 Chirality : 0.038 0.198 2016 Planarity : 0.004 0.054 1956 Dihedral : 7.789 55.429 1748 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 4.56 % Allowed : 19.10 % Favored : 76.34 % 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: 1.97 (0.22), residues: 1500 helix: 1.68 (0.14), residues: 1268 sheet: 0.26 (0.75), residues: 48 loop : -0.85 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 180 HIS 0.004 0.001 HIS C 22 PHE 0.013 0.001 PHE A 39 TYR 0.015 0.001 TYR C 124 ARG 0.003 0.000 ARG C 117 *********************** 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 330 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 272 time to evaluate : 1.315 Fit side-chains REVERT: A 26 LEU cc_start: 0.7987 (OUTLIER) cc_final: 0.7677 (mp) REVERT: A 27 LYS cc_start: 0.7241 (tttt) cc_final: 0.6956 (tmtt) REVERT: A 171 MET cc_start: 0.7688 (tmm) cc_final: 0.7487 (tmm) REVERT: A 197 MET cc_start: 0.7512 (mmm) cc_final: 0.7285 (tmm) REVERT: A 297 MET cc_start: 0.7043 (mpp) cc_final: 0.6708 (mpp) REVERT: B 26 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7660 (mp) REVERT: B 297 MET cc_start: 0.7029 (mpp) cc_final: 0.6678 (mpp) REVERT: B 346 HIS cc_start: 0.7538 (OUTLIER) cc_final: 0.6860 (t-90) REVERT: B 443 GLN cc_start: 0.7879 (tt0) cc_final: 0.7500 (tt0) REVERT: C 67 ILE cc_start: 0.8773 (tp) cc_final: 0.8511 (tt) REVERT: C 121 MET cc_start: 0.7900 (tmm) cc_final: 0.7695 (tmm) REVERT: C 179 GLN cc_start: 0.7236 (tm-30) cc_final: 0.6784 (pm20) REVERT: C 346 HIS cc_start: 0.7554 (OUTLIER) cc_final: 0.6846 (t-90) REVERT: C 443 GLN cc_start: 0.8009 (tt0) cc_final: 0.7525 (tt0) REVERT: D 26 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7671 (mp) REVERT: D 27 LYS cc_start: 0.7282 (tttt) cc_final: 0.7031 (tttm) REVERT: D 179 GLN cc_start: 0.7174 (tm-30) cc_final: 0.6704 (pm20) REVERT: D 346 HIS cc_start: 0.7561 (OUTLIER) cc_final: 0.6869 (t-90) outliers start: 58 outliers final: 40 residues processed: 310 average time/residue: 0.2253 time to fit residues: 101.3717 Evaluate side-chains 285 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 239 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 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 400 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 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 133 optimal weight: 0.5980 chunk 101 optimal weight: 0.0980 chunk 69 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 128 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4078 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= 0.183 Angle : 0.625 12.430 16296 Z= 0.307 Chirality : 0.037 0.164 2016 Planarity : 0.004 0.056 1956 Dihedral : 7.439 51.116 1748 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 5.03 % Allowed : 19.50 % Favored : 75.47 % 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: 2.39 (0.22), residues: 1500 helix: 1.97 (0.14), residues: 1268 sheet: 0.06 (0.76), residues: 48 loop : -0.64 (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 C 22 PHE 0.012 0.001 PHE A 39 TYR 0.017 0.001 TYR D 124 ARG 0.005 0.000 ARG B 117 *********************** 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 339 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 275 time to evaluate : 1.262 Fit side-chains REVERT: A 26 LEU cc_start: 0.7944 (OUTLIER) cc_final: 0.7664 (mp) REVERT: A 121 MET cc_start: 0.7619 (tmm) cc_final: 0.7354 (tmm) REVERT: A 197 MET cc_start: 0.7490 (mmm) cc_final: 0.7235 (tpt) REVERT: A 332 TYR cc_start: 0.7479 (t80) cc_final: 0.7250 (t80) REVERT: B 26 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7754 (mp) REVERT: B 67 ILE cc_start: 0.8775 (tp) cc_final: 0.8504 (tt) REVERT: B 346 HIS cc_start: 0.7489 (OUTLIER) cc_final: 0.6843 (t-90) REVERT: C 67 ILE cc_start: 0.8793 (tp) cc_final: 0.8565 (tt) REVERT: C 346 HIS cc_start: 0.7468 (OUTLIER) cc_final: 0.6832 (t-90) REVERT: C 443 GLN cc_start: 0.7994 (tt0) cc_final: 0.7356 (tt0) REVERT: D 26 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7704 (mp) REVERT: D 67 ILE cc_start: 0.8855 (tp) cc_final: 0.8528 (tt) REVERT: D 179 GLN cc_start: 0.7285 (tm-30) cc_final: 0.6984 (pm20) REVERT: D 346 HIS cc_start: 0.7508 (OUTLIER) cc_final: 0.6863 (t-90) outliers start: 64 outliers final: 38 residues processed: 319 average time/residue: 0.2247 time to fit residues: 105.1612 Evaluate side-chains 295 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 251 time to evaluate : 1.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 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 427 ILE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 359 LEU 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 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 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 119 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 106 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 chunk 122 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.7980 chunk 128 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 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 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 12012 Z= 0.200 Angle : 0.652 12.245 16296 Z= 0.313 Chirality : 0.038 0.162 2016 Planarity : 0.004 0.057 1956 Dihedral : 7.184 50.246 1748 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.66 % Allowed : 22.48 % Favored : 71.86 % 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: 2.63 (0.22), residues: 1500 helix: 2.25 (0.14), residues: 1256 sheet: -0.14 (0.74), residues: 48 loop : -1.19 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 193 HIS 0.003 0.001 HIS C 22 PHE 0.012 0.001 PHE A 39 TYR 0.017 0.001 TYR D 124 ARG 0.005 0.000 ARG C 117 *********************** 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 345 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 273 time to evaluate : 1.342 Fit side-chains REVERT: A 26 LEU cc_start: 0.7860 (OUTLIER) cc_final: 0.7592 (mp) REVERT: A 121 MET cc_start: 0.7592 (tmm) cc_final: 0.7364 (tmm) REVERT: B 26 LEU cc_start: 0.8020 (OUTLIER) cc_final: 0.7750 (mp) REVERT: B 67 ILE cc_start: 0.8821 (tp) cc_final: 0.8546 (tt) REVERT: B 117 ARG cc_start: 0.6984 (ttm110) cc_final: 0.6578 (mtm110) REVERT: B 346 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.6801 (t-90) REVERT: C 27 LYS cc_start: 0.7258 (tttt) cc_final: 0.7014 (tptm) REVERT: C 67 ILE cc_start: 0.8885 (tp) cc_final: 0.8529 (tt) REVERT: C 121 MET cc_start: 0.7901 (tmm) cc_final: 0.7648 (tmm) REVERT: C 297 MET cc_start: 0.6977 (mpp) cc_final: 0.6688 (mpp) REVERT: C 346 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.6781 (t-90) REVERT: C 443 GLN cc_start: 0.8068 (tt0) cc_final: 0.7083 (tt0) REVERT: D 26 LEU cc_start: 0.8030 (OUTLIER) cc_final: 0.7778 (mp) REVERT: D 67 ILE cc_start: 0.8807 (tp) cc_final: 0.8590 (tt) REVERT: D 346 HIS cc_start: 0.7498 (OUTLIER) cc_final: 0.6855 (t-90) outliers start: 72 outliers final: 56 residues processed: 324 average time/residue: 0.2221 time to fit residues: 105.6445 Evaluate side-chains 298 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 236 time to evaluate : 1.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 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 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 400 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 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 408 MET 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 363 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.8980 chunk 128 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 35 optimal weight: 0.0980 chunk 143 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 66 optimal weight: 0.7980 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 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** A 443 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.4734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12012 Z= 0.191 Angle : 0.669 12.166 16296 Z= 0.316 Chirality : 0.037 0.169 2016 Planarity : 0.004 0.056 1956 Dihedral : 7.003 52.399 1748 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 5.42 % Allowed : 21.23 % Favored : 73.35 % 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: 2.86 (0.22), residues: 1500 helix: 2.41 (0.14), residues: 1256 sheet: 0.04 (0.75), residues: 48 loop : -1.20 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 180 HIS 0.004 0.001 HIS C 22 PHE 0.010 0.001 PHE A 39 TYR 0.017 0.001 TYR C 124 ARG 0.005 0.000 ARG D 117 *********************** 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 315 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 246 time to evaluate : 1.371 Fit side-chains REVERT: A 26 LEU cc_start: 0.7849 (OUTLIER) cc_final: 0.7641 (mp) REVERT: A 27 LYS cc_start: 0.7136 (tttt) cc_final: 0.6845 (tmtt) REVERT: A 121 MET cc_start: 0.7587 (tmm) cc_final: 0.7336 (tmm) REVERT: B 26 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7658 (mp) REVERT: B 346 HIS cc_start: 0.7450 (OUTLIER) cc_final: 0.6624 (t-90) REVERT: C 117 ARG cc_start: 0.6960 (ttm110) cc_final: 0.6710 (ttp-110) REVERT: C 125 MET cc_start: 0.7066 (mmt) cc_final: 0.6699 (tpt) REVERT: C 346 HIS cc_start: 0.7473 (OUTLIER) cc_final: 0.6657 (t-90) REVERT: D 26 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7741 (mp) REVERT: D 67 ILE cc_start: 0.8900 (tp) cc_final: 0.8571 (tt) REVERT: D 117 ARG cc_start: 0.6982 (ttm110) cc_final: 0.6754 (ttp-110) REVERT: D 346 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.6655 (t-90) REVERT: D 364 VAL cc_start: 0.5412 (OUTLIER) cc_final: 0.5013 (t) outliers start: 69 outliers final: 49 residues processed: 292 average time/residue: 0.2404 time to fit residues: 102.0535 Evaluate side-chains 292 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 236 time to evaluate : 1.579 ------------------------------------------------------------------------------- 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 395 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 193 TRP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain 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 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 408 MET 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 427 ILE Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 20.0000 chunk 16 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 65 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS B 443 GLN ** 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 D 443 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.4952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12012 Z= 0.233 Angle : 0.703 13.783 16296 Z= 0.330 Chirality : 0.038 0.172 2016 Planarity : 0.004 0.056 1956 Dihedral : 6.794 52.062 1748 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 5.35 % Allowed : 22.25 % Favored : 72.41 % 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: 2.80 (0.22), residues: 1500 helix: 2.41 (0.14), residues: 1256 sheet: -0.30 (0.72), residues: 48 loop : -1.41 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 193 HIS 0.003 0.001 HIS C 22 PHE 0.010 0.001 PHE A 39 TYR 0.015 0.001 TYR D 124 ARG 0.006 0.001 ARG B 117 *********************** 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 313 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 245 time to evaluate : 1.285 Fit side-chains REVERT: A 27 LYS cc_start: 0.7123 (tttt) cc_final: 0.6875 (tmtt) REVERT: B 26 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7699 (mp) REVERT: B 27 LYS cc_start: 0.7229 (tttt) cc_final: 0.6909 (tptt) REVERT: B 117 ARG cc_start: 0.7093 (ttp-110) cc_final: 0.6710 (mtm110) REVERT: B 346 HIS cc_start: 0.7410 (OUTLIER) cc_final: 0.6700 (t-90) REVERT: C 24 PHE cc_start: 0.7921 (t80) cc_final: 0.7330 (t80) REVERT: C 27 LYS cc_start: 0.7182 (tttt) cc_final: 0.6915 (tptt) REVERT: C 346 HIS cc_start: 0.7427 (OUTLIER) cc_final: 0.6734 (t-90) REVERT: D 26 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7702 (mp) REVERT: D 27 LYS cc_start: 0.7257 (tttt) cc_final: 0.6974 (tptt) REVERT: D 346 HIS cc_start: 0.7430 (OUTLIER) cc_final: 0.6773 (t-90) outliers start: 68 outliers final: 54 residues processed: 294 average time/residue: 0.2249 time to fit residues: 96.5327 Evaluate side-chains 297 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 238 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain A residue 193 TRP 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 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 193 TRP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 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 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 408 MET 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 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 428 VAL 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 56 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 97 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 129 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 443 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12012 Z= 0.257 Angle : 0.753 14.051 16296 Z= 0.346 Chirality : 0.039 0.174 2016 Planarity : 0.004 0.054 1956 Dihedral : 6.724 52.853 1748 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 5.50 % Allowed : 22.72 % Favored : 71.78 % 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: 2.73 (0.22), residues: 1500 helix: 2.38 (0.15), residues: 1256 sheet: -0.42 (0.70), residues: 48 loop : -1.55 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 193 HIS 0.007 0.001 HIS A 22 PHE 0.014 0.001 PHE D 444 TYR 0.015 0.001 TYR D 124 ARG 0.007 0.001 ARG C 117 *********************** 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 316 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 246 time to evaluate : 1.238 Fit side-chains REVERT: A 24 PHE cc_start: 0.7826 (t80) cc_final: 0.7347 (t80) REVERT: A 27 LYS cc_start: 0.7080 (tttt) cc_final: 0.6852 (tmtt) REVERT: B 346 HIS cc_start: 0.7439 (OUTLIER) cc_final: 0.6752 (t-90) REVERT: C 24 PHE cc_start: 0.7929 (t80) cc_final: 0.7295 (t80) REVERT: C 297 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6899 (mpp) REVERT: C 346 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.6730 (t-90) REVERT: D 26 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7702 (mp) REVERT: D 117 ARG cc_start: 0.7192 (ttp-110) cc_final: 0.6739 (mtm110) REVERT: D 346 HIS cc_start: 0.7453 (OUTLIER) cc_final: 0.6771 (t-90) outliers start: 70 outliers final: 62 residues processed: 295 average time/residue: 0.2276 time to fit residues: 96.4768 Evaluate side-chains 301 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 234 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 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 395 VAL Chi-restraints excluded: chain A residue 400 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 129 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 443 GLN 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 297 MET Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 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 C residue 408 MET 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 129 VAL Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.9980 chunk 124 optimal weight: 0.7980 chunk 132 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 57 optimal weight: 0.5980 chunk 104 optimal weight: 0.9990 chunk 40 optimal weight: 0.5980 chunk 120 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.5228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12012 Z= 0.205 Angle : 0.759 14.819 16296 Z= 0.342 Chirality : 0.038 0.185 2016 Planarity : 0.004 0.055 1956 Dihedral : 6.636 55.348 1748 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.80 % Allowed : 24.37 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.86 (0.22), residues: 1500 helix: 2.46 (0.14), residues: 1256 sheet: -0.50 (0.70), residues: 48 loop : -1.46 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 180 HIS 0.006 0.001 HIS A 22 PHE 0.013 0.001 PHE B 444 TYR 0.017 0.001 TYR D 124 ARG 0.007 0.000 ARG B 117 *********************** 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 305 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 244 time to evaluate : 1.373 Fit side-chains REVERT: A 24 PHE cc_start: 0.7839 (t80) cc_final: 0.7354 (t80) REVERT: A 27 LYS cc_start: 0.6951 (tttt) cc_final: 0.6744 (tmtt) REVERT: A 117 ARG cc_start: 0.7143 (ttm110) cc_final: 0.6742 (mtm110) REVERT: B 27 LYS cc_start: 0.7182 (tttt) cc_final: 0.6918 (tptt) REVERT: B 117 ARG cc_start: 0.7019 (ttp-110) cc_final: 0.6742 (mtm110) REVERT: B 346 HIS cc_start: 0.7520 (OUTLIER) cc_final: 0.6846 (t-90) REVERT: C 24 PHE cc_start: 0.7853 (t80) cc_final: 0.7289 (t80) REVERT: C 117 ARG cc_start: 0.7126 (ttp-110) cc_final: 0.6736 (mtm110) REVERT: C 346 HIS cc_start: 0.7424 (OUTLIER) cc_final: 0.6782 (t-90) REVERT: D 117 ARG cc_start: 0.7165 (ttp-110) cc_final: 0.6740 (mtm110) REVERT: D 346 HIS cc_start: 0.7478 (OUTLIER) cc_final: 0.6810 (t-90) outliers start: 61 outliers final: 53 residues processed: 284 average time/residue: 0.2302 time to fit residues: 94.6912 Evaluate side-chains 293 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 237 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 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 428 VAL 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 307 HIS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 443 GLN Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 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 408 MET Chi-restraints excluded: chain C residue 443 GLN 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 129 VAL Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 345 LEU Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 359 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 147 optimal weight: 0.5980 chunk 135 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 90 optimal weight: 8.9990 chunk 71 optimal weight: 0.0170 chunk 93 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 22 HIS ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.5353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12012 Z= 0.194 Angle : 0.768 14.922 16296 Z= 0.345 Chirality : 0.039 0.188 2016 Planarity : 0.004 0.056 1956 Dihedral : 6.587 55.270 1748 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 4.40 % Allowed : 24.84 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.92 (0.22), residues: 1500 helix: 2.51 (0.15), residues: 1256 sheet: -0.55 (0.68), residues: 48 loop : -1.43 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 180 HIS 0.006 0.001 HIS B 22 PHE 0.015 0.001 PHE B 444 TYR 0.016 0.001 TYR D 124 ARG 0.007 0.001 ARG B 117 ********************** 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 297 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 241 time to evaluate : 1.342 Fit side-chains REVERT: A 27 LYS cc_start: 0.6881 (tttt) cc_final: 0.6649 (tmtt) REVERT: A 332 TYR cc_start: 0.7942 (t80) cc_final: 0.7444 (t80) REVERT: B 27 LYS cc_start: 0.7077 (tttt) cc_final: 0.6811 (tptt) REVERT: B 117 ARG cc_start: 0.7007 (ttp-110) cc_final: 0.6717 (mtm110) REVERT: B 332 TYR cc_start: 0.7842 (t80) cc_final: 0.7438 (t80) REVERT: B 346 HIS cc_start: 0.7516 (OUTLIER) cc_final: 0.6868 (t-90) REVERT: C 24 PHE cc_start: 0.7873 (t80) cc_final: 0.7290 (t80) REVERT: C 27 LYS cc_start: 0.7129 (tptm) cc_final: 0.6896 (tmtt) REVERT: C 117 ARG cc_start: 0.7182 (ttp-110) cc_final: 0.6736 (mtm110) REVERT: C 332 TYR cc_start: 0.7917 (t80) cc_final: 0.7513 (t80) REVERT: C 346 HIS cc_start: 0.7460 (OUTLIER) cc_final: 0.6850 (t-90) REVERT: D 27 LYS cc_start: 0.7313 (tptm) cc_final: 0.7072 (tmtt) REVERT: D 117 ARG cc_start: 0.7137 (ttp-110) cc_final: 0.6748 (mtm110) REVERT: D 332 TYR cc_start: 0.7864 (t80) cc_final: 0.7442 (t80) REVERT: D 346 HIS cc_start: 0.7474 (OUTLIER) cc_final: 0.6837 (t-90) outliers start: 56 outliers final: 47 residues processed: 279 average time/residue: 0.2213 time to fit residues: 89.5946 Evaluate side-chains 286 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 236 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 THR 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 129 VAL Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 443 GLN Chi-restraints excluded: chain C residue 39 PHE Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 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 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 345 LEU 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 400 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 0.9980 chunk 108 optimal weight: 0.4980 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 0.0570 chunk 117 optimal weight: 0.0030 chunk 49 optimal weight: 0.0470 chunk 120 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 overall best weight: 0.2406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 HIS ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.230651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.194087 restraints weight = 12918.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.199001 restraints weight = 8304.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.202910 restraints weight = 6075.342| |-----------------------------------------------------------------------------| r_work (final): 0.4307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.5519 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= 0.180 Angle : 0.766 15.224 16296 Z= 0.345 Chirality : 0.038 0.188 2016 Planarity : 0.004 0.058 1956 Dihedral : 6.570 57.167 1748 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.62 % Allowed : 26.42 % Favored : 69.97 % 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: 3.06 (0.22), residues: 1500 helix: 2.55 (0.15), residues: 1264 sheet: -0.52 (0.68), residues: 48 loop : -1.12 (0.50), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 193 HIS 0.007 0.001 HIS B 22 PHE 0.019 0.001 PHE B 444 TYR 0.017 0.001 TYR D 124 ARG 0.008 0.001 ARG A 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2519.70 seconds wall clock time: 47 minutes 3.32 seconds (2823.32 seconds total)