Starting phenix.real_space_refine on Fri Mar 15 13:24:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc2_43130/03_2024/8vc2_43130_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc2_43130/03_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_43130/03_2024/8vc2_43130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc2_43130/03_2024/8vc2_43130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc2_43130/03_2024/8vc2_43130_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc2_43130/03_2024/8vc2_43130_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11796 Number of models: 1 Model: "" Number of chains: 8 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: "B" 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: "C" 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: "D" 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 Chain: "B" 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 Chain: "C" 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 Chain: "D" 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 Time building chain proxies: 6.43, per 1000 atoms: 0.55 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 - 3.50 Amino acid : False - 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: 4.34 Conformation dependent library (CDL) restraints added in 2.1 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... running ksdssp... Secondary structure from input PDB file: 40 helices and 4 sheets defined 81.8% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 20 through 31 removed outlier: 3.567A pdb=" N ILE A 25 " --> pdb=" O HIS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 78 Processing helix chain 'A' and resid 90 through 134 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) removed outlier: 3.728A pdb=" N GLY A 113 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) Proline residue: A 115 - end of helix 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 176 removed outlier: 3.989A pdb=" N LEU A 152 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A 175 " --> pdb=" O GLN A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 229 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 287 through 339 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 345 through 389 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 395 through 409 removed outlier: 3.983A pdb=" N MET A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 418 No H-bonds generated for 'chain 'A' and resid 416 through 418' Processing helix chain 'A' and resid 424 through 445 removed outlier: 3.741A pdb=" N LEU A 431 " --> pdb=" O VAL A 428 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR A 435 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU A 438 " --> pdb=" O THR A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 31 removed outlier: 3.568A pdb=" N ILE B 25 " --> pdb=" O HIS B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 78 Processing helix chain 'B' and resid 90 through 134 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) removed outlier: 3.729A pdb=" N GLY B 113 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Proline residue: B 115 - end of helix 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 176 removed outlier: 3.989A pdb=" N LEU B 152 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS B 175 " --> pdb=" O GLN B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 179 through 229 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 287 through 339 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 345 through 389 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 395 through 409 removed outlier: 3.982A pdb=" N MET B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 418 No H-bonds generated for 'chain 'B' and resid 416 through 418' Processing helix chain 'B' and resid 424 through 445 removed outlier: 3.741A pdb=" N LEU B 431 " --> pdb=" O VAL B 428 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR B 435 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU B 438 " --> pdb=" O THR B 435 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 31 removed outlier: 3.568A pdb=" N ILE C 25 " --> pdb=" O HIS C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 78 Processing helix chain 'C' and resid 90 through 134 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) removed outlier: 3.728A pdb=" N GLY C 113 " --> pdb=" O VAL C 109 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) Proline residue: C 115 - end of helix 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 176 removed outlier: 3.989A pdb=" N LEU C 152 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS C 175 " --> pdb=" O GLN C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 179 through 229 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 287 through 339 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 345 through 389 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 395 through 409 removed outlier: 3.983A pdb=" N MET C 408 " --> pdb=" O SER C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 418 No H-bonds generated for 'chain 'C' and resid 416 through 418' Processing helix chain 'C' and resid 424 through 445 removed outlier: 3.742A pdb=" N LEU C 431 " --> pdb=" O VAL C 428 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR C 435 " --> pdb=" O GLY C 432 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N LEU C 438 " --> pdb=" O THR C 435 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 31 removed outlier: 3.567A pdb=" N ILE D 25 " --> pdb=" O HIS D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 78 Processing helix chain 'D' and resid 90 through 134 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) removed outlier: 3.729A pdb=" N GLY D 113 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) Proline residue: D 115 - end of helix 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 176 removed outlier: 3.989A pdb=" N LEU D 152 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS D 175 " --> pdb=" O GLN D 172 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 229 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 287 through 339 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 345 through 389 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 395 through 409 removed outlier: 3.983A pdb=" N MET D 408 " --> pdb=" O SER D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 418 No H-bonds generated for 'chain 'D' and resid 416 through 418' Processing helix chain 'D' and resid 424 through 445 removed outlier: 3.741A pdb=" N LEU D 431 " --> pdb=" O VAL D 428 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N THR D 435 " --> pdb=" O GLY D 432 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU D 438 " --> pdb=" O THR D 435 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 17 through 19 Processing sheet with id= B, first strand: chain 'B' and resid 17 through 19 Processing sheet with id= C, first strand: chain 'C' and resid 17 through 19 Processing sheet with id= D, first strand: chain 'D' and resid 17 through 19 952 hydrogen bonds defined for protein. 2184 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: 3.63 Time building geometry restraints manager: 4.75 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: 100.60 - 107.28: 328 107.28 - 113.96: 7042 113.96 - 120.63: 5089 120.63 - 127.31: 3741 127.31 - 133.99: 96 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: 3885 2.86 - 3.37: 12947 3.37 - 3.88: 19554 3.88 - 4.39: 22038 4.39 - 4.90: 36522 Nonbonded interactions: 94946 Sorted by model distance: nonbonded pdb=" OD2 ASP A 165 " pdb=" NE1 TRP A 354 " model vdw 2.353 2.520 nonbonded pdb=" OD2 ASP B 165 " pdb=" NE1 TRP B 354 " model vdw 2.353 2.520 nonbonded pdb=" OD2 ASP D 165 " pdb=" NE1 TRP D 354 " model vdw 2.353 2.520 nonbonded pdb=" OD2 ASP C 165 " pdb=" NE1 TRP C 354 " model vdw 2.354 2.520 nonbonded pdb=" OE2 GLU A 76 " pdb=" ND2 ASN A 185 " model vdw 2.363 2.520 ... (remaining 94941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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: 1.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.560 Check model and map are aligned: 0.140 Set scattering table: 0.110 Process input model: 33.140 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 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:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.070 ------------------------------------------------------------------------------- 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= 0.368 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 : 1.143 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: 0.2152 time to fit residues: 139.2727 Evaluate side-chains 298 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 297 time to evaluate : 1.373 ------------------------------------------------------------------------------- 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: 0.6980 chunk 112 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 116 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 134 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS A 179 GLN B 22 HIS B 179 GLN ** B 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 HIS C 179 GLN ** C 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS D 179 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12012 Z= 0.199 Angle : 0.638 10.062 16296 Z= 0.335 Chirality : 0.037 0.116 2016 Planarity : 0.006 0.037 1956 Dihedral : 8.717 67.338 1750 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 4.87 % Allowed : 15.49 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.95 (0.21), residues: 1500 helix: 1.07 (0.14), residues: 1244 sheet: 0.13 (0.69), residues: 48 loop : -1.55 (0.42), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.002 0.001 HIS B 326 PHE 0.017 0.002 PHE C 203 TYR 0.018 0.002 TYR D 124 ARG 0.003 0.000 ARG C 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 369 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 307 time to evaluate : 1.319 Fit side-chains revert: symmetry clash REVERT: A 39 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.6773 (p90) REVERT: A 179 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6996 (pm20) REVERT: A 197 MET cc_start: 0.7565 (mmm) cc_final: 0.7303 (tmm) REVERT: B 117 ARG cc_start: 0.7074 (ttm110) cc_final: 0.6492 (mtm110) REVERT: B 346 HIS cc_start: 0.7562 (OUTLIER) cc_final: 0.6864 (t-90) REVERT: C 117 ARG cc_start: 0.7151 (ttm110) cc_final: 0.6497 (mtm110) REVERT: C 167 CYS cc_start: 0.7426 (m) cc_final: 0.6950 (t) REVERT: C 346 HIS cc_start: 0.7606 (OUTLIER) cc_final: 0.6898 (t-90) REVERT: D 117 ARG cc_start: 0.7142 (ttm110) cc_final: 0.6490 (mtm110) REVERT: D 167 CYS cc_start: 0.7499 (m) cc_final: 0.6992 (t) REVERT: D 346 HIS cc_start: 0.7586 (OUTLIER) cc_final: 0.6901 (t-90) REVERT: D 363 LEU cc_start: 0.7042 (mt) cc_final: 0.6833 (tt) outliers start: 62 outliers final: 33 residues processed: 339 average time/residue: 0.2078 time to fit residues: 105.0878 Evaluate side-chains 270 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 232 time to evaluate : 1.260 ------------------------------------------------------------------------------- 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 179 GLN Chi-restraints excluded: chain A residue 184 THR Chi-restraints excluded: chain A residue 357 THR 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 79 VAL Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 179 GLN Chi-restraints excluded: chain B residue 184 THR 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 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 179 GLN Chi-restraints excluded: chain C residue 184 THR 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 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 179 GLN Chi-restraints excluded: chain D residue 184 THR Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 357 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 91 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 145 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12012 Z= 0.323 Angle : 0.730 12.194 16296 Z= 0.372 Chirality : 0.040 0.162 2016 Planarity : 0.006 0.046 1956 Dihedral : 7.807 53.879 1748 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 6.76 % Allowed : 18.08 % Favored : 75.16 % 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: 0.74 (0.21), residues: 1500 helix: 0.96 (0.14), residues: 1240 sheet: 0.25 (0.76), residues: 48 loop : -1.91 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 193 HIS 0.006 0.001 HIS A 358 PHE 0.013 0.001 PHE A 39 TYR 0.012 0.002 TYR B 312 ARG 0.005 0.001 ARG C 42 *********************** 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 355 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 269 time to evaluate : 1.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 MET cc_start: 0.7701 (mmm) cc_final: 0.7217 (tmm) REVERT: A 297 MET cc_start: 0.7249 (mpp) cc_final: 0.6913 (mpp) REVERT: A 377 LYS cc_start: 0.8587 (tppt) cc_final: 0.7654 (tptp) REVERT: A 401 GLU cc_start: 0.8281 (tt0) cc_final: 0.7618 (tt0) REVERT: B 208 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.8014 (tp) REVERT: B 297 MET cc_start: 0.7163 (mpp) cc_final: 0.6920 (mpp) REVERT: B 346 HIS cc_start: 0.7638 (OUTLIER) cc_final: 0.6929 (t-90) REVERT: B 401 GLU cc_start: 0.8317 (tt0) cc_final: 0.7587 (tt0) REVERT: C 67 ILE cc_start: 0.8800 (tp) cc_final: 0.8549 (tt) REVERT: C 197 MET cc_start: 0.7264 (OUTLIER) cc_final: 0.7046 (tmm) REVERT: C 346 HIS cc_start: 0.7676 (OUTLIER) cc_final: 0.6945 (t-90) REVERT: C 401 GLU cc_start: 0.8269 (tt0) cc_final: 0.7582 (tt0) REVERT: C 443 GLN cc_start: 0.7945 (tt0) cc_final: 0.7699 (tt0) REVERT: D 67 ILE cc_start: 0.8767 (tp) cc_final: 0.8527 (tt) REVERT: D 297 MET cc_start: 0.7322 (mpp) cc_final: 0.7034 (mpp) REVERT: D 346 HIS cc_start: 0.7647 (OUTLIER) cc_final: 0.6952 (t-90) REVERT: D 401 GLU cc_start: 0.8244 (tt0) cc_final: 0.7620 (tt0) outliers start: 86 outliers final: 63 residues processed: 328 average time/residue: 0.2196 time to fit residues: 104.1018 Evaluate side-chains 308 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 240 time to evaluate : 1.184 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 307 HIS 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 400 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 441 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 122 LEU Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 285 VAL 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 395 VAL 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 79 VAL Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 197 MET Chi-restraints excluded: chain C residue 285 VAL 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 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 428 VAL 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 122 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 285 VAL 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 395 VAL 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: 1.9990 chunk 101 optimal weight: 4.9990 chunk 69 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 90 optimal weight: 0.0030 chunk 135 optimal weight: 0.0570 chunk 143 optimal weight: 0.8980 chunk 70 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 overall best weight: 0.4908 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN B 410 GLN C 410 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.4238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12012 Z= 0.170 Angle : 0.617 12.306 16296 Z= 0.309 Chirality : 0.037 0.159 2016 Planarity : 0.005 0.050 1956 Dihedral : 7.567 50.148 1748 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.11 % Allowed : 19.81 % Favored : 75.08 % 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: 1.25 (0.22), residues: 1500 helix: 1.33 (0.15), residues: 1240 sheet: 0.27 (0.76), residues: 48 loop : -1.85 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 193 HIS 0.001 0.000 HIS B 326 PHE 0.013 0.001 PHE B 203 TYR 0.018 0.001 TYR D 124 ARG 0.004 0.000 ARG A 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 329 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 264 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: A 117 ARG cc_start: 0.7125 (ttm110) cc_final: 0.6502 (mtm110) REVERT: A 197 MET cc_start: 0.7505 (mmm) cc_final: 0.7210 (tpt) REVERT: A 332 TYR cc_start: 0.7378 (t80) cc_final: 0.7151 (t80) REVERT: A 401 GLU cc_start: 0.8034 (tt0) cc_final: 0.7267 (tt0) REVERT: B 26 LEU cc_start: 0.8448 (mt) cc_final: 0.8246 (mt) REVERT: B 117 ARG cc_start: 0.7015 (ttm110) cc_final: 0.6501 (mtm110) REVERT: B 346 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.6737 (t-90) REVERT: B 401 GLU cc_start: 0.8119 (tt0) cc_final: 0.7252 (tt0) REVERT: C 67 ILE cc_start: 0.8832 (tp) cc_final: 0.8583 (tt) REVERT: C 117 ARG cc_start: 0.7157 (ttm110) cc_final: 0.6521 (mtm110) REVERT: C 346 HIS cc_start: 0.7501 (OUTLIER) cc_final: 0.6742 (t-90) REVERT: C 401 GLU cc_start: 0.8082 (tt0) cc_final: 0.7288 (tt0) REVERT: C 443 GLN cc_start: 0.7936 (tt0) cc_final: 0.7687 (tt0) REVERT: D 67 ILE cc_start: 0.8795 (tp) cc_final: 0.8560 (tt) REVERT: D 117 ARG cc_start: 0.7135 (ttm110) cc_final: 0.6488 (mtm110) REVERT: D 346 HIS cc_start: 0.7511 (OUTLIER) cc_final: 0.6729 (t-90) REVERT: D 401 GLU cc_start: 0.8081 (tt0) cc_final: 0.7338 (tt0) outliers start: 65 outliers final: 41 residues processed: 302 average time/residue: 0.2182 time to fit residues: 94.9947 Evaluate side-chains 289 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 245 time to evaluate : 1.237 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain A residue 153 LEU 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 428 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 153 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 363 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 147 LEU Chi-restraints excluded: chain C residue 152 LEU Chi-restraints excluded: chain C residue 153 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 363 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 147 LEU Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 153 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 363 LEU 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: 0.9990 chunk 81 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 122 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12012 Z= 0.207 Angle : 0.645 13.134 16296 Z= 0.319 Chirality : 0.038 0.169 2016 Planarity : 0.005 0.052 1956 Dihedral : 7.223 49.221 1748 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.27 % Allowed : 21.31 % Favored : 73.43 % 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: 1.35 (0.22), residues: 1500 helix: 1.40 (0.15), residues: 1244 sheet: 0.12 (0.73), residues: 48 loop : -1.81 (0.43), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 193 HIS 0.002 0.001 HIS C 392 PHE 0.011 0.001 PHE A 39 TYR 0.016 0.001 TYR D 124 ARG 0.005 0.000 ARG A 178 *********************** 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 322 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 255 time to evaluate : 1.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 401 GLU cc_start: 0.8199 (tt0) cc_final: 0.7456 (tt0) REVERT: B 67 ILE cc_start: 0.8836 (tp) cc_final: 0.8563 (tt) REVERT: B 346 HIS cc_start: 0.7511 (OUTLIER) cc_final: 0.6777 (t-90) REVERT: B 401 GLU cc_start: 0.8232 (tt0) cc_final: 0.7366 (tt0) REVERT: C 301 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7973 (mp) REVERT: C 346 HIS cc_start: 0.7525 (OUTLIER) cc_final: 0.6800 (t-90) REVERT: C 401 GLU cc_start: 0.8101 (tt0) cc_final: 0.7292 (tt0) REVERT: D 346 HIS cc_start: 0.7526 (OUTLIER) cc_final: 0.6796 (t-90) REVERT: D 401 GLU cc_start: 0.8219 (tt0) cc_final: 0.7413 (tt0) outliers start: 67 outliers final: 53 residues processed: 293 average time/residue: 0.2251 time to fit residues: 95.1544 Evaluate side-chains 296 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 239 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain A residue 153 LEU 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 363 LEU Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 428 VAL 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 152 LEU Chi-restraints excluded: chain B residue 153 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 363 LEU Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 428 VAL 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 152 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 428 VAL 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 152 LEU Chi-restraints excluded: chain D residue 153 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 363 LEU Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.5980 chunk 128 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 0.4980 chunk 143 optimal weight: 0.5980 chunk 118 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 47 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12012 Z= 0.172 Angle : 0.640 12.849 16296 Z= 0.310 Chirality : 0.037 0.178 2016 Planarity : 0.005 0.054 1956 Dihedral : 7.103 52.681 1748 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.72 % Allowed : 21.62 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.62 (0.22), residues: 1500 helix: 1.62 (0.15), residues: 1240 sheet: 0.10 (0.74), residues: 48 loop : -1.91 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 193 HIS 0.002 0.000 HIS C 22 PHE 0.012 0.001 PHE D 39 TYR 0.017 0.001 TYR B 124 ARG 0.004 0.000 ARG B 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 314 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 254 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 VAL cc_start: 0.7380 (t) cc_final: 0.7168 (t) REVERT: A 401 GLU cc_start: 0.8128 (tt0) cc_final: 0.7330 (tt0) REVERT: B 67 ILE cc_start: 0.8853 (tp) cc_final: 0.8550 (tt) REVERT: B 125 MET cc_start: 0.6856 (mmt) cc_final: 0.6642 (tpt) REVERT: B 346 HIS cc_start: 0.7474 (OUTLIER) cc_final: 0.6773 (t-90) REVERT: B 401 GLU cc_start: 0.8082 (tt0) cc_final: 0.7235 (tt0) REVERT: C 117 ARG cc_start: 0.7013 (ttm110) cc_final: 0.6447 (mtm110) REVERT: C 301 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7787 (mp) REVERT: C 346 HIS cc_start: 0.7491 (OUTLIER) cc_final: 0.6704 (t-90) REVERT: C 401 GLU cc_start: 0.8065 (tt0) cc_final: 0.7139 (tt0) REVERT: D 117 ARG cc_start: 0.7000 (ttm110) cc_final: 0.6438 (mtm110) REVERT: D 125 MET cc_start: 0.6869 (mmt) cc_final: 0.6666 (tpt) REVERT: D 346 HIS cc_start: 0.7456 (OUTLIER) cc_final: 0.6763 (t-90) REVERT: D 401 GLU cc_start: 0.8039 (tt0) cc_final: 0.7303 (tt0) outliers start: 60 outliers final: 47 residues processed: 292 average time/residue: 0.2277 time to fit residues: 95.4626 Evaluate side-chains 290 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 239 time to evaluate : 1.268 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain A residue 153 LEU 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 395 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 441 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 152 LEU Chi-restraints excluded: chain B residue 153 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 363 LEU Chi-restraints excluded: chain B residue 379 THR 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 152 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 428 VAL 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 152 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 363 LEU 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: 4.9990 chunk 16 optimal weight: 0.0060 chunk 81 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 120 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 86 optimal weight: 0.0020 chunk 65 optimal weight: 6.9990 chunk 88 optimal weight: 0.8980 overall best weight: 1.1808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 370 HIS A 410 GLN B 370 HIS B 410 GLN C 370 HIS C 410 GLN D 370 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12012 Z= 0.231 Angle : 0.673 13.349 16296 Z= 0.328 Chirality : 0.038 0.174 2016 Planarity : 0.005 0.053 1956 Dihedral : 6.993 53.694 1748 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.82 % Allowed : 22.09 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.50 (0.22), residues: 1500 helix: 1.56 (0.15), residues: 1240 sheet: -0.18 (0.70), residues: 48 loop : -2.04 (0.44), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 193 HIS 0.002 0.001 HIS A 326 PHE 0.010 0.001 PHE C 39 TYR 0.016 0.001 TYR B 124 ARG 0.003 0.000 ARG A 178 *********************** 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 323 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 249 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 401 GLU cc_start: 0.8154 (tt0) cc_final: 0.7406 (tt0) REVERT: B 346 HIS cc_start: 0.7415 (OUTLIER) cc_final: 0.6753 (t-90) REVERT: B 401 GLU cc_start: 0.8251 (tt0) cc_final: 0.7429 (tt0) REVERT: C 301 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7992 (mp) REVERT: C 346 HIS cc_start: 0.7384 (OUTLIER) cc_final: 0.6695 (t-90) REVERT: C 401 GLU cc_start: 0.8221 (tt0) cc_final: 0.7433 (tt0) REVERT: D 346 HIS cc_start: 0.7431 (OUTLIER) cc_final: 0.6806 (t-90) REVERT: D 401 GLU cc_start: 0.8226 (tt0) cc_final: 0.7488 (tt0) outliers start: 74 outliers final: 63 residues processed: 298 average time/residue: 0.2307 time to fit residues: 98.3602 Evaluate side-chains 311 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 244 time to evaluate : 1.280 ------------------------------------------------------------------------------- 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 152 LEU Chi-restraints excluded: chain A residue 153 LEU 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 363 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 A residue 441 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 153 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 363 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 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 152 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 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 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 206 THR 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 363 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 408 MET Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 90 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 70 optimal weight: 0.5980 chunk 13 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 129 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 12012 Z= 0.190 Angle : 0.679 13.359 16296 Z= 0.323 Chirality : 0.037 0.180 2016 Planarity : 0.005 0.054 1956 Dihedral : 6.950 54.531 1748 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.50 % Allowed : 22.88 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.22), residues: 1500 helix: 1.62 (0.15), residues: 1240 sheet: None (None), residues: 0 loop : -1.76 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 193 HIS 0.003 0.000 HIS A 22 PHE 0.009 0.001 PHE D 39 TYR 0.022 0.001 TYR B 124 ARG 0.008 0.000 ARG D 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 321 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 251 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 VAL cc_start: 0.7349 (t) cc_final: 0.7138 (t) REVERT: A 401 GLU cc_start: 0.8156 (tt0) cc_final: 0.7387 (tt0) REVERT: B 346 HIS cc_start: 0.7361 (OUTLIER) cc_final: 0.6816 (t-90) REVERT: B 401 GLU cc_start: 0.8172 (tt0) cc_final: 0.7347 (tt0) REVERT: C 117 ARG cc_start: 0.7011 (ttp-110) cc_final: 0.6567 (mtm110) REVERT: C 301 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7787 (mp) REVERT: C 332 TYR cc_start: 0.7846 (t80) cc_final: 0.7308 (t80) REVERT: C 346 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.6674 (t-90) REVERT: C 401 GLU cc_start: 0.8112 (tt0) cc_final: 0.7307 (tt0) REVERT: D 117 ARG cc_start: 0.6957 (ttp-110) cc_final: 0.6547 (mtm110) REVERT: D 125 MET cc_start: 0.6691 (tpt) cc_final: 0.6483 (tpt) REVERT: D 301 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7789 (mp) REVERT: D 332 TYR cc_start: 0.7824 (t80) cc_final: 0.7259 (t80) REVERT: D 346 HIS cc_start: 0.7396 (OUTLIER) cc_final: 0.6839 (t-90) REVERT: D 401 GLU cc_start: 0.8129 (tt0) cc_final: 0.7386 (tt0) outliers start: 70 outliers final: 56 residues processed: 295 average time/residue: 0.2216 time to fit residues: 94.6718 Evaluate side-chains 302 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 241 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE 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 152 LEU Chi-restraints excluded: chain A residue 153 LEU 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 363 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 A residue 441 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 152 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 428 VAL 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 152 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 427 ILE Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 301 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 363 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 136 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 chunk 80 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 125 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.5359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12012 Z= 0.250 Angle : 0.728 13.794 16296 Z= 0.346 Chirality : 0.039 0.179 2016 Planarity : 0.005 0.053 1956 Dihedral : 6.925 59.072 1748 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.66 % Allowed : 23.11 % Favored : 71.23 % 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: 1.39 (0.22), residues: 1500 helix: 1.50 (0.15), residues: 1240 sheet: None (None), residues: 0 loop : -1.87 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 193 HIS 0.002 0.001 HIS B 22 PHE 0.010 0.001 PHE B 39 TYR 0.017 0.001 TYR D 124 ARG 0.008 0.000 ARG D 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 317 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 245 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 ARG cc_start: 0.7685 (ttp-110) cc_final: 0.6903 (mtm110) REVERT: A 401 GLU cc_start: 0.8261 (tt0) cc_final: 0.7531 (tt0) REVERT: B 332 TYR cc_start: 0.7939 (t80) cc_final: 0.7396 (t80) REVERT: B 346 HIS cc_start: 0.7364 (OUTLIER) cc_final: 0.6814 (t-90) REVERT: B 401 GLU cc_start: 0.8303 (tt0) cc_final: 0.7491 (tt0) REVERT: C 117 ARG cc_start: 0.7069 (ttp-110) cc_final: 0.6687 (mtm110) REVERT: C 301 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7972 (mp) REVERT: C 346 HIS cc_start: 0.7306 (OUTLIER) cc_final: 0.6780 (t-90) REVERT: C 401 GLU cc_start: 0.8258 (tt0) cc_final: 0.7481 (tt0) REVERT: D 117 ARG cc_start: 0.7044 (ttp-110) cc_final: 0.6584 (mtm110) REVERT: D 297 MET cc_start: 0.7215 (mpp) cc_final: 0.6917 (mpp) REVERT: D 301 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7973 (mp) REVERT: D 346 HIS cc_start: 0.7323 (OUTLIER) cc_final: 0.6844 (t-90) REVERT: D 362 MET cc_start: 0.5493 (ttm) cc_final: 0.5279 (ttm) REVERT: D 401 GLU cc_start: 0.8273 (tt0) cc_final: 0.7575 (tt0) outliers start: 72 outliers final: 65 residues processed: 288 average time/residue: 0.2221 time to fit residues: 92.9299 Evaluate side-chains 302 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 232 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 ILE 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 152 LEU Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 206 THR Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 363 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 A residue 441 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 152 LEU Chi-restraints excluded: chain B residue 153 LEU Chi-restraints excluded: chain B residue 171 MET Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 206 THR Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 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 152 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 363 LEU 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 39 PHE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 171 MET Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 301 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 363 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 408 MET 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: 0.9980 chunk 66 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 chunk 117 optimal weight: 9.9990 chunk 12 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 71 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 125 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 410 GLN B 443 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7003 moved from start: 0.5482 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= 0.213 Angle : 0.721 14.018 16296 Z= 0.343 Chirality : 0.038 0.188 2016 Planarity : 0.005 0.055 1956 Dihedral : 6.901 59.737 1748 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.80 % Allowed : 24.06 % Favored : 71.15 % 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: 1.51 (0.22), residues: 1500 helix: 1.60 (0.15), residues: 1236 sheet: None (None), residues: 0 loop : -1.88 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 193 HIS 0.003 0.000 HIS C 22 PHE 0.009 0.001 PHE B 39 TYR 0.023 0.001 TYR C 124 ARG 0.008 0.000 ARG D 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 307 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 246 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 27 LYS cc_start: 0.7518 (tttt) cc_final: 0.7247 (tmtt) REVERT: A 66 VAL cc_start: 0.7392 (t) cc_final: 0.7179 (t) REVERT: A 117 ARG cc_start: 0.7637 (ttp-110) cc_final: 0.6648 (mtm110) REVERT: A 179 GLN cc_start: 0.7186 (pp30) cc_final: 0.6965 (pp30) REVERT: A 332 TYR cc_start: 0.7889 (t80) cc_final: 0.7306 (t80) REVERT: A 401 GLU cc_start: 0.8159 (tt0) cc_final: 0.7402 (tt0) REVERT: B 332 TYR cc_start: 0.7920 (t80) cc_final: 0.7378 (t80) REVERT: B 346 HIS cc_start: 0.7348 (OUTLIER) cc_final: 0.6878 (t-90) REVERT: B 401 GLU cc_start: 0.8215 (tt0) cc_final: 0.7360 (tt0) REVERT: C 117 ARG cc_start: 0.7028 (ttp-110) cc_final: 0.6622 (mtm110) REVERT: C 301 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7790 (mp) REVERT: C 332 TYR cc_start: 0.7907 (t80) cc_final: 0.7284 (t80) REVERT: C 346 HIS cc_start: 0.7342 (OUTLIER) cc_final: 0.6824 (t-90) REVERT: C 362 MET cc_start: 0.5490 (ttm) cc_final: 0.5259 (ttm) REVERT: C 401 GLU cc_start: 0.8170 (tt0) cc_final: 0.7367 (tt0) REVERT: D 117 ARG cc_start: 0.7026 (ttp-110) cc_final: 0.6609 (mtm110) REVERT: D 301 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7792 (mp) REVERT: D 332 TYR cc_start: 0.7903 (t80) cc_final: 0.7284 (t80) REVERT: D 346 HIS cc_start: 0.7365 (OUTLIER) cc_final: 0.6920 (t-90) REVERT: D 401 GLU cc_start: 0.8173 (tt0) cc_final: 0.7435 (tt0) outliers start: 61 outliers final: 53 residues processed: 282 average time/residue: 0.2312 time to fit residues: 93.1070 Evaluate side-chains 300 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 242 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 129 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 363 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 A residue 441 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 152 LEU Chi-restraints excluded: chain B residue 153 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 363 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 410 GLN 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 152 LEU Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 441 LEU Chi-restraints excluded: chain D residue 39 PHE Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 301 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 1.9990 chunk 108 optimal weight: 0.0970 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 0.5980 chunk 117 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 120 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 410 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.222204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.186103 restraints weight = 13246.559| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.191155 restraints weight = 8686.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.194752 restraints weight = 6389.723| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.175 12012 Z= 0.267 Angle : 0.927 59.187 16296 Z= 0.500 Chirality : 0.038 0.413 2016 Planarity : 0.005 0.055 1956 Dihedral : 6.908 59.729 1748 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.80 % Allowed : 24.45 % Favored : 70.75 % Cbeta Deviations : 0.07 % 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: 1.52 (0.22), residues: 1500 helix: 1.61 (0.15), residues: 1236 sheet: None (None), residues: 0 loop : -1.87 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 193 HIS 0.004 0.000 HIS C 22 PHE 0.009 0.001 PHE B 39 TYR 0.021 0.001 TYR C 124 ARG 0.006 0.000 ARG C 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2497.22 seconds wall clock time: 45 minutes 46.12 seconds (2746.12 seconds total)