Starting phenix.real_space_refine on Mon Aug 5 01:01:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc2_43130/08_2024/8vc2_43130.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc2_43130/08_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_43130/08_2024/8vc2_43130.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc2_43130/08_2024/8vc2_43130.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc2_43130/08_2024/8vc2_43130.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8vc2_43130/08_2024/8vc2_43130.cif" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 120 5.16 5 C 7720 2.51 5 N 1932 2.21 5 O 2020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 7.20, per 1000 atoms: 0.61 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: 4.40 Conformation dependent library (CDL) restraints added in 2.2 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2856 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 85.5% alpha, 2.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 21 through 32 Processing helix chain 'A' and resid 51 through 79 Processing helix chain 'A' and resid 89 through 112 removed outlier: 3.669A pdb=" N VAL A 102 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N VAL A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 135 removed outlier: 4.555A pdb=" N GLU A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN A 127 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU A 134 " --> pdb=" O ALA A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 175 removed outlier: 4.070A pdb=" N GLU A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU A 153 " --> pdb=" O ALA A 149 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 230 removed outlier: 3.533A pdb=" N TYR A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY A 188 " --> pdb=" O THR A 184 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE A 189 " --> pdb=" O ASN A 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER A 226 " --> pdb=" O ASN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 340 removed outlier: 5.042A pdb=" N GLY A 292 " --> pdb=" O CYS A 288 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS A 302 " --> pdb=" O ARG A 298 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU A 314 " --> pdb=" O ASP A 310 " (cutoff:3.500A) Proline residue: A 315 - end of helix removed outlier: 3.635A pdb=" N LEU A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Proline residue: A 331 - end of helix Processing helix chain 'A' and resid 344 through 390 removed outlier: 4.128A pdb=" N MET A 362 " --> pdb=" O HIS A 358 " (cutoff:3.500A) Proline residue: A 368 - end of helix removed outlier: 3.724A pdb=" N GLU A 375 " --> pdb=" O TYR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 410 removed outlier: 3.983A pdb=" N MET A 408 " --> pdb=" O SER A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 419 Processing helix chain 'A' and resid 424 through 446 removed outlier: 3.650A pdb=" N VAL A 428 " --> pdb=" O ARG A 424 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR A 436 " --> pdb=" O GLY A 432 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 439 " --> pdb=" O THR A 435 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE A 444 " --> pdb=" O ILE A 440 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 32 Processing helix chain 'B' and resid 51 through 79 Processing helix chain 'B' and resid 89 through 112 removed outlier: 3.669A pdb=" N VAL B 102 " --> pdb=" O CYS B 98 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N VAL B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 135 removed outlier: 4.555A pdb=" N GLU B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN B 127 " --> pdb=" O SER B 123 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU B 134 " --> pdb=" O ALA B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 175 removed outlier: 4.070A pdb=" N GLU B 144 " --> pdb=" O SER B 140 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 153 " --> pdb=" O ALA B 149 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 230 removed outlier: 3.533A pdb=" N TYR B 186 " --> pdb=" O ILE B 182 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLY B 188 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N PHE B 189 " --> pdb=" O ASN B 185 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA B 225 " --> pdb=" O LEU B 221 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 340 removed outlier: 5.042A pdb=" N GLY B 292 " --> pdb=" O CYS B 288 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS B 302 " --> pdb=" O ARG B 298 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR B 305 " --> pdb=" O LEU B 301 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU B 314 " --> pdb=" O ASP B 310 " (cutoff:3.500A) Proline residue: B 315 - end of helix removed outlier: 3.633A pdb=" N LEU B 320 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Proline residue: B 331 - end of helix Processing helix chain 'B' and resid 344 through 390 removed outlier: 4.129A pdb=" N MET B 362 " --> pdb=" O HIS B 358 " (cutoff:3.500A) Proline residue: B 368 - end of helix removed outlier: 3.724A pdb=" N GLU B 375 " --> pdb=" O TYR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 394 through 410 removed outlier: 3.982A pdb=" N MET B 408 " --> pdb=" O SER B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 419 Processing helix chain 'B' and resid 424 through 446 removed outlier: 3.650A pdb=" N VAL B 428 " --> pdb=" O ARG B 424 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR B 436 " --> pdb=" O GLY B 432 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 444 " --> pdb=" O ILE B 440 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN B 445 " --> pdb=" O LEU B 441 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 32 Processing helix chain 'C' and resid 51 through 79 Processing helix chain 'C' and resid 89 through 112 removed outlier: 3.668A pdb=" N VAL C 102 " --> pdb=" O CYS C 98 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL C 103 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 113 through 135 removed outlier: 4.555A pdb=" N GLU C 126 " --> pdb=" O LEU C 122 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ASN C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU C 134 " --> pdb=" O ALA C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 140 through 175 removed outlier: 4.069A pdb=" N GLU C 144 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU C 153 " --> pdb=" O ALA C 149 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE C 154 " --> pdb=" O LEU C 150 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU C 155 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 230 removed outlier: 3.533A pdb=" N TYR C 186 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLY C 188 " --> pdb=" O THR C 184 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N PHE C 189 " --> pdb=" O ASN C 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 211 " --> pdb=" O ALA C 207 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR C 224 " --> pdb=" O ALA C 220 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N SER C 226 " --> pdb=" O ASN C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 340 removed outlier: 5.042A pdb=" N GLY C 292 " --> pdb=" O CYS C 288 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N CYS C 302 " --> pdb=" O ARG C 298 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR C 305 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU C 314 " --> pdb=" O ASP C 310 " (cutoff:3.500A) Proline residue: C 315 - end of helix removed outlier: 3.634A pdb=" N LEU C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Proline residue: C 331 - end of helix Processing helix chain 'C' and resid 344 through 390 removed outlier: 4.128A pdb=" N MET C 362 " --> pdb=" O HIS C 358 " (cutoff:3.500A) Proline residue: C 368 - end of helix removed outlier: 3.724A pdb=" N GLU C 375 " --> pdb=" O TYR C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 410 removed outlier: 3.983A pdb=" N MET C 408 " --> pdb=" O SER C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 415 through 419 Processing helix chain 'C' and resid 424 through 446 removed outlier: 3.650A pdb=" N VAL C 428 " --> pdb=" O ARG C 424 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR C 436 " --> pdb=" O GLY C 432 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL C 439 " --> pdb=" O THR C 435 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE C 444 " --> pdb=" O ILE C 440 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN C 445 " --> pdb=" O LEU C 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 32 Processing helix chain 'D' and resid 51 through 79 Processing helix chain 'D' and resid 89 through 112 removed outlier: 3.668A pdb=" N VAL D 102 " --> pdb=" O CYS D 98 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL D 103 " --> pdb=" O ASP D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 135 removed outlier: 4.556A pdb=" N GLU D 126 " --> pdb=" O LEU D 122 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLU D 134 " --> pdb=" O ALA D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 140 through 175 removed outlier: 4.070A pdb=" N GLU D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU D 155 " --> pdb=" O LEU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 230 removed outlier: 3.533A pdb=" N TYR D 186 " --> pdb=" O ILE D 182 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N GLY D 188 " --> pdb=" O THR D 184 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N PHE D 189 " --> pdb=" O ASN D 185 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU D 208 " --> pdb=" O ALA D 204 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG D 211 " --> pdb=" O ALA D 207 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N THR D 224 " --> pdb=" O ALA D 220 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA D 225 " --> pdb=" O LEU D 221 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER D 226 " --> pdb=" O ASN D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 340 removed outlier: 5.042A pdb=" N GLY D 292 " --> pdb=" O CYS D 288 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS D 302 " --> pdb=" O ARG D 298 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N THR D 305 " --> pdb=" O LEU D 301 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LEU D 314 " --> pdb=" O ASP D 310 " (cutoff:3.500A) Proline residue: D 315 - end of helix removed outlier: 3.633A pdb=" N LEU D 320 " --> pdb=" O LEU D 316 " (cutoff:3.500A) Proline residue: D 331 - end of helix Processing helix chain 'D' and resid 344 through 390 removed outlier: 4.129A pdb=" N MET D 362 " --> pdb=" O HIS D 358 " (cutoff:3.500A) Proline residue: D 368 - end of helix removed outlier: 3.725A pdb=" N GLU D 375 " --> pdb=" O TYR D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 410 removed outlier: 3.983A pdb=" N MET D 408 " --> pdb=" O SER D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 415 through 419 Processing helix chain 'D' and resid 424 through 446 removed outlier: 3.651A pdb=" N VAL D 428 " --> pdb=" O ARG D 424 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR D 436 " --> pdb=" O GLY D 432 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL D 439 " --> pdb=" O THR D 435 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N PHE D 444 " --> pdb=" O ILE D 440 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN D 445 " --> pdb=" O LEU D 441 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 19 Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 19 Processing sheet with id=AA4, first strand: chain 'D' and resid 17 through 19 988 hydrogen bonds defined for protein. 2940 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.59 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: 3829 2.86 - 3.37: 12927 3.37 - 3.88: 19578 3.88 - 4.39: 21966 4.39 - 4.90: 36502 Nonbonded interactions: 94802 Sorted by model distance: nonbonded pdb=" OD2 ASP A 165 " pdb=" NE1 TRP A 354 " model vdw 2.353 3.120 nonbonded pdb=" OD2 ASP B 165 " pdb=" NE1 TRP B 354 " model vdw 2.353 3.120 nonbonded pdb=" OD2 ASP D 165 " pdb=" NE1 TRP D 354 " model vdw 2.353 3.120 nonbonded pdb=" OD2 ASP C 165 " pdb=" NE1 TRP C 354 " model vdw 2.354 3.120 nonbonded pdb=" OE2 GLU A 76 " pdb=" ND2 ASN A 185 " model vdw 2.363 3.120 ... (remaining 94797 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 33.690 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6874 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 12012 Z= 0.360 Angle : 0.843 16.784 16296 Z= 0.468 Chirality : 0.036 0.144 2016 Planarity : 0.010 0.087 1956 Dihedral : 14.087 119.212 4332 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.31 % Allowed : 1.18 % Favored : 98.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.20), residues: 1500 helix: -0.33 (0.14), residues: 1232 sheet: 0.54 (0.71), residues: 48 loop : -1.91 (0.43), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.007 TRP D 354 HIS 0.008 0.003 HIS D 358 PHE 0.010 0.002 PHE C 203 TYR 0.037 0.006 TYR B 124 ARG 0.019 0.003 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 449 time to evaluate : 1.292 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: 0.2286 time to fit residues: 148.4243 Evaluate side-chains 298 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 297 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 124 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 70 optimal weight: 0.5980 chunk 86 optimal weight: 40.0000 chunk 134 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 179 GLN ** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12012 Z= 0.214 Angle : 0.649 10.264 16296 Z= 0.330 Chirality : 0.037 0.126 2016 Planarity : 0.004 0.043 1956 Dihedral : 8.704 67.786 1750 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 4.95 % Allowed : 14.31 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.22), residues: 1500 helix: 1.38 (0.14), residues: 1264 sheet: 0.05 (0.70), residues: 48 loop : -0.82 (0.50), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 193 HIS 0.003 0.001 HIS B 326 PHE 0.016 0.002 PHE C 203 TYR 0.018 0.002 TYR D 124 ARG 0.003 0.000 ARG A 344 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 321 time to evaluate : 1.246 Fit side-chains REVERT: A 26 LEU cc_start: 0.7910 (OUTLIER) cc_final: 0.7636 (mp) REVERT: A 39 PHE cc_start: 0.6958 (OUTLIER) cc_final: 0.6754 (p90) REVERT: A 197 MET cc_start: 0.7544 (mmm) cc_final: 0.7285 (tmm) REVERT: B 26 LEU cc_start: 0.7839 (OUTLIER) cc_final: 0.7633 (mp) REVERT: B 125 MET cc_start: 0.7028 (mmt) cc_final: 0.6740 (tpt) REVERT: B 346 HIS cc_start: 0.7596 (OUTLIER) cc_final: 0.6877 (t-90) REVERT: C 179 GLN cc_start: 0.7211 (tm-30) cc_final: 0.6795 (pm20) REVERT: C 346 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.6873 (t-90) REVERT: C 401 GLU cc_start: 0.7933 (tt0) cc_final: 0.7478 (tt0) REVERT: D 26 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7617 (mp) REVERT: D 179 GLN cc_start: 0.7207 (tm-30) cc_final: 0.6822 (pm20) REVERT: D 346 HIS cc_start: 0.7594 (OUTLIER) cc_final: 0.6858 (t-90) REVERT: D 401 GLU cc_start: 0.7908 (tt0) cc_final: 0.7314 (tt0) outliers start: 63 outliers final: 30 residues processed: 362 average time/residue: 0.2102 time to fit residues: 110.4817 Evaluate side-chains 286 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 249 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 395 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 chunk 111 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 119 optimal weight: 0.5980 chunk 133 optimal weight: 0.8980 chunk 45 optimal weight: 0.2980 chunk 108 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 358 HIS B 358 HIS C 358 HIS D 358 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12012 Z= 0.192 Angle : 0.652 11.988 16296 Z= 0.319 Chirality : 0.038 0.201 2016 Planarity : 0.004 0.054 1956 Dihedral : 7.778 57.244 1748 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 3.77 % Allowed : 18.95 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.22), residues: 1500 helix: 1.77 (0.14), residues: 1268 sheet: 0.26 (0.76), residues: 48 loop : -0.84 (0.50), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 180 HIS 0.004 0.001 HIS C 22 PHE 0.014 0.001 PHE C 203 TYR 0.017 0.001 TYR C 124 ARG 0.003 0.000 ARG A 293 *********************** 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 323 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 275 time to evaluate : 1.265 Fit side-chains REVERT: A 26 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7598 (mp) REVERT: A 27 LYS cc_start: 0.7193 (tttt) cc_final: 0.6928 (tmtt) REVERT: A 117 ARG cc_start: 0.7055 (ttm110) cc_final: 0.6257 (mtm110) REVERT: A 297 MET cc_start: 0.6978 (mpp) cc_final: 0.6649 (mpp) REVERT: B 26 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7578 (mp) REVERT: B 117 ARG cc_start: 0.6952 (ttm110) cc_final: 0.6501 (mtm110) REVERT: B 297 MET cc_start: 0.7004 (mpp) cc_final: 0.6630 (mpp) REVERT: B 346 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.6837 (t-90) REVERT: B 443 GLN cc_start: 0.7825 (tt0) cc_final: 0.7242 (tt0) REVERT: C 67 ILE cc_start: 0.8775 (tp) cc_final: 0.8480 (tt) REVERT: C 117 ARG cc_start: 0.6965 (ttm110) cc_final: 0.6509 (mtm110) REVERT: C 179 GLN cc_start: 0.7210 (tm-30) cc_final: 0.6773 (pm20) REVERT: C 208 LEU cc_start: 0.8311 (tp) cc_final: 0.8105 (tp) REVERT: C 297 MET cc_start: 0.7069 (mpp) cc_final: 0.6797 (mpp) REVERT: C 346 HIS cc_start: 0.7529 (OUTLIER) cc_final: 0.6827 (t-90) REVERT: D 26 LEU cc_start: 0.7955 (OUTLIER) cc_final: 0.7603 (mp) REVERT: D 27 LYS cc_start: 0.7235 (tttt) cc_final: 0.7006 (tttm) REVERT: D 117 ARG cc_start: 0.6940 (ttm110) cc_final: 0.6460 (mtm110) REVERT: D 179 GLN cc_start: 0.7169 (tm-30) cc_final: 0.6681 (pm20) REVERT: D 297 MET cc_start: 0.7225 (mpp) cc_final: 0.6866 (mpp) REVERT: D 346 HIS cc_start: 0.7536 (OUTLIER) cc_final: 0.6851 (t-90) outliers start: 48 outliers final: 30 residues processed: 305 average time/residue: 0.2144 time to fit residues: 94.9756 Evaluate side-chains 276 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 240 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 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: 7.9990 chunk 69 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 64 optimal weight: 3.9990 chunk 90 optimal weight: 9.9990 chunk 135 optimal weight: 0.6980 chunk 143 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 128 optimal weight: 5.9990 chunk 38 optimal weight: 0.7980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.4095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12012 Z= 0.218 Angle : 0.646 12.705 16296 Z= 0.317 Chirality : 0.038 0.162 2016 Planarity : 0.004 0.056 1956 Dihedral : 7.299 50.805 1748 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 5.42 % Allowed : 18.95 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.37 (0.22), residues: 1500 helix: 1.98 (0.14), residues: 1268 sheet: -0.01 (0.75), residues: 48 loop : -0.78 (0.49), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 193 HIS 0.002 0.001 HIS A 326 PHE 0.012 0.001 PHE A 39 TYR 0.015 0.001 TYR A 124 ARG 0.003 0.000 ARG B 117 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 277 time to evaluate : 1.258 Fit side-chains REVERT: A 26 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7659 (mp) REVERT: A 67 ILE cc_start: 0.8777 (tp) cc_final: 0.8495 (tt) REVERT: A 121 MET cc_start: 0.7637 (tmm) cc_final: 0.7412 (tmm) REVERT: A 332 TYR cc_start: 0.7612 (t80) cc_final: 0.7363 (t80) REVERT: B 26 LEU cc_start: 0.8068 (OUTLIER) cc_final: 0.7781 (mp) REVERT: B 67 ILE cc_start: 0.8795 (tp) cc_final: 0.8540 (tt) REVERT: B 346 HIS cc_start: 0.7491 (OUTLIER) cc_final: 0.6847 (t-90) REVERT: C 24 PHE cc_start: 0.7893 (t80) cc_final: 0.7664 (t80) REVERT: C 67 ILE cc_start: 0.8798 (tp) cc_final: 0.8570 (tt) REVERT: C 346 HIS cc_start: 0.7491 (OUTLIER) cc_final: 0.6823 (t-90) REVERT: C 443 GLN cc_start: 0.7997 (tt0) cc_final: 0.7401 (tt0) REVERT: D 26 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7809 (mp) REVERT: D 67 ILE cc_start: 0.8719 (tp) cc_final: 0.8477 (tt) REVERT: D 179 GLN cc_start: 0.7311 (tm-30) cc_final: 0.7102 (pm20) REVERT: D 346 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.6866 (t-90) outliers start: 69 outliers final: 48 residues processed: 323 average time/residue: 0.2100 time to fit residues: 99.0819 Evaluate side-chains 305 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 251 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 427 ILE Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 427 ILE Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 119 optimal weight: 6.9990 chunk 81 optimal weight: 0.6980 chunk 2 optimal weight: 9.9990 chunk 106 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 122 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 chunk 128 optimal weight: 2.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6991 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12012 Z= 0.207 Angle : 0.661 12.057 16296 Z= 0.317 Chirality : 0.038 0.161 2016 Planarity : 0.004 0.055 1956 Dihedral : 7.082 51.351 1748 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 5.58 % Allowed : 19.89 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.63 (0.22), residues: 1500 helix: 2.25 (0.14), residues: 1256 sheet: -0.22 (0.72), residues: 48 loop : -1.22 (0.47), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 193 HIS 0.003 0.001 HIS C 22 PHE 0.012 0.001 PHE B 31 TYR 0.018 0.001 TYR D 124 ARG 0.005 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 269 time to evaluate : 1.235 Fit side-chains REVERT: A 26 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7641 (mp) REVERT: A 67 ILE cc_start: 0.8785 (tp) cc_final: 0.8574 (tt) REVERT: A 121 MET cc_start: 0.7586 (tmm) cc_final: 0.7376 (tmm) REVERT: B 26 LEU cc_start: 0.8004 (OUTLIER) cc_final: 0.7768 (mp) REVERT: B 67 ILE cc_start: 0.8837 (tp) cc_final: 0.8555 (tt) REVERT: B 346 HIS cc_start: 0.7498 (OUTLIER) cc_final: 0.6795 (t-90) REVERT: C 27 LYS cc_start: 0.7269 (tttt) cc_final: 0.7005 (tptm) REVERT: C 67 ILE cc_start: 0.8898 (tp) cc_final: 0.8533 (tt) REVERT: C 346 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.6797 (t-90) REVERT: C 443 GLN cc_start: 0.8090 (tt0) cc_final: 0.7213 (tt0) REVERT: D 26 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7827 (mp) REVERT: D 346 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.6842 (t-90) outliers start: 71 outliers final: 50 residues processed: 316 average time/residue: 0.2093 time to fit residues: 96.7135 Evaluate side-chains 298 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 242 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 122 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 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 C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 122 LEU Chi-restraints excluded: chain C residue 123 SER Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 400 LEU Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 48 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 28 optimal weight: 5.9990 chunk 83 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 143 optimal weight: 0.1980 chunk 118 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 7.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 HIS ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.4744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12012 Z= 0.208 Angle : 0.660 11.828 16296 Z= 0.316 Chirality : 0.037 0.164 2016 Planarity : 0.004 0.055 1956 Dihedral : 6.904 52.363 1748 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 5.50 % Allowed : 20.91 % Favored : 73.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.22), residues: 1500 helix: 2.39 (0.14), residues: 1256 sheet: -0.12 (0.75), residues: 48 loop : -1.15 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 193 HIS 0.004 0.001 HIS C 22 PHE 0.010 0.001 PHE A 39 TYR 0.017 0.001 TYR B 124 ARG 0.006 0.000 ARG D 117 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 252 time to evaluate : 1.481 Fit side-chains REVERT: A 26 LEU cc_start: 0.7847 (OUTLIER) cc_final: 0.7631 (mp) REVERT: A 67 ILE cc_start: 0.8890 (tp) cc_final: 0.8528 (tt) REVERT: B 26 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7723 (mp) REVERT: B 346 HIS cc_start: 0.7468 (OUTLIER) cc_final: 0.6746 (t-90) REVERT: C 117 ARG cc_start: 0.7007 (ttm110) cc_final: 0.6524 (mtm110) REVERT: C 125 MET cc_start: 0.7075 (mmt) cc_final: 0.6814 (tpt) REVERT: C 297 MET cc_start: 0.7100 (mpp) cc_final: 0.6804 (mpp) REVERT: C 301 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7889 (mp) REVERT: C 346 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.6677 (t-90) REVERT: C 443 GLN cc_start: 0.7800 (tt0) cc_final: 0.7495 (tt0) REVERT: D 26 LEU cc_start: 0.7959 (OUTLIER) cc_final: 0.7733 (mp) REVERT: D 346 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.6747 (t-90) outliers start: 70 outliers final: 49 residues processed: 297 average time/residue: 0.2224 time to fit residues: 96.1602 Evaluate side-chains 295 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 239 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 395 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 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 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 379 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 138 optimal weight: 20.0000 chunk 16 optimal weight: 0.0270 chunk 81 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 120 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 65 optimal weight: 6.9990 chunk 88 optimal weight: 0.9980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 HIS A 443 GLN ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 443 GLN ** C 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12012 Z= 0.203 Angle : 0.693 14.034 16296 Z= 0.323 Chirality : 0.037 0.170 2016 Planarity : 0.004 0.057 1956 Dihedral : 6.751 53.319 1748 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 5.19 % Allowed : 21.78 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.22), residues: 1500 helix: 2.48 (0.14), residues: 1256 sheet: -0.51 (0.71), residues: 48 loop : -1.26 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 193 HIS 0.004 0.001 HIS C 22 PHE 0.009 0.001 PHE B 39 TYR 0.016 0.001 TYR D 124 ARG 0.007 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 305 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 239 time to evaluate : 1.300 Fit side-chains REVERT: A 27 LYS cc_start: 0.7112 (tttt) cc_final: 0.6854 (tmtt) REVERT: A 67 ILE cc_start: 0.8882 (tp) cc_final: 0.8530 (tt) REVERT: B 26 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7663 (mp) REVERT: B 27 LYS cc_start: 0.7240 (tttt) cc_final: 0.6942 (tptt) REVERT: B 346 HIS cc_start: 0.7417 (OUTLIER) cc_final: 0.6789 (t-90) REVERT: C 27 LYS cc_start: 0.7174 (tttt) cc_final: 0.6973 (tptt) REVERT: C 125 MET cc_start: 0.7158 (mmt) cc_final: 0.6947 (tpt) REVERT: C 301 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7845 (mp) REVERT: C 346 HIS cc_start: 0.7416 (OUTLIER) cc_final: 0.6725 (t-90) REVERT: D 26 LEU cc_start: 0.7900 (OUTLIER) cc_final: 0.7674 (mp) REVERT: D 27 LYS cc_start: 0.7225 (tttt) cc_final: 0.6897 (tptt) REVERT: D 346 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.6781 (t-90) outliers start: 66 outliers final: 50 residues processed: 290 average time/residue: 0.2159 time to fit residues: 91.2700 Evaluate side-chains 283 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 227 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain B residue 26 LEU Chi-restraints excluded: chain B residue 39 PHE Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 359 LEU Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 359 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 428 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 90 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 70 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 370 HIS ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 370 HIS ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12012 Z= 0.287 Angle : 0.756 14.140 16296 Z= 0.354 Chirality : 0.040 0.171 2016 Planarity : 0.005 0.053 1956 Dihedral : 6.677 51.510 1748 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 5.19 % Allowed : 22.96 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.22), residues: 1500 helix: 2.32 (0.15), residues: 1256 sheet: -0.63 (0.69), residues: 48 loop : -1.52 (0.46), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 193 HIS 0.007 0.001 HIS A 22 PHE 0.010 0.001 PHE C 31 TYR 0.014 0.001 TYR A 124 ARG 0.007 0.001 ARG C 117 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 233 time to evaluate : 1.352 Fit side-chains REVERT: A 24 PHE cc_start: 0.7938 (t80) cc_final: 0.7465 (t80) REVERT: A 27 LYS cc_start: 0.7095 (tttt) cc_final: 0.6841 (tmtt) REVERT: A 117 ARG cc_start: 0.7415 (ttm110) cc_final: 0.7098 (ttp-110) REVERT: A 401 GLU cc_start: 0.8233 (tt0) cc_final: 0.7781 (tt0) REVERT: B 117 ARG cc_start: 0.7069 (ttp-110) cc_final: 0.6567 (mtm110) REVERT: B 346 HIS cc_start: 0.7453 (OUTLIER) cc_final: 0.6807 (t-90) REVERT: B 401 GLU cc_start: 0.8282 (tt0) cc_final: 0.7827 (tt0) REVERT: C 301 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.8068 (mp) REVERT: C 346 HIS cc_start: 0.7448 (OUTLIER) cc_final: 0.6751 (t-90) REVERT: C 401 GLU cc_start: 0.8266 (tt0) cc_final: 0.7835 (tt0) REVERT: D 26 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7698 (mp) REVERT: D 117 ARG cc_start: 0.7176 (ttp-110) cc_final: 0.6777 (mtm110) REVERT: D 346 HIS cc_start: 0.7494 (OUTLIER) cc_final: 0.6860 (t-90) REVERT: D 401 GLU cc_start: 0.8275 (tt0) cc_final: 0.7799 (tt0) outliers start: 66 outliers final: 53 residues processed: 284 average time/residue: 0.2213 time to fit residues: 91.6408 Evaluate side-chains 289 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 231 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 193 TRP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 364 VAL 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 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 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 364 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 395 VAL Chi-restraints excluded: chain B residue 400 LEU Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain D residue 26 LEU Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 395 VAL Chi-restraints excluded: chain D residue 408 MET 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: 2.9990 chunk 132 optimal weight: 10.0000 chunk 80 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 104 optimal weight: 0.8980 chunk 40 optimal weight: 20.0000 chunk 120 optimal weight: 0.6980 chunk 125 optimal weight: 0.6980 chunk 87 optimal weight: 2.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 443 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.5252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12012 Z= 0.212 Angle : 0.737 13.829 16296 Z= 0.338 Chirality : 0.039 0.181 2016 Planarity : 0.004 0.054 1956 Dihedral : 6.588 55.082 1748 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 4.56 % Allowed : 24.14 % Favored : 71.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.22), residues: 1500 helix: 2.51 (0.15), residues: 1256 sheet: -0.67 (0.68), residues: 48 loop : -1.43 (0.48), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 180 HIS 0.009 0.001 HIS B 22 PHE 0.010 0.001 PHE B 39 TYR 0.016 0.001 TYR C 124 ARG 0.006 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 295 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 237 time to evaluate : 1.299 Fit side-chains REVERT: A 24 PHE cc_start: 0.7904 (t80) cc_final: 0.7414 (t80) REVERT: A 27 LYS cc_start: 0.6907 (tttt) cc_final: 0.6672 (tmtt) REVERT: A 117 ARG cc_start: 0.7311 (ttm110) cc_final: 0.6907 (ttp-110) REVERT: A 332 TYR cc_start: 0.7924 (t80) cc_final: 0.7356 (t80) REVERT: B 24 PHE cc_start: 0.7844 (t80) cc_final: 0.7252 (t80) REVERT: B 27 LYS cc_start: 0.7205 (tttt) cc_final: 0.6908 (tptt) REVERT: B 117 ARG cc_start: 0.6941 (ttp-110) cc_final: 0.6470 (mtm110) REVERT: B 332 TYR cc_start: 0.7882 (t80) cc_final: 0.7409 (t80) REVERT: B 346 HIS cc_start: 0.7515 (OUTLIER) cc_final: 0.6887 (t-90) REVERT: C 24 PHE cc_start: 0.7924 (t80) cc_final: 0.7343 (t80) REVERT: C 27 LYS cc_start: 0.6989 (tttt) cc_final: 0.6755 (tptt) REVERT: C 301 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7856 (mp) REVERT: C 346 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.6862 (t-90) REVERT: D 117 ARG cc_start: 0.7132 (ttp-110) cc_final: 0.6778 (mtm110) REVERT: D 346 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.6886 (t-90) REVERT: D 419 MET cc_start: 0.7658 (mtp) cc_final: 0.7343 (ttm) outliers start: 58 outliers final: 51 residues processed: 278 average time/residue: 0.2212 time to fit residues: 88.9405 Evaluate side-chains 288 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 233 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 193 TRP Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 338 ILE Chi-restraints excluded: chain C residue 345 LEU Chi-restraints excluded: chain C residue 346 HIS Chi-restraints excluded: chain C residue 353 LEU Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 363 LEU Chi-restraints excluded: chain C residue 364 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain 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 193 TRP Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 427 ILE Chi-restraints excluded: chain D residue 443 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 85 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 147 optimal weight: 0.9990 chunk 135 optimal weight: 0.5980 chunk 117 optimal weight: 0.0010 chunk 12 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 93 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN D 22 HIS ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6975 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12012 Z= 0.203 Angle : 0.744 14.702 16296 Z= 0.339 Chirality : 0.039 0.183 2016 Planarity : 0.004 0.055 1956 Dihedral : 6.548 54.827 1748 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 4.40 % Allowed : 24.69 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.22), residues: 1500 helix: 2.50 (0.14), residues: 1256 sheet: -0.70 (0.68), residues: 48 loop : -1.43 (0.49), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 193 HIS 0.006 0.001 HIS D 22 PHE 0.012 0.001 PHE D 31 TYR 0.016 0.001 TYR A 124 ARG 0.006 0.000 ARG C 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 288 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 232 time to evaluate : 1.481 Fit side-chains REVERT: A 24 PHE cc_start: 0.7911 (t80) cc_final: 0.7446 (t80) REVERT: A 27 LYS cc_start: 0.6846 (tttt) cc_final: 0.6609 (tmtt) REVERT: A 117 ARG cc_start: 0.7256 (ttm110) cc_final: 0.6897 (ttp-110) REVERT: B 27 LYS cc_start: 0.7110 (tttt) cc_final: 0.6832 (tptt) REVERT: B 117 ARG cc_start: 0.6942 (ttp-110) cc_final: 0.6485 (mtm110) REVERT: B 332 TYR cc_start: 0.7855 (t80) cc_final: 0.7494 (t80) REVERT: B 346 HIS cc_start: 0.7478 (OUTLIER) cc_final: 0.6864 (t-90) REVERT: C 24 PHE cc_start: 0.7798 (t80) cc_final: 0.7261 (t80) REVERT: C 27 LYS cc_start: 0.6907 (tttt) cc_final: 0.6688 (tptt) REVERT: C 117 ARG cc_start: 0.7082 (ttp-110) cc_final: 0.6629 (mtm110) REVERT: C 301 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7802 (mp) REVERT: C 332 TYR cc_start: 0.7926 (t80) cc_final: 0.7412 (t80) REVERT: C 346 HIS cc_start: 0.7499 (OUTLIER) cc_final: 0.6855 (t-90) REVERT: D 27 LYS cc_start: 0.7082 (tttt) cc_final: 0.6742 (tptt) REVERT: D 117 ARG cc_start: 0.7122 (ttp-110) cc_final: 0.6789 (mtm110) REVERT: D 125 MET cc_start: 0.7404 (tpt) cc_final: 0.7044 (tpt) REVERT: D 332 TYR cc_start: 0.7914 (t80) cc_final: 0.7397 (t80) REVERT: D 346 HIS cc_start: 0.7467 (OUTLIER) cc_final: 0.6915 (t-90) outliers start: 56 outliers final: 50 residues processed: 273 average time/residue: 0.2222 time to fit residues: 87.3767 Evaluate side-chains 280 residues out of total 1324 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 226 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 98 CYS Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 193 TRP Chi-restraints excluded: chain A residue 307 HIS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 379 THR Chi-restraints excluded: chain A residue 400 LEU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 98 CYS Chi-restraints excluded: chain B residue 123 SER Chi-restraints excluded: chain B residue 193 TRP Chi-restraints excluded: chain B residue 307 HIS Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 346 HIS Chi-restraints excluded: chain B residue 353 LEU Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain B residue 379 THR Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 98 CYS Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain C residue 307 HIS Chi-restraints excluded: chain C residue 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 364 VAL Chi-restraints excluded: chain C residue 379 THR Chi-restraints excluded: chain C residue 400 LEU Chi-restraints excluded: chain C residue 408 MET Chi-restraints excluded: chain C residue 428 VAL Chi-restraints excluded: chain C residue 443 GLN Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 98 CYS Chi-restraints excluded: chain D residue 193 TRP Chi-restraints excluded: chain D residue 307 HIS Chi-restraints excluded: chain D residue 338 ILE Chi-restraints excluded: chain D residue 346 HIS Chi-restraints excluded: chain D residue 353 LEU Chi-restraints excluded: chain D residue 357 THR Chi-restraints excluded: chain D residue 359 LEU Chi-restraints excluded: chain D residue 363 LEU Chi-restraints excluded: chain D residue 364 VAL Chi-restraints excluded: chain D residue 379 THR Chi-restraints excluded: chain D residue 427 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 35 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 49 optimal weight: 0.0070 chunk 120 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 6 optimal weight: 0.0870 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 HIS ** A 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 HIS ** B 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 443 GLN ** D 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.224010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.188773 restraints weight = 12963.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.191542 restraints weight = 8904.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.193396 restraints weight = 6828.160| |-----------------------------------------------------------------------------| r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12012 Z= 0.212 Angle : 0.745 14.668 16296 Z= 0.338 Chirality : 0.039 0.179 2016 Planarity : 0.004 0.056 1956 Dihedral : 6.521 54.898 1748 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 4.56 % Allowed : 24.84 % Favored : 70.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.22), residues: 1500 helix: 2.42 (0.15), residues: 1268 sheet: -0.72 (0.67), residues: 48 loop : -1.21 (0.51), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 193 HIS 0.007 0.001 HIS B 22 PHE 0.009 0.001 PHE B 39 TYR 0.015 0.001 TYR D 124 ARG 0.007 0.000 ARG C 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2421.11 seconds wall clock time: 44 minutes 9.69 seconds (2649.69 seconds total)