Starting phenix.real_space_refine on Sun Nov 17 15:01:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op9_17045/11_2024/8op9_17045.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op9_17045/11_2024/8op9_17045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op9_17045/11_2024/8op9_17045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op9_17045/11_2024/8op9_17045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op9_17045/11_2024/8op9_17045.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8op9_17045/11_2024/8op9_17045.cif" } resolution = 3.36 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= 0.000 sd= 0.001 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 S 75 5.16 5 Cl 1 4.86 5 C 9070 2.51 5 N 2195 2.21 5 O 2470 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13811 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2701 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 2701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2701 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 318} Chain breaks: 1 Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 67 Unusual residues: {' CL': 1, 'ABU': 2, 'HEX': 4, 'NAG': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Unusual residues: {'HEX': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 66 Unusual residues: {'ABU': 2, 'HEX': 4, 'NAG': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 52 Unusual residues: {'HEX': 4, 'NAG': 2} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 7 Unusual residues: {'ABU': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Restraints were copied for chains: E, C, D Time building chain proxies: 12.91, per 1000 atoms: 0.93 Number of scatterers: 13811 At special positions: 0 Unit cell: (95.0235, 97.6815, 137.551, 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) Cl 1 17.00 S 75 16.00 O 2470 8.00 N 2195 7.00 C 9070 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 212 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 212 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 602 " - " ASN A 140 " " NAG A 603 " - " ASN A 234 " " NAG B 501 " - " ASN B 140 " " NAG B 502 " - " ASN B 234 " " NAG C 603 " - " ASN C 140 " " NAG C 604 " - " ASN C 234 " " NAG D 501 " - " ASN D 140 " " NAG D 502 " - " ASN D 234 " " NAG E 602 " - " ASN E 140 " " NAG E 603 " - " ASN E 234 " Time building additional restraints: 3.76 Conformation dependent library (CDL) restraints added in 1.8 seconds 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3220 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 15 sheets defined 41.0% alpha, 40.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.51 Creating SS restraints... Processing helix chain 'A' and resid 80 through 84 Processing helix chain 'A' and resid 131 through 134 Processing helix chain 'A' and resid 147 through 153 removed outlier: 3.601A pdb=" N LYS A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 235 Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 288 through 298 Processing helix chain 'A' and resid 299 through 304 removed outlier: 3.814A pdb=" N SER A 302 " --> pdb=" O SER A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 334 Proline residue: A 315 - end of helix removed outlier: 4.210A pdb=" N SER A 334 " --> pdb=" O GLY A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 380 removed outlier: 3.608A pdb=" N VAL A 359 " --> pdb=" O VAL A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 478 removed outlier: 4.072A pdb=" N ILE A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Proline residue: A 464 - end of helix Processing helix chain 'B' and resid 80 through 84 Processing helix chain 'B' and resid 131 through 134 Processing helix chain 'B' and resid 147 through 153 removed outlier: 3.601A pdb=" N LYS B 151 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 235 Processing helix chain 'B' and resid 281 through 288 Processing helix chain 'B' and resid 288 through 298 Processing helix chain 'B' and resid 299 through 304 removed outlier: 3.814A pdb=" N SER B 302 " --> pdb=" O SER B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 334 Proline residue: B 315 - end of helix removed outlier: 4.210A pdb=" N SER B 334 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 380 removed outlier: 3.609A pdb=" N VAL B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 478 removed outlier: 4.072A pdb=" N ILE B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Proline residue: B 464 - end of helix Processing helix chain 'C' and resid 80 through 84 Processing helix chain 'C' and resid 131 through 134 Processing helix chain 'C' and resid 147 through 153 removed outlier: 3.600A pdb=" N LYS C 151 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 235 Processing helix chain 'C' and resid 281 through 288 Processing helix chain 'C' and resid 288 through 298 Processing helix chain 'C' and resid 299 through 304 removed outlier: 3.814A pdb=" N SER C 302 " --> pdb=" O SER C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 309 through 334 Proline residue: C 315 - end of helix removed outlier: 4.210A pdb=" N SER C 334 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 380 removed outlier: 3.608A pdb=" N VAL C 359 " --> pdb=" O VAL C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 453 through 478 removed outlier: 4.072A pdb=" N ILE C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Proline residue: C 464 - end of helix Processing helix chain 'D' and resid 80 through 84 Processing helix chain 'D' and resid 131 through 134 Processing helix chain 'D' and resid 147 through 153 removed outlier: 3.600A pdb=" N LYS D 151 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 235 Processing helix chain 'D' and resid 281 through 288 Processing helix chain 'D' and resid 288 through 298 Processing helix chain 'D' and resid 299 through 304 removed outlier: 3.814A pdb=" N SER D 302 " --> pdb=" O SER D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 309 through 334 Proline residue: D 315 - end of helix removed outlier: 4.210A pdb=" N SER D 334 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 380 removed outlier: 3.608A pdb=" N VAL D 359 " --> pdb=" O VAL D 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 453 through 478 removed outlier: 4.072A pdb=" N ILE D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Proline residue: D 464 - end of helix Processing helix chain 'E' and resid 80 through 84 Processing helix chain 'E' and resid 131 through 134 Processing helix chain 'E' and resid 147 through 153 removed outlier: 3.601A pdb=" N LYS E 151 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 235 Processing helix chain 'E' and resid 281 through 288 Processing helix chain 'E' and resid 288 through 298 Processing helix chain 'E' and resid 299 through 304 removed outlier: 3.814A pdb=" N SER E 302 " --> pdb=" O SER E 299 " (cutoff:3.500A) Processing helix chain 'E' and resid 309 through 334 Proline residue: E 315 - end of helix removed outlier: 4.210A pdb=" N SER E 334 " --> pdb=" O GLY E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 380 removed outlier: 3.609A pdb=" N VAL E 359 " --> pdb=" O VAL E 355 " (cutoff:3.500A) Processing helix chain 'E' and resid 453 through 478 removed outlier: 4.073A pdb=" N ILE E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Proline residue: E 464 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 145 removed outlier: 4.460A pdb=" N LEU A 178 " --> pdb=" O PHE A 145 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP A 117 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER A 110 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 163 through 168 removed outlier: 7.027A pdb=" N THR A 195 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER A 166 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR A 193 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE A 168 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ARG A 191 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP A 117 " --> pdb=" O SER A 110 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER A 110 " --> pdb=" O ASP A 117 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.710A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER A 218 " --> pdb=" O ASN A 269 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN A 269 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY A 266 " --> pdb=" O PHE A 261 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE A 261 " --> pdb=" O GLY A 266 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR A 268 " --> pdb=" O LEU A 259 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU A 259 " --> pdb=" O TYR A 268 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG A 270 " --> pdb=" O THR A 257 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR A 257 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR A 272 " --> pdb=" O THR A 255 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR A 255 " --> pdb=" O TYR A 272 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN A 274 " --> pdb=" O PHE A 253 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE A 253 " --> pdb=" O ASN A 274 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 143 through 145 removed outlier: 4.460A pdb=" N LEU B 178 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP B 117 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER B 110 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 163 through 168 removed outlier: 7.028A pdb=" N THR B 195 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER B 166 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR B 193 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE B 168 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ARG B 191 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP B 117 " --> pdb=" O SER B 110 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N SER B 110 " --> pdb=" O ASP B 117 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.709A pdb=" N GLU B 215 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N SER B 218 " --> pdb=" O ASN B 269 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASN B 269 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY B 266 " --> pdb=" O PHE B 261 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE B 261 " --> pdb=" O GLY B 266 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR B 268 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU B 259 " --> pdb=" O TYR B 268 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG B 270 " --> pdb=" O THR B 257 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR B 257 " --> pdb=" O ARG B 270 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR B 272 " --> pdb=" O THR B 255 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N THR B 255 " --> pdb=" O TYR B 272 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ASN B 274 " --> pdb=" O PHE B 253 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE B 253 " --> pdb=" O ASN B 274 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 143 through 145 removed outlier: 4.459A pdb=" N LEU C 178 " --> pdb=" O PHE C 145 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP C 117 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER C 110 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS C 129 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 163 through 168 removed outlier: 7.028A pdb=" N THR C 195 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N SER C 166 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR C 193 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE C 168 " --> pdb=" O ARG C 191 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ARG C 191 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP C 117 " --> pdb=" O SER C 110 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER C 110 " --> pdb=" O ASP C 117 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS C 129 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 158 through 161 removed outlier: 4.710A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER C 218 " --> pdb=" O ASN C 269 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN C 269 " --> pdb=" O SER C 218 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY C 266 " --> pdb=" O PHE C 261 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE C 261 " --> pdb=" O GLY C 266 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR C 268 " --> pdb=" O LEU C 259 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N LEU C 259 " --> pdb=" O TYR C 268 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG C 270 " --> pdb=" O THR C 257 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR C 257 " --> pdb=" O ARG C 270 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N TYR C 272 " --> pdb=" O THR C 255 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR C 255 " --> pdb=" O TYR C 272 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN C 274 " --> pdb=" O PHE C 253 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE C 253 " --> pdb=" O ASN C 274 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 143 through 145 removed outlier: 4.460A pdb=" N LEU D 178 " --> pdb=" O PHE D 145 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP D 117 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER D 110 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS D 129 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 163 through 168 removed outlier: 7.027A pdb=" N THR D 195 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER D 166 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR D 193 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE D 168 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ARG D 191 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP D 117 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER D 110 " --> pdb=" O ASP D 117 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS D 129 " --> pdb=" O PRO D 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.708A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N SER D 218 " --> pdb=" O ASN D 269 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN D 269 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY D 266 " --> pdb=" O PHE D 261 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N PHE D 261 " --> pdb=" O GLY D 266 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TYR D 268 " --> pdb=" O LEU D 259 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU D 259 " --> pdb=" O TYR D 268 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ARG D 270 " --> pdb=" O THR D 257 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N THR D 257 " --> pdb=" O ARG D 270 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR D 272 " --> pdb=" O THR D 255 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR D 255 " --> pdb=" O TYR D 272 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN D 274 " --> pdb=" O PHE D 253 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE D 253 " --> pdb=" O ASN D 274 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 143 through 145 removed outlier: 4.460A pdb=" N LEU E 178 " --> pdb=" O PHE E 145 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP E 117 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER E 110 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 163 through 168 removed outlier: 7.028A pdb=" N THR E 195 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N SER E 166 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N THR E 193 " --> pdb=" O SER E 166 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N ILE E 168 " --> pdb=" O ARG E 191 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ARG E 191 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N ASP E 117 " --> pdb=" O SER E 110 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N SER E 110 " --> pdb=" O ASP E 117 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.709A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N SER E 218 " --> pdb=" O ASN E 269 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN E 269 " --> pdb=" O SER E 218 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLY E 266 " --> pdb=" O PHE E 261 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N PHE E 261 " --> pdb=" O GLY E 266 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N TYR E 268 " --> pdb=" O LEU E 259 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LEU E 259 " --> pdb=" O TYR E 268 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARG E 270 " --> pdb=" O THR E 257 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N THR E 257 " --> pdb=" O ARG E 270 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N TYR E 272 " --> pdb=" O THR E 255 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N THR E 255 " --> pdb=" O TYR E 272 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ASN E 274 " --> pdb=" O PHE E 253 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE E 253 " --> pdb=" O ASN E 274 " (cutoff:3.500A) 785 hydrogen bonds defined for protein. 2205 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: 4.66 Time building geometry restraints manager: 4.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4105 1.34 - 1.46: 3298 1.46 - 1.58: 6607 1.58 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 14150 Sorted by residual: bond pdb=" C2 HEX C 608 " pdb=" C3 HEX C 608 " ideal model delta sigma weight residual 1.524 1.554 -0.030 2.00e-02 2.50e+03 2.25e+00 bond pdb=" C4 HEX E 607 " pdb=" C5 HEX E 607 " ideal model delta sigma weight residual 1.524 1.554 -0.030 2.00e-02 2.50e+03 2.22e+00 bond pdb=" C2 HEX E 607 " pdb=" C3 HEX E 607 " ideal model delta sigma weight residual 1.524 1.553 -0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C2 HEX D 506 " pdb=" C3 HEX D 506 " ideal model delta sigma weight residual 1.524 1.553 -0.029 2.00e-02 2.50e+03 2.16e+00 bond pdb=" C4 HEX C 608 " pdb=" C5 HEX C 608 " ideal model delta sigma weight residual 1.524 1.553 -0.029 2.00e-02 2.50e+03 2.15e+00 ... (remaining 14145 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 18138 1.02 - 2.04: 838 2.04 - 3.06: 115 3.06 - 4.08: 72 4.08 - 5.10: 32 Bond angle restraints: 19195 Sorted by residual: angle pdb=" CA TYR E 362 " pdb=" CB TYR E 362 " pdb=" CG TYR E 362 " ideal model delta sigma weight residual 113.90 109.23 4.67 1.80e+00 3.09e-01 6.73e+00 angle pdb=" CA TYR B 362 " pdb=" CB TYR B 362 " pdb=" CG TYR B 362 " ideal model delta sigma weight residual 113.90 109.24 4.66 1.80e+00 3.09e-01 6.69e+00 angle pdb=" CA TYR A 362 " pdb=" CB TYR A 362 " pdb=" CG TYR A 362 " ideal model delta sigma weight residual 113.90 109.25 4.65 1.80e+00 3.09e-01 6.69e+00 angle pdb=" CA TYR C 362 " pdb=" CB TYR C 362 " pdb=" CG TYR C 362 " ideal model delta sigma weight residual 113.90 109.25 4.65 1.80e+00 3.09e-01 6.68e+00 angle pdb=" CA TYR D 362 " pdb=" CB TYR D 362 " pdb=" CG TYR D 362 " ideal model delta sigma weight residual 113.90 109.25 4.65 1.80e+00 3.09e-01 6.66e+00 ... (remaining 19190 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.19: 8124 16.19 - 32.38: 212 32.38 - 48.57: 35 48.57 - 64.77: 5 64.77 - 80.96: 10 Dihedral angle restraints: 8386 sinusoidal: 3431 harmonic: 4955 Sorted by residual: dihedral pdb=" CA SER D 107 " pdb=" C SER D 107 " pdb=" N LEU D 108 " pdb=" CA LEU D 108 " ideal model delta harmonic sigma weight residual 180.00 164.27 15.73 0 5.00e+00 4.00e-02 9.90e+00 dihedral pdb=" CA SER A 107 " pdb=" C SER A 107 " pdb=" N LEU A 108 " pdb=" CA LEU A 108 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.85e+00 dihedral pdb=" CA SER B 107 " pdb=" C SER B 107 " pdb=" N LEU B 108 " pdb=" CA LEU B 108 " ideal model delta harmonic sigma weight residual 180.00 164.31 15.69 0 5.00e+00 4.00e-02 9.85e+00 ... (remaining 8383 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1648 0.044 - 0.088: 411 0.088 - 0.132: 136 0.132 - 0.176: 10 0.176 - 0.219: 5 Chirality restraints: 2210 Sorted by residual: chirality pdb=" C1 NAG D 501 " pdb=" ND2 ASN D 140 " pdb=" C2 NAG D 501 " pdb=" O5 NAG D 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1 NAG E 602 " pdb=" ND2 ASN E 140 " pdb=" C2 NAG E 602 " pdb=" O5 NAG E 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1 NAG A 602 " pdb=" ND2 ASN A 140 " pdb=" C2 NAG A 602 " pdb=" O5 NAG A 602 " both_signs ideal model delta sigma weight residual False -2.40 -2.62 0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 2207 not shown) Planarity restraints: 2340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " 0.276 2.00e-02 2.50e+03 3.13e-01 1.22e+03 pdb=" CG ASN D 234 " -0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " -0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " -0.487 2.00e-02 2.50e+03 pdb=" C1 NAG D 502 " 0.397 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 234 " -0.276 2.00e-02 2.50e+03 3.12e-01 1.22e+03 pdb=" CG ASN A 234 " 0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN A 234 " 0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN A 234 " 0.486 2.00e-02 2.50e+03 pdb=" C1 NAG A 603 " -0.397 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " 0.276 2.00e-02 2.50e+03 3.12e-01 1.22e+03 pdb=" CG ASN B 234 " -0.108 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.079 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " -0.487 2.00e-02 2.50e+03 pdb=" C1 NAG B 502 " 0.397 2.00e-02 2.50e+03 ... (remaining 2337 not shown) Histogram of nonbonded interaction distances: 2.01 - 2.59: 68 2.59 - 3.17: 10780 3.17 - 3.74: 20342 3.74 - 4.32: 29602 4.32 - 4.90: 49441 Nonbonded interactions: 110233 Sorted by model distance: nonbonded pdb=" OD1 ASN C 234 " pdb=" O5 NAG C 604 " model vdw 2.012 3.040 nonbonded pdb=" OD1 ASN D 234 " pdb=" O5 NAG D 502 " model vdw 2.013 3.040 nonbonded pdb=" OD1 ASN A 234 " pdb=" O5 NAG A 603 " model vdw 2.013 3.040 nonbonded pdb=" OD1 ASN B 234 " pdb=" O5 NAG B 502 " model vdw 2.013 3.040 nonbonded pdb=" OD1 ASN E 234 " pdb=" O5 NAG E 603 " model vdw 2.014 3.040 ... (remaining 110228 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' and (resid 78 through 479 or resid 605 through 606)) selection = (chain 'B' and (resid 78 through 479 or resid 505 through 506)) selection = (chain 'C' and (resid 78 through 479 or resid 605 through 606)) selection = (chain 'D' and (resid 78 through 479 or resid 505 through 506)) selection = (chain 'E' and (resid 78 through 479 or resid 605 through 606)) } 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 individual isotropic 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: 4.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.640 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.370 Find NCS groups from input model: 0.820 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 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 : 0.003 0.030 14150 Z= 0.172 Angle : 0.546 5.097 19195 Z= 0.285 Chirality : 0.043 0.219 2210 Planarity : 0.004 0.029 2330 Dihedral : 8.964 80.958 5160 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 0.34 % Allowed : 0.34 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 2.02 (0.21), residues: 1640 helix: 1.73 (0.21), residues: 600 sheet: 1.63 (0.24), residues: 395 loop : 0.94 (0.25), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 475 HIS 0.002 0.000 HIS E 84 PHE 0.010 0.001 PHE D 253 TYR 0.019 0.001 TYR D 362 ARG 0.003 0.001 ARG D 374 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 331 time to evaluate : 1.511 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 THR cc_start: 0.8107 (m) cc_final: 0.7869 (p) REVERT: C 143 MET cc_start: 0.7993 (mmm) cc_final: 0.7782 (mmt) REVERT: D 326 THR cc_start: 0.7879 (m) cc_final: 0.7652 (p) REVERT: D 349 TRP cc_start: 0.6951 (m100) cc_final: 0.6481 (m100) REVERT: E 335 MET cc_start: 0.4174 (mmm) cc_final: 0.3965 (mpp) outliers start: 5 outliers final: 0 residues processed: 336 average time/residue: 0.2869 time to fit residues: 136.0369 Evaluate side-chains 215 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.7980 chunk 125 optimal weight: 0.1980 chunk 69 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 66 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 96 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 247 GLN C 287 GLN D 287 GLN E 287 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 14150 Z= 0.342 Angle : 0.675 7.322 19195 Z= 0.358 Chirality : 0.051 0.358 2210 Planarity : 0.005 0.052 2330 Dihedral : 7.387 87.767 2115 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 3.70 % Allowed : 5.99 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.30 (0.20), residues: 1640 helix: 1.46 (0.20), residues: 600 sheet: 1.11 (0.25), residues: 400 loop : 0.25 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 230 HIS 0.007 0.002 HIS C 280 PHE 0.021 0.002 PHE D 159 TYR 0.023 0.002 TYR C 362 ARG 0.011 0.001 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 229 time to evaluate : 1.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7833 (ptp90) cc_final: 0.7593 (ptp90) REVERT: A 158 MET cc_start: 0.7944 (mmm) cc_final: 0.7736 (mmm) REVERT: C 115 ASP cc_start: 0.8054 (m-30) cc_final: 0.7854 (m-30) REVERT: D 185 LYS cc_start: 0.8442 (mttp) cc_final: 0.8128 (mtpp) REVERT: D 203 SER cc_start: 0.8584 (t) cc_final: 0.7670 (p) REVERT: E 115 ASP cc_start: 0.8002 (m-30) cc_final: 0.7474 (m-30) REVERT: E 322 LEU cc_start: 0.7672 (tt) cc_final: 0.7441 (mp) REVERT: E 335 MET cc_start: 0.4639 (mmm) cc_final: 0.4300 (mmt) outliers start: 55 outliers final: 35 residues processed: 259 average time/residue: 0.3158 time to fit residues: 113.3349 Evaluate side-chains 243 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 1.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 338 VAL Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 293 THR Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 199 ASN Chi-restraints excluded: chain E residue 319 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 150 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 133 optimal weight: 0.0770 chunk 148 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 120 optimal weight: 0.9980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN B 247 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14150 Z= 0.167 Angle : 0.503 10.020 19195 Z= 0.270 Chirality : 0.045 0.355 2210 Planarity : 0.004 0.045 2330 Dihedral : 6.591 89.748 2115 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.69 % Allowed : 7.88 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.61 (0.20), residues: 1640 helix: 1.99 (0.21), residues: 600 sheet: 1.09 (0.25), residues: 415 loop : 0.24 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 128 HIS 0.003 0.001 HIS B 254 PHE 0.013 0.001 PHE A 282 TYR 0.018 0.001 TYR E 362 ARG 0.005 0.000 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7755 (ptp90) cc_final: 0.7381 (ptp90) REVERT: A 375 LYS cc_start: 0.7394 (mtpt) cc_final: 0.7101 (ttpt) REVERT: B 265 THR cc_start: 0.7689 (p) cc_final: 0.7419 (p) REVERT: B 308 ARG cc_start: 0.7105 (mtm-85) cc_final: 0.6811 (mtp180) REVERT: C 185 LYS cc_start: 0.8344 (mttp) cc_final: 0.8114 (mmmm) REVERT: D 88 MET cc_start: 0.8821 (mtm) cc_final: 0.8529 (mtm) REVERT: D 148 ARG cc_start: 0.7768 (ptt-90) cc_final: 0.7555 (ptt-90) REVERT: D 185 LYS cc_start: 0.8417 (mttp) cc_final: 0.8183 (mmmm) REVERT: D 203 SER cc_start: 0.8553 (t) cc_final: 0.7668 (p) REVERT: D 457 LYS cc_start: 0.7716 (tttp) cc_final: 0.7502 (tptt) REVERT: E 85 ASP cc_start: 0.7493 (p0) cc_final: 0.7282 (p0) REVERT: E 115 ASP cc_start: 0.8099 (m-30) cc_final: 0.7851 (m-30) REVERT: E 148 ARG cc_start: 0.7549 (ptt-90) cc_final: 0.7334 (ptt-90) REVERT: E 308 ARG cc_start: 0.6454 (mtm180) cc_final: 0.6228 (mtt-85) REVERT: E 335 MET cc_start: 0.4735 (mmm) cc_final: 0.4416 (mmt) outliers start: 40 outliers final: 27 residues processed: 238 average time/residue: 0.3233 time to fit residues: 106.0566 Evaluate side-chains 224 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 197 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 236 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 236 SER Chi-restraints excluded: chain D residue 255 THR Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 265 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 150 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.4263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14150 Z= 0.239 Angle : 0.546 6.220 19195 Z= 0.293 Chirality : 0.045 0.272 2210 Planarity : 0.004 0.041 2330 Dihedral : 6.642 87.654 2115 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.70 % Allowed : 7.88 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.31 (0.20), residues: 1640 helix: 1.85 (0.21), residues: 600 sheet: 0.96 (0.25), residues: 410 loop : -0.08 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 230 HIS 0.004 0.001 HIS B 280 PHE 0.014 0.002 PHE D 159 TYR 0.021 0.002 TYR B 362 ARG 0.005 0.000 ARG E 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 213 time to evaluate : 1.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7796 (ptp90) cc_final: 0.7398 (ptp90) REVERT: A 375 LYS cc_start: 0.7305 (mtpt) cc_final: 0.7055 (ttpt) REVERT: B 265 THR cc_start: 0.7760 (p) cc_final: 0.7538 (p) REVERT: B 308 ARG cc_start: 0.7071 (mtm-85) cc_final: 0.6784 (mtp180) REVERT: C 88 MET cc_start: 0.8809 (mtm) cc_final: 0.8582 (mtt) REVERT: D 116 MET cc_start: 0.7961 (mtm) cc_final: 0.7711 (mtm) REVERT: D 203 SER cc_start: 0.8596 (t) cc_final: 0.7958 (p) REVERT: E 85 ASP cc_start: 0.7494 (p0) cc_final: 0.7189 (p0) REVERT: E 115 ASP cc_start: 0.8212 (m-30) cc_final: 0.7977 (m-30) REVERT: E 148 ARG cc_start: 0.7751 (ptt-90) cc_final: 0.7535 (ptt-90) REVERT: E 170 ASP cc_start: 0.7263 (t0) cc_final: 0.6895 (p0) outliers start: 55 outliers final: 45 residues processed: 248 average time/residue: 0.3153 time to fit residues: 109.5055 Evaluate side-chains 236 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 173 THR Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 259 LEU Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 265 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 143 optimal weight: 0.9980 chunk 40 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.4555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14150 Z= 0.241 Angle : 0.526 6.424 19195 Z= 0.282 Chirality : 0.044 0.258 2210 Planarity : 0.004 0.045 2330 Dihedral : 6.321 82.424 2115 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.70 % Allowed : 9.16 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.17 (0.20), residues: 1640 helix: 1.84 (0.21), residues: 600 sheet: 0.73 (0.25), residues: 415 loop : -0.16 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 230 HIS 0.004 0.001 HIS A 280 PHE 0.013 0.001 PHE E 205 TYR 0.020 0.002 TYR E 362 ARG 0.006 0.000 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 202 time to evaluate : 1.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7838 (ptp90) cc_final: 0.7455 (ptp90) REVERT: A 375 LYS cc_start: 0.7314 (mtpt) cc_final: 0.7083 (ttpt) REVERT: B 265 THR cc_start: 0.7728 (p) cc_final: 0.7510 (p) REVERT: B 308 ARG cc_start: 0.7074 (mtm-85) cc_final: 0.6782 (mtp180) REVERT: D 148 ARG cc_start: 0.7854 (ptt-90) cc_final: 0.7568 (ptt-90) REVERT: D 203 SER cc_start: 0.8744 (t) cc_final: 0.7975 (p) REVERT: E 115 ASP cc_start: 0.8180 (m-30) cc_final: 0.7957 (m-30) REVERT: E 170 ASP cc_start: 0.7162 (t0) cc_final: 0.6883 (p0) outliers start: 55 outliers final: 45 residues processed: 237 average time/residue: 0.3356 time to fit residues: 108.9646 Evaluate side-chains 244 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 199 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 263 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 263 SER Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 93 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 159 optimal weight: 0.9990 chunk 132 optimal weight: 0.6980 chunk 73 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14150 Z= 0.182 Angle : 0.494 5.656 19195 Z= 0.264 Chirality : 0.043 0.245 2210 Planarity : 0.004 0.047 2330 Dihedral : 5.976 77.555 2115 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 3.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.90 % Allowed : 10.51 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.24 (0.20), residues: 1640 helix: 1.97 (0.21), residues: 600 sheet: 0.70 (0.25), residues: 415 loop : -0.15 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 128 HIS 0.003 0.001 HIS A 280 PHE 0.011 0.001 PHE B 282 TYR 0.018 0.001 TYR E 362 ARG 0.005 0.000 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 1.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7824 (ptp90) cc_final: 0.7445 (ptp90) REVERT: A 375 LYS cc_start: 0.7262 (mtpt) cc_final: 0.7038 (ttpt) REVERT: B 265 THR cc_start: 0.7631 (p) cc_final: 0.7424 (p) REVERT: B 308 ARG cc_start: 0.7099 (mtm-85) cc_final: 0.6811 (mtp180) REVERT: B 335 MET cc_start: 0.6192 (tpt) cc_final: 0.5564 (tmm) REVERT: C 88 MET cc_start: 0.8788 (mtm) cc_final: 0.8582 (mtt) REVERT: D 148 ARG cc_start: 0.7808 (ptt-90) cc_final: 0.7506 (ptt-90) REVERT: D 185 LYS cc_start: 0.8453 (mttp) cc_final: 0.8065 (mtpp) REVERT: D 203 SER cc_start: 0.8722 (t) cc_final: 0.7964 (p) REVERT: D 457 LYS cc_start: 0.7932 (tttp) cc_final: 0.7643 (tptt) REVERT: E 335 MET cc_start: 0.5207 (tpt) cc_final: 0.4833 (tmm) outliers start: 43 outliers final: 41 residues processed: 230 average time/residue: 0.3422 time to fit residues: 108.4959 Evaluate side-chains 229 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 188 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 256 THR Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 96 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 14150 Z= 0.360 Angle : 0.588 5.835 19195 Z= 0.314 Chirality : 0.046 0.240 2210 Planarity : 0.005 0.046 2330 Dihedral : 5.961 66.099 2115 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.64 % Allowed : 9.56 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 0.87 (0.20), residues: 1640 helix: 1.66 (0.21), residues: 600 sheet: 0.52 (0.25), residues: 415 loop : -0.38 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 230 HIS 0.006 0.002 HIS B 280 PHE 0.016 0.002 PHE D 159 TYR 0.022 0.002 TYR E 362 ARG 0.009 0.001 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 197 time to evaluate : 1.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7897 (ptp90) cc_final: 0.7496 (ptp90) REVERT: A 375 LYS cc_start: 0.7333 (mtpt) cc_final: 0.7118 (ttpt) REVERT: B 265 THR cc_start: 0.7838 (p) cc_final: 0.7627 (p) REVERT: B 308 ARG cc_start: 0.7088 (mtm-85) cc_final: 0.6802 (mtp180) REVERT: C 215 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8078 (mt-10) REVERT: D 203 SER cc_start: 0.8744 (t) cc_final: 0.8024 (p) REVERT: E 148 ARG cc_start: 0.7819 (ptt-90) cc_final: 0.7580 (ptt-90) outliers start: 54 outliers final: 47 residues processed: 233 average time/residue: 0.3286 time to fit residues: 105.9609 Evaluate side-chains 242 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 195 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 246 SER Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 142 SER Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 198 CYS Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain C residue 371 VAL Chi-restraints excluded: chain D residue 81 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 176 VAL Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 198 CYS Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 0.1980 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 78 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 125 optimal weight: 0.5980 chunk 144 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14150 Z= 0.154 Angle : 0.484 8.015 19195 Z= 0.257 Chirality : 0.042 0.218 2210 Planarity : 0.004 0.047 2330 Dihedral : 5.303 54.339 2115 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.42 % Allowed : 11.45 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.20 (0.20), residues: 1640 helix: 2.01 (0.21), residues: 600 sheet: 0.64 (0.25), residues: 410 loop : -0.23 (0.24), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 128 HIS 0.003 0.001 HIS E 169 PHE 0.013 0.001 PHE B 282 TYR 0.014 0.001 TYR E 362 ARG 0.004 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 210 time to evaluate : 1.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7813 (ptp90) cc_final: 0.7478 (ptp90) REVERT: A 375 LYS cc_start: 0.7248 (mtpt) cc_final: 0.7032 (ttpt) REVERT: B 148 ARG cc_start: 0.7734 (ptt-90) cc_final: 0.7390 (ptt90) REVERT: B 185 LYS cc_start: 0.8398 (mttp) cc_final: 0.8016 (mttt) REVERT: B 265 THR cc_start: 0.7571 (p) cc_final: 0.7355 (p) REVERT: B 308 ARG cc_start: 0.7101 (mtm-85) cc_final: 0.6806 (mtp180) REVERT: B 335 MET cc_start: 0.6094 (tpt) cc_final: 0.5487 (tmm) REVERT: C 148 ARG cc_start: 0.7747 (ptt-90) cc_final: 0.7539 (ptt-90) REVERT: C 185 LYS cc_start: 0.8446 (mttp) cc_final: 0.8057 (mtmt) REVERT: D 185 LYS cc_start: 0.8464 (mttp) cc_final: 0.8053 (mtpp) REVERT: D 203 SER cc_start: 0.8700 (t) cc_final: 0.7977 (p) REVERT: D 284 PHE cc_start: 0.7568 (m-80) cc_final: 0.7264 (m-80) REVERT: D 457 LYS cc_start: 0.7900 (tttp) cc_final: 0.7596 (tptt) REVERT: E 148 ARG cc_start: 0.7741 (ptt-90) cc_final: 0.7533 (ptt-90) outliers start: 36 outliers final: 33 residues processed: 236 average time/residue: 0.2741 time to fit residues: 87.2236 Evaluate side-chains 239 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 206 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 177 MET Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 255 THR Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 89 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 133 optimal weight: 0.1980 chunk 140 optimal weight: 0.0980 chunk 147 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14150 Z= 0.181 Angle : 0.507 8.362 19195 Z= 0.266 Chirality : 0.043 0.214 2210 Planarity : 0.004 0.045 2330 Dihedral : 5.174 47.489 2115 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.49 % Allowed : 11.58 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.18 (0.20), residues: 1640 helix: 2.06 (0.21), residues: 600 sheet: 0.55 (0.25), residues: 415 loop : -0.24 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 128 HIS 0.003 0.001 HIS B 280 PHE 0.012 0.001 PHE B 282 TYR 0.019 0.001 TYR E 362 ARG 0.005 0.000 ARG C 148 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 202 time to evaluate : 1.701 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7831 (ptp90) cc_final: 0.7461 (ptp90) REVERT: B 148 ARG cc_start: 0.7718 (ptt-90) cc_final: 0.7350 (ptt90) REVERT: B 265 THR cc_start: 0.7559 (p) cc_final: 0.7339 (p) REVERT: B 308 ARG cc_start: 0.7116 (mtm-85) cc_final: 0.6825 (mtp180) REVERT: B 335 MET cc_start: 0.6102 (tpt) cc_final: 0.5542 (tmm) REVERT: D 185 LYS cc_start: 0.8468 (mttp) cc_final: 0.8047 (mtpp) REVERT: D 203 SER cc_start: 0.8695 (t) cc_final: 0.7992 (p) REVERT: D 457 LYS cc_start: 0.7922 (tttp) cc_final: 0.7613 (tptt) REVERT: E 148 ARG cc_start: 0.7778 (ptt-90) cc_final: 0.7530 (ptt-90) REVERT: E 375 LYS cc_start: 0.7194 (mtpt) cc_final: 0.6946 (ttpt) outliers start: 37 outliers final: 36 residues processed: 229 average time/residue: 0.3481 time to fit residues: 108.1691 Evaluate side-chains 236 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 200 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 278 ARG Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 chunk 151 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 101 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14150 Z= 0.206 Angle : 0.517 8.303 19195 Z= 0.273 Chirality : 0.043 0.206 2210 Planarity : 0.004 0.045 2330 Dihedral : 5.076 42.076 2115 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.63 % Allowed : 11.52 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.11 (0.20), residues: 1640 helix: 1.99 (0.21), residues: 600 sheet: 0.52 (0.25), residues: 415 loop : -0.29 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 128 HIS 0.004 0.001 HIS B 280 PHE 0.012 0.001 PHE E 205 TYR 0.019 0.001 TYR E 362 ARG 0.012 0.000 ARG D 148 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3280 Ramachandran restraints generated. 1640 Oldfield, 0 Emsley, 1640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 196 time to evaluate : 1.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 148 ARG cc_start: 0.7851 (ptp90) cc_final: 0.7488 (ptp90) REVERT: B 265 THR cc_start: 0.7631 (p) cc_final: 0.7411 (p) REVERT: B 308 ARG cc_start: 0.7108 (mtm-85) cc_final: 0.6821 (mtp180) REVERT: B 335 MET cc_start: 0.6082 (tpt) cc_final: 0.5579 (tmm) REVERT: C 148 ARG cc_start: 0.7707 (ptt-90) cc_final: 0.7498 (ptt-90) REVERT: D 203 SER cc_start: 0.8695 (t) cc_final: 0.8013 (p) REVERT: E 148 ARG cc_start: 0.7802 (ptt-90) cc_final: 0.7544 (ptt-90) REVERT: E 375 LYS cc_start: 0.7249 (mtpt) cc_final: 0.7019 (ttpt) outliers start: 39 outliers final: 37 residues processed: 224 average time/residue: 0.3379 time to fit residues: 103.3504 Evaluate side-chains 231 residues out of total 1540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 194 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 335 MET Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain B residue 108 LEU Chi-restraints excluded: chain B residue 114 VAL Chi-restraints excluded: chain B residue 194 VAL Chi-restraints excluded: chain B residue 246 SER Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 246 SER Chi-restraints excluded: chain C residue 299 SER Chi-restraints excluded: chain C residue 365 VAL Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain D residue 142 SER Chi-restraints excluded: chain D residue 177 MET Chi-restraints excluded: chain D residue 194 VAL Chi-restraints excluded: chain D residue 246 SER Chi-restraints excluded: chain D residue 278 ARG Chi-restraints excluded: chain D residue 299 SER Chi-restraints excluded: chain D residue 302 SER Chi-restraints excluded: chain D residue 365 VAL Chi-restraints excluded: chain D residue 369 THR Chi-restraints excluded: chain D residue 371 VAL Chi-restraints excluded: chain E residue 114 VAL Chi-restraints excluded: chain E residue 142 SER Chi-restraints excluded: chain E residue 255 THR Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 365 VAL Chi-restraints excluded: chain E residue 371 VAL Chi-restraints excluded: chain E residue 476 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 134 optimal weight: 0.0370 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.142300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.119603 restraints weight = 15530.463| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.05 r_work: 0.3151 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.5159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14150 Z= 0.208 Angle : 0.522 8.116 19195 Z= 0.276 Chirality : 0.043 0.202 2210 Planarity : 0.004 0.043 2330 Dihedral : 5.141 39.303 2115 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.69 % Allowed : 11.92 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.08 (0.20), residues: 1640 helix: 1.96 (0.21), residues: 600 sheet: 0.52 (0.25), residues: 415 loop : -0.32 (0.24), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 128 HIS 0.004 0.001 HIS B 280 PHE 0.012 0.001 PHE E 205 TYR 0.018 0.001 TYR E 362 ARG 0.011 0.000 ARG D 148 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3209.81 seconds wall clock time: 67 minutes 19.27 seconds (4039.27 seconds total)