Starting phenix.real_space_refine on Sat Sep 12 03:20:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6cjt_7483/09_2026/6cjt_7483.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cjt_7483/09_2026/6cjt_7483.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6cjt_7483/09_2026/6cjt_7483.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6cjt_7483/09_2026/6cjt_7483.cif" model { file = "/net/cci-nas-00/data/ceres_data/6cjt_7483/09_2026/6cjt_7483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cjt_7483/09_2026/6cjt_7483.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cjt_7483/09_2026/6cjt_7483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cjt_7483/09_2026/6cjt_7483.map" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 28 5.16 5 C 8748 2.51 5 N 2128 2.21 5 O 2296 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13208 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3155 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 24, 'TRANS': 371} Chain breaks: 1 Chain: "D" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 396, 3155 Classifications: {'peptide': 396} Link IDs: {'PTRANS': 24, 'TRANS': 371} Chain breaks: 1 Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Unusual residues: {'PCG': 1, 'PGW': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGW:plan-1': 4, 'PGW:plan-2': 4, 'PGW:plan-3': 6} Unresolved non-hydrogen planarities: 44 Chain: "D" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 147 Unusual residues: {'PCG': 1, 'PGW': 6} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 182 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGW:plan-3': 6, 'PGW:plan-1': 4, 'PGW:plan-2': 4} Unresolved non-hydrogen planarities: 44 Restraints were copied for chains: B, C Time building chain proxies: 4.10, per 1000 atoms: 0.31 Number of scatterers: 13208 At special positions: 0 Unit cell: (106.322, 106.322, 120.571, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 P 8 15.00 O 2296 8.00 N 2128 7.00 C 8748 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 153 " - pdb=" SG CYS B 153 " distance=0.00 Simple disulfide: pdb=" SG CYS B 387 " - pdb=" SG CYS B 387 " distance=0.00 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 592.8 milliseconds 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3008 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 66.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 10 through 35 removed outlier: 4.683A pdb=" N VAL A 14 " --> pdb=" O THR A 10 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP A 15 " --> pdb=" O TYR A 11 " (cutoff:3.500A) Proline residue: A 31 - end of helix removed outlier: 3.732A pdb=" N VAL A 35 " --> pdb=" O PRO A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 68 removed outlier: 6.496A pdb=" N LEU A 43 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Proline residue: A 45 - end of helix removed outlier: 4.446A pdb=" N ILE A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Proline residue: A 59 - end of helix removed outlier: 4.926A pdb=" N PHE A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU A 65 " --> pdb=" O ASP A 61 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG A 67 " --> pdb=" O ALA A 63 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ARG A 68 " --> pdb=" O PHE A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 88 Processing helix chain 'A' and resid 91 through 98 removed outlier: 4.825A pdb=" N VAL A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE A 96 " --> pdb=" O ASP A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 104 No H-bonds generated for 'chain 'A' and resid 103 through 104' Processing helix chain 'A' and resid 105 through 114 removed outlier: 3.760A pdb=" N ARG A 111 " --> pdb=" O SER A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 126 removed outlier: 4.056A pdb=" N ARG A 124 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 158 removed outlier: 3.864A pdb=" N GLY A 150 " --> pdb=" O LEU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 181 removed outlier: 3.868A pdb=" N TYR A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA A 173 " --> pdb=" O ARG A 169 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU A 181 " --> pdb=" O THR A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 224 removed outlier: 3.835A pdb=" N TYR A 199 " --> pdb=" O THR A 195 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.506A pdb=" N VAL A 239 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 240 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 267 removed outlier: 3.703A pdb=" N ARG A 267 " --> pdb=" O LEU A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 278 removed outlier: 4.054A pdb=" N LYS A 277 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU A 278 " --> pdb=" O GLU A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 Processing helix chain 'A' and resid 293 through 298 removed outlier: 4.298A pdb=" N GLU A 297 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 298' Processing helix chain 'A' and resid 307 through 316 removed outlier: 3.617A pdb=" N ASP A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 315 " --> pdb=" O ARG A 311 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N HIS A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 4.837A pdb=" N ILE A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU A 373 " --> pdb=" O MET A 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 368 through 373' Processing helix chain 'A' and resid 394 through 403 removed outlier: 4.787A pdb=" N ARG A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 412 removed outlier: 4.089A pdb=" N GLN A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 35 removed outlier: 4.683A pdb=" N VAL B 14 " --> pdb=" O THR B 10 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP B 15 " --> pdb=" O TYR B 11 " (cutoff:3.500A) Proline residue: B 31 - end of helix removed outlier: 3.732A pdb=" N VAL B 35 " --> pdb=" O PRO B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 68 removed outlier: 6.496A pdb=" N LEU B 43 " --> pdb=" O LEU B 39 " (cutoff:3.500A) Proline residue: B 45 - end of helix removed outlier: 4.446A pdb=" N ILE B 58 " --> pdb=" O LEU B 54 " (cutoff:3.500A) Proline residue: B 59 - end of helix removed outlier: 4.926A pdb=" N PHE B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU B 65 " --> pdb=" O ASP B 61 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ARG B 68 " --> pdb=" O PHE B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 91 through 98 removed outlier: 4.825A pdb=" N VAL B 95 " --> pdb=" O LEU B 91 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE B 96 " --> pdb=" O ASP B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 104 No H-bonds generated for 'chain 'B' and resid 103 through 104' Processing helix chain 'B' and resid 105 through 114 removed outlier: 3.760A pdb=" N ARG B 111 " --> pdb=" O SER B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 126 removed outlier: 4.056A pdb=" N ARG B 124 " --> pdb=" O ARG B 120 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 158 removed outlier: 3.864A pdb=" N GLY B 150 " --> pdb=" O LEU B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 181 removed outlier: 3.868A pdb=" N TYR B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 181 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 224 removed outlier: 3.835A pdb=" N TYR B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS B 224 " --> pdb=" O SER B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 245 removed outlier: 3.506A pdb=" N VAL B 239 " --> pdb=" O ARG B 235 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR B 240 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR B 245 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 267 removed outlier: 3.703A pdb=" N ARG B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 278 removed outlier: 4.054A pdb=" N LYS B 277 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU B 278 " --> pdb=" O GLU B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 292 Processing helix chain 'B' and resid 293 through 298 removed outlier: 4.298A pdb=" N GLU B 297 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 293 through 298' Processing helix chain 'B' and resid 307 through 316 removed outlier: 3.617A pdb=" N ASP B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU B 315 " --> pdb=" O ARG B 311 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N HIS B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 4.837A pdb=" N ILE B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU B 373 " --> pdb=" O MET B 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 368 through 373' Processing helix chain 'B' and resid 394 through 403 removed outlier: 4.787A pdb=" N ARG B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 412 removed outlier: 4.089A pdb=" N GLN B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 35 removed outlier: 4.683A pdb=" N VAL C 14 " --> pdb=" O THR C 10 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP C 15 " --> pdb=" O TYR C 11 " (cutoff:3.500A) Proline residue: C 31 - end of helix removed outlier: 3.732A pdb=" N VAL C 35 " --> pdb=" O PRO C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 68 removed outlier: 6.496A pdb=" N LEU C 43 " --> pdb=" O LEU C 39 " (cutoff:3.500A) Proline residue: C 45 - end of helix removed outlier: 4.446A pdb=" N ILE C 58 " --> pdb=" O LEU C 54 " (cutoff:3.500A) Proline residue: C 59 - end of helix removed outlier: 4.926A pdb=" N PHE C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU C 65 " --> pdb=" O ASP C 61 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG C 67 " --> pdb=" O ALA C 63 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ARG C 68 " --> pdb=" O PHE C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 88 Processing helix chain 'C' and resid 91 through 98 removed outlier: 4.825A pdb=" N VAL C 95 " --> pdb=" O LEU C 91 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 104 No H-bonds generated for 'chain 'C' and resid 103 through 104' Processing helix chain 'C' and resid 105 through 114 removed outlier: 3.760A pdb=" N ARG C 111 " --> pdb=" O SER C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 126 removed outlier: 4.056A pdb=" N ARG C 124 " --> pdb=" O ARG C 120 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU C 126 " --> pdb=" O ALA C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 158 removed outlier: 3.864A pdb=" N GLY C 150 " --> pdb=" O LEU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 181 removed outlier: 3.868A pdb=" N TYR C 170 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA C 173 " --> pdb=" O ARG C 169 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU C 181 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 224 removed outlier: 3.835A pdb=" N TYR C 199 " --> pdb=" O THR C 195 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS C 224 " --> pdb=" O SER C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 245 removed outlier: 3.506A pdb=" N VAL C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR C 240 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR C 245 " --> pdb=" O ALA C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 267 removed outlier: 3.703A pdb=" N ARG C 267 " --> pdb=" O LEU C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 278 removed outlier: 4.054A pdb=" N LYS C 277 " --> pdb=" O ARG C 273 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU C 278 " --> pdb=" O GLU C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 292 Processing helix chain 'C' and resid 293 through 298 removed outlier: 4.298A pdb=" N GLU C 297 " --> pdb=" O GLY C 293 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS C 298 " --> pdb=" O ASP C 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 293 through 298' Processing helix chain 'C' and resid 307 through 316 removed outlier: 3.617A pdb=" N ASP C 312 " --> pdb=" O GLU C 308 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 315 " --> pdb=" O ARG C 311 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N HIS C 316 " --> pdb=" O ASP C 312 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 4.837A pdb=" N ILE C 372 " --> pdb=" O GLU C 368 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU C 373 " --> pdb=" O MET C 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 368 through 373' Processing helix chain 'C' and resid 394 through 403 removed outlier: 4.787A pdb=" N ARG C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 405 through 412 removed outlier: 4.089A pdb=" N GLN C 412 " --> pdb=" O ALA C 408 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 35 removed outlier: 4.683A pdb=" N VAL D 14 " --> pdb=" O THR D 10 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N TRP D 15 " --> pdb=" O TYR D 11 " (cutoff:3.500A) Proline residue: D 31 - end of helix removed outlier: 3.732A pdb=" N VAL D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 68 removed outlier: 6.496A pdb=" N LEU D 43 " --> pdb=" O LEU D 39 " (cutoff:3.500A) Proline residue: D 45 - end of helix removed outlier: 4.446A pdb=" N ILE D 58 " --> pdb=" O LEU D 54 " (cutoff:3.500A) Proline residue: D 59 - end of helix removed outlier: 4.926A pdb=" N PHE D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLU D 65 " --> pdb=" O ASP D 61 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ARG D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ARG D 68 " --> pdb=" O PHE D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 88 Processing helix chain 'D' and resid 91 through 98 removed outlier: 4.825A pdb=" N VAL D 95 " --> pdb=" O LEU D 91 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N PHE D 96 " --> pdb=" O ASP D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 104 No H-bonds generated for 'chain 'D' and resid 103 through 104' Processing helix chain 'D' and resid 105 through 114 removed outlier: 3.760A pdb=" N ARG D 111 " --> pdb=" O SER D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 126 removed outlier: 4.056A pdb=" N ARG D 124 " --> pdb=" O ARG D 120 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU D 126 " --> pdb=" O ALA D 122 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 158 removed outlier: 3.864A pdb=" N GLY D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 181 removed outlier: 3.868A pdb=" N TYR D 170 " --> pdb=" O ALA D 166 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA D 173 " --> pdb=" O ARG D 169 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU D 181 " --> pdb=" O THR D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 224 removed outlier: 3.835A pdb=" N TYR D 199 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS D 224 " --> pdb=" O SER D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 245 removed outlier: 3.506A pdb=" N VAL D 239 " --> pdb=" O ARG D 235 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR D 240 " --> pdb=" O VAL D 236 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N TYR D 245 " --> pdb=" O ALA D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 267 removed outlier: 3.703A pdb=" N ARG D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 278 removed outlier: 4.054A pdb=" N LYS D 277 " --> pdb=" O ARG D 273 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N GLU D 278 " --> pdb=" O GLU D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 292 Processing helix chain 'D' and resid 293 through 298 removed outlier: 4.298A pdb=" N GLU D 297 " --> pdb=" O GLY D 293 " (cutoff:3.500A) removed outlier: 6.144A pdb=" N LYS D 298 " --> pdb=" O ASP D 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 293 through 298' Processing helix chain 'D' and resid 307 through 316 removed outlier: 3.617A pdb=" N ASP D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU D 315 " --> pdb=" O ARG D 311 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N HIS D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 4.837A pdb=" N ILE D 372 " --> pdb=" O GLU D 368 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU D 373 " --> pdb=" O MET D 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 368 through 373' Processing helix chain 'D' and resid 394 through 403 removed outlier: 4.787A pdb=" N ARG D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 412 removed outlier: 4.089A pdb=" N GLN D 412 " --> pdb=" O ALA D 408 " (cutoff:3.500A) 592 hydrogen bonds defined for protein. 1704 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: 1.89 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3220 1.33 - 1.45: 2404 1.45 - 1.57: 7788 1.57 - 1.69: 24 1.69 - 1.81: 48 Bond restraints: 13484 Sorted by residual: bond pdb=" O1A PCG A 500 " pdb=" PA PCG A 500 " ideal model delta sigma weight residual 1.582 1.457 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" O1A PCG B 500 " pdb=" PA PCG B 500 " ideal model delta sigma weight residual 1.582 1.457 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" O1A PCG D 500 " pdb=" PA PCG D 500 " ideal model delta sigma weight residual 1.582 1.457 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" O1A PCG C 500 " pdb=" PA PCG C 500 " ideal model delta sigma weight residual 1.582 1.457 0.125 2.00e-02 2.50e+03 3.90e+01 bond pdb=" O2A PCG C 500 " pdb=" PA PCG C 500 " ideal model delta sigma weight residual 1.473 1.584 -0.111 2.00e-02 2.50e+03 3.10e+01 ... (remaining 13479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 16656 2.11 - 4.21: 1072 4.21 - 6.32: 320 6.32 - 8.43: 140 8.43 - 10.53: 48 Bond angle restraints: 18236 Sorted by residual: angle pdb=" C ASP B 92 " pdb=" N LEU B 93 " pdb=" CA LEU B 93 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C ASP C 92 " pdb=" N LEU C 93 " pdb=" CA LEU C 93 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C ASP D 92 " pdb=" N LEU D 93 " pdb=" CA LEU D 93 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C ASP A 92 " pdb=" N LEU A 93 " pdb=" CA LEU A 93 " ideal model delta sigma weight residual 121.54 131.48 -9.94 1.91e+00 2.74e-01 2.71e+01 angle pdb=" C LEU C 39 " pdb=" N PHE C 40 " pdb=" CA PHE C 40 " ideal model delta sigma weight residual 121.54 129.84 -8.30 1.91e+00 2.74e-01 1.89e+01 ... (remaining 18231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.92: 8024 33.92 - 67.83: 196 67.83 - 101.75: 24 101.75 - 135.66: 16 135.66 - 169.58: 4 Dihedral angle restraints: 8264 sinusoidal: 3604 harmonic: 4660 Sorted by residual: dihedral pdb=" CB CYS B 153 " pdb=" SG CYS B 153 " pdb=" SG CYS B 153 " pdb=" CB CYS B 153 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CB CYS B 387 " pdb=" SG CYS B 387 " pdb=" SG CYS B 387 " pdb=" CB CYS B 387 " ideal model delta sinusoidal sigma weight residual 0.00 0.00 0.00 1 1.00e+01 1.00e-02 0.00e+00 dihedral pdb=" CA LEU D 276 " pdb=" C LEU D 276 " pdb=" N LYS D 277 " pdb=" CA LYS D 277 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 8261 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1944 0.111 - 0.222: 164 0.222 - 0.333: 8 0.333 - 0.445: 4 0.445 - 0.556: 4 Chirality restraints: 2124 Sorted by residual: chirality pdb=" PA PCG D 500 " pdb=" O2A PCG D 500 " pdb=" O3' PCG D 500 " pdb=" O5' PCG D 500 " both_signs ideal model delta sigma weight residual True 2.70 -3.25 -0.56 2.00e-01 2.50e+01 7.72e+00 chirality pdb=" PA PCG A 500 " pdb=" O2A PCG A 500 " pdb=" O3' PCG A 500 " pdb=" O5' PCG A 500 " both_signs ideal model delta sigma weight residual True 2.70 -3.25 -0.56 2.00e-01 2.50e+01 7.72e+00 chirality pdb=" PA PCG C 500 " pdb=" O2A PCG C 500 " pdb=" O3' PCG C 500 " pdb=" O5' PCG C 500 " both_signs ideal model delta sigma weight residual True 2.70 -3.25 -0.56 2.00e-01 2.50e+01 7.72e+00 ... (remaining 2121 not shown) Planarity restraints: 2200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 93 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C LEU A 93 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU A 93 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU A 94 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 93 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C LEU D 93 " 0.056 2.00e-02 2.50e+03 pdb=" O LEU D 93 " -0.021 2.00e-02 2.50e+03 pdb=" N LEU D 94 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 93 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C LEU C 93 " -0.056 2.00e-02 2.50e+03 pdb=" O LEU C 93 " 0.021 2.00e-02 2.50e+03 pdb=" N LEU C 94 " 0.019 2.00e-02 2.50e+03 ... (remaining 2197 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 3428 2.80 - 3.33: 11648 3.33 - 3.85: 21056 3.85 - 4.38: 23012 4.38 - 4.90: 41232 Nonbonded interactions: 100376 Sorted by model distance: nonbonded pdb=" OD2 ASP B 312 " pdb=" OH TYR B 404 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP C 312 " pdb=" OH TYR C 404 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP D 312 " pdb=" OH TYR D 404 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP A 312 " pdb=" OH TYR A 404 " model vdw 2.280 3.040 nonbonded pdb=" O12 PGW A 501 " pdb=" OAE PGW A 501 " model vdw 2.295 3.040 ... (remaining 100371 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: 0.04 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 10 through 412 or (resid 503 and (name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24 or name C25 or name C26 or name C27 or name C28)) or (resid 505 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or resid 506 \ or (resid 501 and (name C15 or name C16 or name C17 or name C18 or name C19 or \ name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28)))) selection = (chain 'B' and (resid 10 through 412 or (resid 503 and (name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24 or name C25 or name C26 or name C27 or name C28)) or (resid 505 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or resid 506 \ or (resid 501 and (name C15 or name C16 or name C17 or name C18 or name C19 or \ name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28)))) selection = (chain 'C' and (resid 10 through 412 or (resid 503 and (name C15 or name C16 or \ name C17 or name C18 or name C19 or name C20 or name C21 or name C22 or name C23 \ or name C24 or name C25 or name C26 or name C27 or name C28)) or (resid 505 and \ (name C1 or name C2 or name C3 or name C4 or name C5 or name C6 )) or resid 506 \ or (resid 501 and (name C15 or name C16 or name C17 or name C18 or name C19 or \ name C20 or name C21 or name C22 or name C23 or name C24 or name C25 or name C26 \ or name C27 or name C28)))) selection = (chain 'D' and (resid 10 through 412 or resid 502 or (resid 504 and (name C1 or \ name C2 or name C3 or name C4 or name C5 or name C6 )) or (resid 505 and (name C \ 15 or name C16 or name C17 or name C18 or name C19 or name C20 or name C21 or na \ me C22 or name C23 or name C24 or name C25 or name C26 or name C27 or name C28 o \ r name C29 or name C30)) or (resid 506 and (name C15 or name C16 or name C17 or \ name C18 or name C19 or name C20 or name C21 or name C22 or name C23 or name C24 \ or name C25 or name C26 or name C27 or name C28)))) } 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: 1.210 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.870 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 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 : 0.010 0.125 13484 Z= 0.430 Angle : 1.430 10.534 18238 Z= 0.674 Chirality : 0.070 0.556 2124 Planarity : 0.008 0.058 2200 Dihedral : 15.920 169.580 5252 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 0.59 % Allowed : 7.06 % Favored : 92.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.58 (0.18), residues: 1568 helix: -2.14 (0.14), residues: 924 sheet: -2.51 (0.39), residues: 84 loop : -2.47 (0.24), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 111 TYR 0.030 0.004 TYR D 211 PHE 0.012 0.002 PHE B 36 TRP 0.021 0.003 TRP A 264 HIS 0.005 0.001 HIS D 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00962 / 0.43 (13484) covalent geometry : angle 1.42986 / 0.67 (18236) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.13946 / 9.74 ( 592) hydrogen bonds : angle 5.68759 / 4.01 ( 1704) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 236 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.7501 (tm) cc_final: 0.7279 (mt) REVERT: A 158 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9092 (pp) REVERT: A 229 LYS cc_start: 0.8980 (tmtp) cc_final: 0.8746 (ttmt) REVERT: A 272 GLU cc_start: 0.8313 (tm-30) cc_final: 0.7878 (tm-30) REVERT: A 388 ASP cc_start: 0.8234 (m-30) cc_final: 0.7799 (t0) REVERT: B 77 LEU cc_start: 0.7492 (tm) cc_final: 0.7291 (mt) REVERT: B 229 LYS cc_start: 0.8974 (tmtp) cc_final: 0.8755 (ttmt) REVERT: B 272 GLU cc_start: 0.8304 (tm-30) cc_final: 0.7858 (tm-30) REVERT: B 388 ASP cc_start: 0.8204 (m-30) cc_final: 0.7820 (t0) REVERT: C 77 LEU cc_start: 0.7528 (tm) cc_final: 0.7309 (mt) REVERT: C 272 GLU cc_start: 0.8356 (tm-30) cc_final: 0.7939 (tm-30) REVERT: C 388 ASP cc_start: 0.8222 (m-30) cc_final: 0.7971 (t0) REVERT: D 77 LEU cc_start: 0.7519 (tm) cc_final: 0.7295 (mt) REVERT: D 158 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.9067 (pp) REVERT: D 229 LYS cc_start: 0.8981 (tmtp) cc_final: 0.8738 (ttmt) REVERT: D 272 GLU cc_start: 0.8351 (tm-30) cc_final: 0.7908 (tm-30) REVERT: D 388 ASP cc_start: 0.8216 (m-30) cc_final: 0.7814 (t0) outliers start: 8 outliers final: 0 residues processed: 240 average time/residue: 0.1435 time to fit residues: 47.9091 Evaluate side-chains 97 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 95 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain D residue 158 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.118507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.087885 restraints weight = 23964.204| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.17 r_work: 0.2958 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13484 Z= 0.131 Angle : 0.716 8.558 18238 Z= 0.336 Chirality : 0.043 0.178 2124 Planarity : 0.005 0.047 2200 Dihedral : 17.816 175.112 2252 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.01 % Allowed : 10.37 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.39 (0.21), residues: 1568 helix: -0.37 (0.17), residues: 944 sheet: -1.62 (0.47), residues: 92 loop : -1.60 (0.28), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 124 TYR 0.018 0.001 TYR B 128 PHE 0.009 0.001 PHE A 242 TRP 0.012 0.001 TRP A 264 HIS 0.002 0.001 HIS C 281 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (13484) covalent geometry : angle 0.71580 / 0.34 (18236) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03903 / 2.65 ( 592) hydrogen bonds : angle 3.89250 / 2.74 ( 1704) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 131 time to evaluate : 0.580 Fit side-chains REVERT: A 77 LEU cc_start: 0.7514 (tm) cc_final: 0.7259 (mt) REVERT: A 171 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8857 (tp) REVERT: A 272 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7861 (tm-30) REVERT: A 369 MET cc_start: 0.8202 (mmm) cc_final: 0.7951 (mmt) REVERT: A 388 ASP cc_start: 0.8508 (m-30) cc_final: 0.7963 (t0) REVERT: B 28 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8805 (mm) REVERT: B 77 LEU cc_start: 0.7353 (tm) cc_final: 0.7105 (mt) REVERT: B 272 GLU cc_start: 0.8321 (tm-30) cc_final: 0.7907 (tm-30) REVERT: B 369 MET cc_start: 0.8287 (mmm) cc_final: 0.8029 (mmt) REVERT: B 388 ASP cc_start: 0.8488 (m-30) cc_final: 0.7984 (t0) REVERT: C 77 LEU cc_start: 0.7391 (tm) cc_final: 0.7122 (mt) REVERT: C 171 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8843 (tp) REVERT: C 272 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7904 (tm-30) REVERT: C 369 MET cc_start: 0.8203 (mmm) cc_final: 0.7952 (mmt) REVERT: C 388 ASP cc_start: 0.8521 (m-30) cc_final: 0.8035 (t0) REVERT: D 77 LEU cc_start: 0.7552 (tm) cc_final: 0.7283 (mt) REVERT: D 171 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8851 (tp) REVERT: D 272 GLU cc_start: 0.8266 (tm-30) cc_final: 0.7871 (tm-30) REVERT: D 369 MET cc_start: 0.8162 (mmm) cc_final: 0.7919 (mmt) REVERT: D 388 ASP cc_start: 0.8518 (m-30) cc_final: 0.7996 (t0) outliers start: 41 outliers final: 8 residues processed: 170 average time/residue: 0.1314 time to fit residues: 32.2750 Evaluate side-chains 108 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 203 ILE Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 203 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 142 optimal weight: 6.9990 chunk 56 optimal weight: 0.0170 chunk 8 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 96 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 148 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 overall best weight: 2.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.114251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.086841 restraints weight = 24452.776| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.37 r_work: 0.2849 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 13484 Z= 0.232 Angle : 0.769 14.591 18238 Z= 0.355 Chirality : 0.046 0.198 2124 Planarity : 0.005 0.035 2200 Dihedral : 17.641 178.419 2248 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.46 % Allowed : 13.01 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.22), residues: 1568 helix: 0.45 (0.18), residues: 944 sheet: -1.01 (0.48), residues: 92 loop : -1.26 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 374 TYR 0.021 0.002 TYR B 11 PHE 0.008 0.001 PHE B 36 TRP 0.013 0.002 TRP A 264 HIS 0.004 0.001 HIS B 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00564 / 0.23 (13484) covalent geometry : angle 0.76907 / 0.35 (18236) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.04379 / 2.99 ( 592) hydrogen bonds : angle 3.77794 / 2.68 ( 1704) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 104 time to evaluate : 0.523 Fit side-chains REVERT: A 60 LEU cc_start: 0.8317 (tp) cc_final: 0.8110 (tt) REVERT: A 77 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7090 (mt) REVERT: A 272 GLU cc_start: 0.8399 (tm-30) cc_final: 0.7969 (tm-30) REVERT: A 334 MET cc_start: 0.7812 (ttm) cc_final: 0.7508 (mmm) REVERT: A 369 MET cc_start: 0.8320 (mmm) cc_final: 0.8115 (mmm) REVERT: A 388 ASP cc_start: 0.8669 (m-30) cc_final: 0.8111 (t0) REVERT: B 60 LEU cc_start: 0.8292 (tp) cc_final: 0.8077 (tt) REVERT: B 77 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7097 (mt) REVERT: B 272 GLU cc_start: 0.8434 (tm-30) cc_final: 0.7997 (tm-30) REVERT: B 369 MET cc_start: 0.8307 (mmm) cc_final: 0.8104 (mmm) REVERT: B 388 ASP cc_start: 0.8658 (m-30) cc_final: 0.8132 (t0) REVERT: C 77 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7094 (mt) REVERT: C 171 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8855 (tp) REVERT: C 230 LEU cc_start: 0.9091 (OUTLIER) cc_final: 0.8889 (mp) REVERT: C 272 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8008 (tm-30) REVERT: C 369 MET cc_start: 0.8182 (mmm) cc_final: 0.7981 (mmm) REVERT: C 388 ASP cc_start: 0.8644 (m-30) cc_final: 0.8136 (t0) REVERT: D 60 LEU cc_start: 0.8299 (tp) cc_final: 0.8080 (tt) REVERT: D 77 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7104 (mt) REVERT: D 171 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8862 (tp) REVERT: D 272 GLU cc_start: 0.8435 (tm-30) cc_final: 0.7994 (tm-30) REVERT: D 334 MET cc_start: 0.7932 (ttm) cc_final: 0.7590 (mmm) REVERT: D 369 MET cc_start: 0.8182 (mmm) cc_final: 0.7969 (mmm) REVERT: D 388 ASP cc_start: 0.8655 (m-30) cc_final: 0.8122 (t0) outliers start: 47 outliers final: 26 residues processed: 143 average time/residue: 0.1134 time to fit residues: 24.4419 Evaluate side-chains 115 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 82 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 125 ILE Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 314 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 88 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 76 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 54 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.116350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.088521 restraints weight = 24203.582| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.39 r_work: 0.2888 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13484 Z= 0.123 Angle : 0.670 13.691 18238 Z= 0.304 Chirality : 0.042 0.177 2124 Planarity : 0.004 0.027 2200 Dihedral : 17.028 179.819 2248 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.34 % Allowed : 13.60 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.23), residues: 1568 helix: 0.93 (0.18), residues: 952 sheet: -0.46 (0.51), residues: 92 loop : -0.95 (0.30), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 399 TYR 0.011 0.001 TYR C 128 PHE 0.006 0.001 PHE A 242 TRP 0.014 0.001 TRP C 264 HIS 0.002 0.000 HIS C 149 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (13484) covalent geometry : angle 0.66983 / 0.30 (18236) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03514 / 2.38 ( 592) hydrogen bonds : angle 3.45169 / 2.45 ( 1704) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 116 time to evaluate : 0.627 Fit side-chains REVERT: A 60 LEU cc_start: 0.8341 (tp) cc_final: 0.8140 (tt) REVERT: A 77 LEU cc_start: 0.7472 (OUTLIER) cc_final: 0.7095 (mt) REVERT: A 221 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9011 (tt) REVERT: A 272 GLU cc_start: 0.8272 (tm-30) cc_final: 0.8021 (tm-30) REVERT: A 334 MET cc_start: 0.7803 (ttm) cc_final: 0.7471 (tpp) REVERT: A 369 MET cc_start: 0.8184 (mmm) cc_final: 0.7979 (mmm) REVERT: A 388 ASP cc_start: 0.8653 (m-30) cc_final: 0.8015 (t0) REVERT: B 60 LEU cc_start: 0.8325 (tp) cc_final: 0.8118 (tt) REVERT: B 77 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7115 (mt) REVERT: B 221 LEU cc_start: 0.9419 (OUTLIER) cc_final: 0.9005 (tt) REVERT: B 235 ARG cc_start: 0.8811 (ttp80) cc_final: 0.8597 (ttt180) REVERT: B 272 GLU cc_start: 0.8336 (tm-30) cc_final: 0.8086 (tm-30) REVERT: B 334 MET cc_start: 0.7860 (ttm) cc_final: 0.7492 (tpp) REVERT: B 369 MET cc_start: 0.8197 (mmm) cc_final: 0.7995 (mmm) REVERT: B 388 ASP cc_start: 0.8654 (m-30) cc_final: 0.8032 (t0) REVERT: C 77 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7083 (mt) REVERT: C 171 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8874 (tp) REVERT: C 221 LEU cc_start: 0.9423 (OUTLIER) cc_final: 0.9018 (tt) REVERT: C 272 GLU cc_start: 0.8358 (tm-30) cc_final: 0.8122 (tm-30) REVERT: C 334 MET cc_start: 0.7906 (ttm) cc_final: 0.7509 (tpp) REVERT: C 388 ASP cc_start: 0.8603 (m-30) cc_final: 0.8034 (t0) REVERT: D 77 LEU cc_start: 0.7476 (OUTLIER) cc_final: 0.7101 (mt) REVERT: D 221 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9011 (tt) REVERT: D 272 GLU cc_start: 0.8317 (tm-30) cc_final: 0.8074 (tm-30) REVERT: D 334 MET cc_start: 0.7943 (ttm) cc_final: 0.7513 (tpp) REVERT: D 369 MET cc_start: 0.8189 (mmm) cc_final: 0.7968 (mmm) REVERT: D 388 ASP cc_start: 0.8648 (m-30) cc_final: 0.8024 (t0) outliers start: 59 outliers final: 32 residues processed: 165 average time/residue: 0.1068 time to fit residues: 27.3832 Evaluate side-chains 138 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 97 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 20 optimal weight: 1.9990 chunk 88 optimal weight: 0.7980 chunk 87 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 152 optimal weight: 6.9990 chunk 77 optimal weight: 0.3980 chunk 38 optimal weight: 0.9990 chunk 139 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 112 optimal weight: 4.9990 chunk 47 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.117908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.090584 restraints weight = 24294.161| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 2.29 r_work: 0.2929 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13484 Z= 0.106 Angle : 0.670 15.537 18238 Z= 0.295 Chirality : 0.041 0.175 2124 Planarity : 0.004 0.025 2200 Dihedral : 16.302 179.999 2248 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.60 % Allowed : 15.22 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.23), residues: 1568 helix: 1.16 (0.18), residues: 960 sheet: -0.41 (0.54), residues: 92 loop : -0.82 (0.31), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 399 TYR 0.027 0.001 TYR B 11 PHE 0.004 0.001 PHE D 40 TRP 0.012 0.001 TRP D 264 HIS 0.002 0.000 HIS A 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (13484) covalent geometry : angle 0.67023 / 0.29 (18236) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03182 / 2.15 ( 592) hydrogen bonds : angle 3.23417 / 2.28 ( 1704) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 106 time to evaluate : 0.626 Fit side-chains REVERT: A 77 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7113 (mt) REVERT: A 171 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8818 (tp) REVERT: A 221 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9038 (tt) REVERT: A 334 MET cc_start: 0.7943 (ttm) cc_final: 0.7600 (tpp) REVERT: A 369 MET cc_start: 0.8243 (mmm) cc_final: 0.8025 (mmm) REVERT: A 388 ASP cc_start: 0.8516 (m-30) cc_final: 0.8066 (t0) REVERT: B 77 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7135 (mt) REVERT: B 221 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9038 (tt) REVERT: B 235 ARG cc_start: 0.8833 (ttp80) cc_final: 0.8616 (ttt180) REVERT: B 334 MET cc_start: 0.7974 (ttm) cc_final: 0.7611 (tpp) REVERT: B 369 MET cc_start: 0.8362 (mmm) cc_final: 0.8128 (mmm) REVERT: B 388 ASP cc_start: 0.8523 (m-30) cc_final: 0.8068 (t0) REVERT: C 77 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7108 (mt) REVERT: C 171 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8825 (tp) REVERT: C 221 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9058 (tt) REVERT: C 334 MET cc_start: 0.7890 (ttm) cc_final: 0.7574 (tpp) REVERT: C 388 ASP cc_start: 0.8510 (m-30) cc_final: 0.8071 (t0) REVERT: D 77 LEU cc_start: 0.7482 (OUTLIER) cc_final: 0.7098 (mt) REVERT: D 171 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8819 (tp) REVERT: D 221 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9054 (tt) REVERT: D 334 MET cc_start: 0.7987 (ttm) cc_final: 0.7621 (tpp) REVERT: D 369 MET cc_start: 0.8206 (mmm) cc_final: 0.7985 (mmm) REVERT: D 388 ASP cc_start: 0.8519 (m-30) cc_final: 0.8078 (t0) outliers start: 49 outliers final: 26 residues processed: 147 average time/residue: 0.1072 time to fit residues: 24.0702 Evaluate side-chains 130 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 93 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 102 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 41 optimal weight: 0.0870 chunk 126 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.118725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.090458 restraints weight = 24288.850| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 2.31 r_work: 0.2931 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13484 Z= 0.105 Angle : 0.688 18.064 18238 Z= 0.300 Chirality : 0.041 0.180 2124 Planarity : 0.004 0.024 2200 Dihedral : 15.558 179.855 2248 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.90 % Allowed : 16.18 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.23), residues: 1568 helix: 1.39 (0.18), residues: 944 sheet: -0.41 (0.56), residues: 92 loop : -0.67 (0.30), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 399 TYR 0.009 0.001 TYR D 128 PHE 0.005 0.001 PHE D 40 TRP 0.011 0.001 TRP B 264 HIS 0.002 0.000 HIS B 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (13484) covalent geometry : angle 0.68790 / 0.30 (18236) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03113 / 2.09 ( 592) hydrogen bonds : angle 3.17117 / 2.22 ( 1704) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 104 time to evaluate : 0.548 Fit side-chains REVERT: A 62 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8106 (mm) REVERT: A 77 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7111 (mt) REVERT: A 171 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8829 (tp) REVERT: A 221 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9055 (tt) REVERT: A 334 MET cc_start: 0.7918 (ttm) cc_final: 0.7464 (tpt) REVERT: A 388 ASP cc_start: 0.8478 (m-30) cc_final: 0.8202 (t0) REVERT: B 77 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7127 (mt) REVERT: B 221 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9056 (tt) REVERT: B 235 ARG cc_start: 0.8822 (ttp80) cc_final: 0.8614 (ttt180) REVERT: B 334 MET cc_start: 0.7942 (ttm) cc_final: 0.7480 (tpt) REVERT: B 388 ASP cc_start: 0.8495 (m-30) cc_final: 0.8201 (t0) REVERT: C 77 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7025 (mt) REVERT: C 171 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8832 (tp) REVERT: C 221 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9059 (tt) REVERT: C 334 MET cc_start: 0.7968 (ttm) cc_final: 0.7484 (tpt) REVERT: C 369 MET cc_start: 0.8616 (mmt) cc_final: 0.8384 (mmt) REVERT: C 388 ASP cc_start: 0.8484 (m-30) cc_final: 0.8220 (t0) REVERT: D 62 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8135 (mm) REVERT: D 77 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7118 (mt) REVERT: D 171 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8834 (tp) REVERT: D 221 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9047 (tt) REVERT: D 334 MET cc_start: 0.7964 (ttm) cc_final: 0.7648 (tpp) REVERT: D 369 MET cc_start: 0.8137 (mmm) cc_final: 0.7932 (mmm) REVERT: D 388 ASP cc_start: 0.8489 (m-30) cc_final: 0.8212 (t0) outliers start: 53 outliers final: 31 residues processed: 148 average time/residue: 0.1123 time to fit residues: 25.5592 Evaluate side-chains 134 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 90 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 143 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 116 optimal weight: 0.3980 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 7.9990 chunk 147 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 153 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.118374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.091169 restraints weight = 24107.703| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 2.22 r_work: 0.2944 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13484 Z= 0.104 Angle : 0.656 15.458 18238 Z= 0.287 Chirality : 0.041 0.186 2124 Planarity : 0.004 0.024 2200 Dihedral : 15.077 179.934 2248 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.82 % Allowed : 16.25 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.23), residues: 1568 helix: 1.46 (0.18), residues: 944 sheet: -0.66 (0.55), residues: 92 loop : -0.57 (0.30), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 399 TYR 0.022 0.001 TYR B 11 PHE 0.005 0.001 PHE D 40 TRP 0.011 0.001 TRP B 264 HIS 0.002 0.000 HIS D 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 (13484) covalent geometry : angle 0.65596 / 0.29 (18236) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03038 / 2.04 ( 592) hydrogen bonds : angle 3.19509 / 2.24 ( 1704) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 89 time to evaluate : 0.602 Fit side-chains REVERT: A 62 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8073 (mm) REVERT: A 77 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.7077 (mt) REVERT: A 221 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9073 (tt) REVERT: A 334 MET cc_start: 0.7942 (ttm) cc_final: 0.7669 (tpp) REVERT: A 388 ASP cc_start: 0.8425 (m-30) cc_final: 0.8046 (t0) REVERT: B 77 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7093 (mt) REVERT: B 221 LEU cc_start: 0.9328 (OUTLIER) cc_final: 0.9061 (tt) REVERT: B 334 MET cc_start: 0.7927 (ttm) cc_final: 0.7688 (tpp) REVERT: B 388 ASP cc_start: 0.8444 (m-30) cc_final: 0.8059 (t0) REVERT: C 77 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.7020 (mt) REVERT: C 171 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8822 (tp) REVERT: C 221 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9085 (tt) REVERT: C 369 MET cc_start: 0.8679 (mmt) cc_final: 0.8412 (mmt) REVERT: C 388 ASP cc_start: 0.8405 (m-30) cc_final: 0.8087 (t0) REVERT: D 62 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8078 (mm) REVERT: D 77 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.7046 (mt) REVERT: D 171 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8820 (tp) REVERT: D 221 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9072 (tt) REVERT: D 334 MET cc_start: 0.7933 (ttm) cc_final: 0.7556 (tpt) REVERT: D 369 MET cc_start: 0.8176 (mmm) cc_final: 0.7972 (mmm) REVERT: D 388 ASP cc_start: 0.8417 (m-30) cc_final: 0.8079 (t0) outliers start: 52 outliers final: 34 residues processed: 131 average time/residue: 0.1122 time to fit residues: 22.4748 Evaluate side-chains 126 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 80 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 152 optimal weight: 20.0000 chunk 67 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 96 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.090585 restraints weight = 24074.713| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.20 r_work: 0.2947 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 13484 Z= 0.106 Angle : 0.645 13.065 18238 Z= 0.285 Chirality : 0.041 0.185 2124 Planarity : 0.004 0.024 2200 Dihedral : 14.847 179.405 2248 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 3.53 % Allowed : 16.99 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.23), residues: 1568 helix: 1.49 (0.18), residues: 948 sheet: -0.57 (0.56), residues: 92 loop : -0.42 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 374 TYR 0.034 0.001 TYR D 11 PHE 0.005 0.001 PHE D 40 TRP 0.011 0.001 TRP B 264 HIS 0.002 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (13484) covalent geometry : angle 0.64459 / 0.29 (18236) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03045 / 2.04 ( 592) hydrogen bonds : angle 3.19827 / 2.24 ( 1704) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 90 time to evaluate : 0.525 Fit side-chains REVERT: A 62 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.8117 (mm) REVERT: A 77 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7078 (mt) REVERT: A 221 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9099 (tt) REVERT: A 388 ASP cc_start: 0.8402 (m-30) cc_final: 0.7966 (t0) REVERT: B 77 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7016 (mt) REVERT: B 221 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9094 (tt) REVERT: B 388 ASP cc_start: 0.8417 (m-30) cc_final: 0.7979 (t0) REVERT: C 62 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8019 (mm) REVERT: C 77 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7051 (mt) REVERT: C 171 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8812 (tp) REVERT: C 221 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9098 (tt) REVERT: C 369 MET cc_start: 0.8716 (mmt) cc_final: 0.8436 (mmt) REVERT: C 388 ASP cc_start: 0.8414 (m-30) cc_final: 0.7991 (t0) REVERT: D 62 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8049 (mm) REVERT: D 77 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7072 (mt) REVERT: D 171 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8807 (tp) REVERT: D 221 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9097 (tt) REVERT: D 369 MET cc_start: 0.8129 (mmm) cc_final: 0.7911 (mmm) REVERT: D 388 ASP cc_start: 0.8433 (m-30) cc_final: 0.7975 (t0) outliers start: 48 outliers final: 29 residues processed: 130 average time/residue: 0.1097 time to fit residues: 22.0683 Evaluate side-chains 124 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 82 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 86 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 147 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.089186 restraints weight = 24363.097| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.23 r_work: 0.2947 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13484 Z= 0.110 Angle : 0.686 12.946 18238 Z= 0.297 Chirality : 0.042 0.181 2124 Planarity : 0.004 0.024 2200 Dihedral : 14.758 179.089 2248 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.46 % Allowed : 17.28 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.23), residues: 1568 helix: 1.53 (0.18), residues: 948 sheet: -0.63 (0.56), residues: 92 loop : -0.44 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 374 TYR 0.008 0.001 TYR C 128 PHE 0.005 0.001 PHE D 40 TRP 0.011 0.001 TRP B 264 HIS 0.002 0.001 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.11 (13484) covalent geometry : angle 0.68557 / 0.30 (18236) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.03038 / 2.04 ( 592) hydrogen bonds : angle 3.19550 / 2.24 ( 1704) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 94 time to evaluate : 0.540 Fit side-chains REVERT: A 62 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8055 (mm) REVERT: A 77 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7096 (mt) REVERT: A 221 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9093 (tt) REVERT: A 369 MET cc_start: 0.8384 (mmm) cc_final: 0.8146 (mmm) REVERT: A 388 ASP cc_start: 0.8390 (m-30) cc_final: 0.7947 (t0) REVERT: B 62 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8001 (mm) REVERT: B 77 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7133 (mt) REVERT: B 221 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9086 (tt) REVERT: B 303 LYS cc_start: 0.7407 (mptt) cc_final: 0.6620 (mmtt) REVERT: B 369 MET cc_start: 0.8369 (mmm) cc_final: 0.8125 (mmm) REVERT: B 388 ASP cc_start: 0.8390 (m-30) cc_final: 0.7965 (t0) REVERT: C 62 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8014 (mm) REVERT: C 77 LEU cc_start: 0.7529 (OUTLIER) cc_final: 0.7067 (mt) REVERT: C 221 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9085 (tt) REVERT: C 369 MET cc_start: 0.8722 (mmt) cc_final: 0.8445 (mmt) REVERT: C 388 ASP cc_start: 0.8394 (m-30) cc_final: 0.7991 (t0) REVERT: D 62 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8046 (mm) REVERT: D 77 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7075 (mt) REVERT: D 221 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9099 (tt) REVERT: D 369 MET cc_start: 0.8151 (mmm) cc_final: 0.7932 (mmm) REVERT: D 388 ASP cc_start: 0.8410 (m-30) cc_final: 0.7988 (t0) outliers start: 47 outliers final: 31 residues processed: 131 average time/residue: 0.1159 time to fit residues: 23.0425 Evaluate side-chains 126 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 83 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 314 ILE Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 80 optimal weight: 0.3980 chunk 116 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 73 optimal weight: 0.3980 chunk 65 optimal weight: 0.7980 chunk 132 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.118280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.087952 restraints weight = 24245.274| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.16 r_work: 0.2951 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13484 Z= 0.101 Angle : 0.682 12.718 18238 Z= 0.295 Chirality : 0.041 0.180 2124 Planarity : 0.004 0.025 2200 Dihedral : 14.639 179.007 2248 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.24 % Allowed : 17.65 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.23), residues: 1568 helix: 1.77 (0.18), residues: 924 sheet: -0.65 (0.56), residues: 92 loop : -0.49 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 374 TYR 0.035 0.001 TYR A 11 PHE 0.005 0.001 PHE D 40 TRP 0.011 0.001 TRP B 264 HIS 0.002 0.000 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00228 / 0.10 (13484) covalent geometry : angle 0.68247 / 0.30 (18236) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.02909 / 1.95 ( 592) hydrogen bonds : angle 3.14461 / 2.21 ( 1704) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3136 Ramachandran restraints generated. 1568 Oldfield, 0 Emsley, 1568 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 90 time to evaluate : 0.520 Fit side-chains REVERT: A 62 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.8043 (mm) REVERT: A 77 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7111 (mt) REVERT: A 303 LYS cc_start: 0.7465 (mptt) cc_final: 0.6699 (mmtt) REVERT: A 369 MET cc_start: 0.8448 (mmm) cc_final: 0.8193 (mmm) REVERT: A 388 ASP cc_start: 0.8333 (m-30) cc_final: 0.7935 (t0) REVERT: B 62 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7929 (mm) REVERT: B 77 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7155 (mt) REVERT: B 221 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9078 (tt) REVERT: B 303 LYS cc_start: 0.7464 (mptt) cc_final: 0.6699 (mmtt) REVERT: B 369 MET cc_start: 0.8427 (mmm) cc_final: 0.8165 (mmm) REVERT: B 388 ASP cc_start: 0.8336 (m-30) cc_final: 0.7939 (t0) REVERT: C 62 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7938 (mm) REVERT: C 77 LEU cc_start: 0.7546 (OUTLIER) cc_final: 0.7084 (mt) REVERT: C 221 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9071 (tt) REVERT: C 369 MET cc_start: 0.8710 (mmt) cc_final: 0.8472 (mmm) REVERT: C 388 ASP cc_start: 0.8351 (m-30) cc_final: 0.7957 (t0) REVERT: D 62 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7977 (mm) REVERT: D 77 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7114 (mt) REVERT: D 221 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.9083 (tt) REVERT: D 369 MET cc_start: 0.8096 (mmm) cc_final: 0.7860 (mmm) REVERT: D 388 ASP cc_start: 0.8382 (m-30) cc_final: 0.8068 (t0) outliers start: 44 outliers final: 31 residues processed: 124 average time/residue: 0.1115 time to fit residues: 21.3430 Evaluate side-chains 127 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 24 LEU Chi-restraints excluded: chain A residue 26 TYR Chi-restraints excluded: chain A residue 62 LEU Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain B residue 19 ILE Chi-restraints excluded: chain B residue 24 LEU Chi-restraints excluded: chain B residue 26 TYR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 230 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 26 TYR Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 77 LEU Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 205 LEU Chi-restraints excluded: chain C residue 221 LEU Chi-restraints excluded: chain C residue 389 LEU Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 24 LEU Chi-restraints excluded: chain D residue 26 TYR Chi-restraints excluded: chain D residue 60 LEU Chi-restraints excluded: chain D residue 62 LEU Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 171 LEU Chi-restraints excluded: chain D residue 205 LEU Chi-restraints excluded: chain D residue 221 LEU Chi-restraints excluded: chain D residue 230 LEU Chi-restraints excluded: chain D residue 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 116 optimal weight: 0.0270 chunk 84 optimal weight: 0.1980 chunk 121 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 chunk 136 optimal weight: 1.9990 chunk 117 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.5842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.118722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.088377 restraints weight = 24246.712| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.16 r_work: 0.2966 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13484 Z= 0.099 Angle : 0.679 13.084 18238 Z= 0.291 Chirality : 0.041 0.178 2124 Planarity : 0.003 0.023 2200 Dihedral : 14.504 178.982 2248 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.38 % Allowed : 17.65 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.23), residues: 1568 helix: 1.81 (0.18), residues: 924 sheet: -0.61 (0.57), residues: 92 loop : -0.47 (0.29), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 374 TYR 0.006 0.001 TYR C 128 PHE 0.005 0.001 PHE D 40 TRP 0.011 0.001 TRP B 264 HIS 0.002 0.000 HIS C 232 Details of bonding type rmsd/Z covalent geometry : bond 0.00219 / 0.10 (13484) covalent geometry : angle 0.67883 / 0.29 (18236) SS BOND : angle 0.00000 / 0.00 ( 2) hydrogen bonds : bond 0.02848 / 1.91 ( 592) hydrogen bonds : angle 3.09780 / 2.17 ( 1704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2753.29 seconds wall clock time: 48 minutes 12.85 seconds (2892.85 seconds total)