Starting phenix.real_space_refine on Tue Nov 18 10:35:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cjt_7483/11_2025/6cjt_7483.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cjt_7483/11_2025/6cjt_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6cjt_7483/11_2025/6cjt_7483.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cjt_7483/11_2025/6cjt_7483.map" model { file = "/net/cci-nas-00/data/ceres_data/6cjt_7483/11_2025/6cjt_7483.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cjt_7483/11_2025/6cjt_7483.cif" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/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: 184 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: 184 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: 3.41, per 1000 atoms: 0.26 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: 1.12 Conformation dependent library (CDL) restraints added in 572.1 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: 0.42 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: 2.40 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 - 35.00: 8072 35.00 - 70.00: 184 70.00 - 105.01: 36 105.01 - 140.01: 28 140.01 - 175.01: 12 Dihedral angle restraints: 8332 sinusoidal: 3672 harmonic: 4660 Sorted by residual: 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 dihedral pdb=" CA LEU A 276 " pdb=" C LEU A 276 " pdb=" N LYS A 277 " pdb=" CA LYS A 277 " ideal model delta harmonic sigma weight residual 180.00 156.83 23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA LEU C 276 " pdb=" C LEU C 276 " pdb=" N LYS C 277 " pdb=" CA LYS C 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 8329 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: 1.130 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 13.490 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:1.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 18.918 175.011 5320 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 covalent geometry : bond 0.00962 (13484) covalent geometry : angle 1.42986 (18236) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.13946 ( 592) hydrogen bonds : angle 5.68759 ( 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 : 0.537 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: 0.9091 (pp) REVERT: A 229 LYS cc_start: 0.8979 (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: 0.7800 (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: 0.7938 (tm-30) REVERT: C 388 ASP cc_start: 0.8222 (m-30) cc_final: 0.7970 (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: 0.9066 (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: 0.7815 (t0) outliers start: 8 outliers final: 0 residues processed: 240 average time/residue: 0.1477 time to fit residues: 48.6208 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 : 0.339 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3600 r_free = 0.3600 target = 0.118554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.089891 restraints weight = 24004.010| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.28 r_work: 0.2946 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2017 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 8.561 18238 Z= 0.335 Chirality : 0.043 0.172 2124 Planarity : 0.005 0.046 2200 Dihedral : 21.891 175.278 2320 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.16 % Allowed : 10.29 % Favored : 86.54 % 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: -1.37 (0.21), residues: 1568 helix: -0.35 (0.17), residues: 944 sheet: -1.63 (0.46), residues: 92 loop : -1.60 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 374 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 149 Details of bonding type rmsd covalent geometry : bond 0.00300 (13484) covalent geometry : angle 0.71564 (18236) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03878 ( 592) hydrogen bonds : angle 3.88084 ( 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 174 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 131 time to evaluate : 0.409 Fit side-chains REVERT: A 77 LEU cc_start: 0.7499 (tm) cc_final: 0.7253 (mt) REVERT: A 171 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8849 (tp) REVERT: A 272 GLU cc_start: 0.8261 (tm-30) cc_final: 0.7886 (tm-30) REVERT: A 369 MET cc_start: 0.8192 (mmm) cc_final: 0.7963 (mmt) REVERT: A 388 ASP cc_start: 0.8527 (m-30) cc_final: 0.8025 (t0) REVERT: B 28 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8836 (mm) REVERT: B 77 LEU cc_start: 0.7335 (tm) cc_final: 0.7097 (mt) REVERT: B 171 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8844 (tp) REVERT: B 272 GLU cc_start: 0.8329 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 369 MET cc_start: 0.8290 (mmm) cc_final: 0.8052 (mmt) REVERT: B 388 ASP cc_start: 0.8505 (m-30) cc_final: 0.8043 (t0) REVERT: C 77 LEU cc_start: 0.7372 (tm) cc_final: 0.7114 (mt) REVERT: C 171 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8837 (tp) REVERT: C 272 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7931 (tm-30) REVERT: C 369 MET cc_start: 0.8190 (mmm) cc_final: 0.7965 (mmt) REVERT: C 388 ASP cc_start: 0.8543 (m-30) cc_final: 0.8171 (t0) REVERT: D 77 LEU cc_start: 0.7536 (tm) cc_final: 0.7279 (mt) REVERT: D 171 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8846 (tp) REVERT: D 272 GLU cc_start: 0.8273 (tm-30) cc_final: 0.7930 (tm-30) REVERT: D 369 MET cc_start: 0.8148 (mmm) cc_final: 0.7927 (mmt) REVERT: D 388 ASP cc_start: 0.8540 (m-30) cc_final: 0.8060 (t0) outliers start: 43 outliers final: 8 residues processed: 172 average time/residue: 0.1313 time to fit residues: 32.4699 Evaluate side-chains 110 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.523 ------------------------------------------------------------------------------- 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 171 LEU 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: 3.9990 chunk 8 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 96 optimal weight: 0.8980 chunk 6 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 117 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.113153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.086336 restraints weight = 24621.535| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.61 r_work: 0.2813 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 13484 Z= 0.277 Angle : 0.818 15.426 18238 Z= 0.379 Chirality : 0.047 0.201 2124 Planarity : 0.005 0.036 2200 Dihedral : 21.409 178.697 2316 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.90 % Allowed : 12.72 % Favored : 83.38 % 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: -0.39 (0.22), residues: 1568 helix: 0.44 (0.18), residues: 944 sheet: -0.99 (0.48), residues: 92 loop : -1.26 (0.29), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 238 TYR 0.023 0.002 TYR B 11 PHE 0.009 0.002 PHE B 36 TRP 0.013 0.002 TRP B 264 HIS 0.004 0.001 HIS D 149 Details of bonding type rmsd covalent geometry : bond 0.00664 (13484) covalent geometry : angle 0.81760 (18236) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.04649 ( 592) hydrogen bonds : angle 3.87248 ( 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 152 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 99 time to evaluate : 0.328 Fit side-chains REVERT: A 77 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.7118 (mt) REVERT: A 171 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8842 (tp) REVERT: A 230 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8848 (mt) REVERT: A 272 GLU cc_start: 0.8456 (tm-30) cc_final: 0.7998 (tm-30) REVERT: A 277 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8695 (ttpt) REVERT: A 334 MET cc_start: 0.7844 (ttm) cc_final: 0.7473 (mmm) REVERT: A 369 MET cc_start: 0.8239 (mmm) cc_final: 0.8021 (mmm) REVERT: A 388 ASP cc_start: 0.8748 (m-30) cc_final: 0.8133 (t0) REVERT: B 77 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7124 (mt) REVERT: B 171 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8841 (tp) REVERT: B 230 LEU cc_start: 0.9110 (OUTLIER) cc_final: 0.8857 (mt) REVERT: B 369 MET cc_start: 0.8245 (mmm) cc_final: 0.8025 (mmm) REVERT: B 388 ASP cc_start: 0.8731 (m-30) cc_final: 0.8153 (t0) REVERT: C 77 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7087 (mt) REVERT: C 171 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8870 (tp) REVERT: C 230 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8866 (mt) REVERT: C 272 GLU cc_start: 0.8487 (tm-30) cc_final: 0.8027 (tm-30) REVERT: C 369 MET cc_start: 0.8233 (mmm) cc_final: 0.8008 (mmm) REVERT: C 388 ASP cc_start: 0.8729 (m-30) cc_final: 0.8171 (t0) REVERT: D 77 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.7096 (mt) REVERT: D 171 LEU cc_start: 0.9170 (OUTLIER) cc_final: 0.8830 (tp) REVERT: D 230 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8865 (mt) REVERT: D 272 GLU cc_start: 0.8481 (tm-30) cc_final: 0.8011 (tm-30) REVERT: D 334 MET cc_start: 0.7968 (ttm) cc_final: 0.7559 (mmm) REVERT: D 369 MET cc_start: 0.8213 (mmm) cc_final: 0.7995 (mmm) REVERT: D 388 ASP cc_start: 0.8728 (m-30) cc_final: 0.8153 (t0) outliers start: 53 outliers final: 28 residues processed: 143 average time/residue: 0.1087 time to fit residues: 23.3661 Evaluate side-chains 119 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 78 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 230 LEU Chi-restraints excluded: chain A residue 277 LYS 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 77 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 125 ILE Chi-restraints excluded: chain B residue 171 LEU 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 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 C residue 389 LEU 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 230 LEU Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 389 LEU 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: 0.0980 chunk 45 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 54 optimal weight: 0.5980 chunk 146 optimal weight: 2.9990 chunk 127 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3594 r_free = 0.3594 target = 0.117904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.090884 restraints weight = 24170.487| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.31 r_work: 0.2934 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 13484 Z= 0.106 Angle : 0.662 15.231 18238 Z= 0.299 Chirality : 0.042 0.178 2124 Planarity : 0.004 0.026 2200 Dihedral : 19.177 179.963 2316 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.97 % Allowed : 13.82 % Favored : 82.21 % 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: -0.52 (0.50), residues: 92 loop : -0.94 (0.30), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 399 TYR 0.011 0.001 TYR B 128 PHE 0.005 0.001 PHE A 242 TRP 0.014 0.001 TRP C 264 HIS 0.001 0.000 HIS B 292 Details of bonding type rmsd covalent geometry : bond 0.00243 (13484) covalent geometry : angle 0.66229 (18236) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03224 ( 592) hydrogen bonds : angle 3.38342 ( 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: 54 poor density : 121 time to evaluate : 0.530 Fit side-chains REVERT: A 77 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7127 (mt) REVERT: A 221 LEU cc_start: 0.9395 (OUTLIER) cc_final: 0.9030 (tt) REVERT: A 334 MET cc_start: 0.7761 (ttm) cc_final: 0.7481 (tpp) REVERT: A 369 MET cc_start: 0.8159 (mmm) cc_final: 0.7958 (mmm) REVERT: A 388 ASP cc_start: 0.8605 (m-30) cc_final: 0.7991 (t0) REVERT: B 77 LEU cc_start: 0.7481 (OUTLIER) cc_final: 0.7124 (mt) REVERT: B 221 LEU cc_start: 0.9403 (OUTLIER) cc_final: 0.9031 (tt) REVERT: B 334 MET cc_start: 0.7854 (ttm) cc_final: 0.7525 (tpp) REVERT: B 388 ASP cc_start: 0.8594 (m-30) cc_final: 0.8025 (t0) REVERT: C 77 LEU cc_start: 0.7473 (OUTLIER) cc_final: 0.7102 (mt) REVERT: C 221 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9029 (tt) REVERT: C 334 MET cc_start: 0.7872 (ttm) cc_final: 0.7532 (tpp) REVERT: C 388 ASP cc_start: 0.8584 (m-30) cc_final: 0.8017 (t0) REVERT: D 77 LEU cc_start: 0.7465 (OUTLIER) cc_final: 0.7097 (mt) REVERT: D 221 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.9033 (tt) REVERT: D 334 MET cc_start: 0.7910 (ttm) cc_final: 0.7528 (tpp) REVERT: D 369 MET cc_start: 0.8160 (mmm) cc_final: 0.7942 (mmm) REVERT: D 388 ASP cc_start: 0.8591 (m-30) cc_final: 0.8005 (t0) outliers start: 54 outliers final: 22 residues processed: 165 average time/residue: 0.1119 time to fit residues: 27.8957 Evaluate side-chains 124 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE 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 B residue 19 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 171 LEU 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 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 D residue 19 ILE Chi-restraints excluded: chain D residue 24 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 314 ILE 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: 2.9990 chunk 18 optimal weight: 0.9990 chunk 152 optimal weight: 5.9990 chunk 77 optimal weight: 0.0770 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 112 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 overall best weight: 0.6942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.117731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.090845 restraints weight = 24310.506| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 2.32 r_work: 0.2937 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.3123 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= 0.108 Angle : 0.699 17.238 18238 Z= 0.304 Chirality : 0.042 0.174 2124 Planarity : 0.004 0.025 2200 Dihedral : 17.439 179.739 2316 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.09 % Allowed : 16.40 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.22 (0.18), residues: 948 sheet: -0.43 (0.53), residues: 92 loop : -0.90 (0.30), residues: 528 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 0.005 0.001 PHE D 40 TRP 0.012 0.001 TRP D 264 HIS 0.002 0.000 HIS B 149 Details of bonding type rmsd covalent geometry : bond 0.00245 (13484) covalent geometry : angle 0.69906 (18236) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03191 ( 592) hydrogen bonds : angle 3.20873 ( 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 147 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 105 time to evaluate : 0.541 Fit side-chains REVERT: A 77 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7139 (mt) REVERT: A 171 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8835 (tp) REVERT: A 221 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9043 (tt) REVERT: A 334 MET cc_start: 0.7918 (ttm) cc_final: 0.7605 (tpp) REVERT: A 388 ASP cc_start: 0.8539 (m-30) cc_final: 0.8073 (t0) REVERT: B 77 LEU cc_start: 0.7595 (OUTLIER) cc_final: 0.7121 (mt) REVERT: B 171 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8831 (tp) REVERT: B 221 LEU cc_start: 0.9369 (OUTLIER) cc_final: 0.9050 (tt) REVERT: B 334 MET cc_start: 0.7926 (ttm) cc_final: 0.7611 (tpp) REVERT: B 388 ASP cc_start: 0.8530 (m-30) cc_final: 0.8083 (t0) REVERT: C 77 LEU cc_start: 0.7520 (OUTLIER) cc_final: 0.7118 (mt) REVERT: C 171 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8824 (tp) REVERT: C 221 LEU cc_start: 0.9358 (OUTLIER) cc_final: 0.9045 (tt) REVERT: C 334 MET cc_start: 0.7941 (ttm) cc_final: 0.7616 (tpp) REVERT: C 369 MET cc_start: 0.8174 (mmm) cc_final: 0.7973 (mmt) REVERT: C 388 ASP cc_start: 0.8541 (m-30) cc_final: 0.8085 (t0) REVERT: C 398 ASP cc_start: 0.8561 (m-30) cc_final: 0.8198 (t0) REVERT: D 77 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7109 (mt) REVERT: D 171 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8834 (tp) REVERT: D 221 LEU cc_start: 0.9368 (OUTLIER) cc_final: 0.9051 (tt) REVERT: D 334 MET cc_start: 0.7939 (ttm) cc_final: 0.7596 (tpp) REVERT: D 388 ASP cc_start: 0.8519 (m-30) cc_final: 0.8060 (t0) outliers start: 42 outliers final: 24 residues processed: 139 average time/residue: 0.1050 time to fit residues: 22.5691 Evaluate side-chains 126 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 90 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE 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 171 LEU 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 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: 2.9990 chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 130 optimal weight: 5.9990 chunk 41 optimal weight: 0.0980 chunk 126 optimal weight: 0.7980 chunk 116 optimal weight: 0.3980 chunk 85 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.118405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.091803 restraints weight = 24138.815| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.29 r_work: 0.2957 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3332 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= 0.100 Angle : 0.659 15.108 18238 Z= 0.288 Chirality : 0.041 0.187 2124 Planarity : 0.004 0.025 2200 Dihedral : 16.912 179.967 2316 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.68 % Allowed : 16.69 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.44 (0.18), residues: 940 sheet: -0.45 (0.56), residues: 92 loop : -0.57 (0.30), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 399 TYR 0.009 0.001 TYR B 128 PHE 0.005 0.001 PHE B 365 TRP 0.012 0.001 TRP A 264 HIS 0.002 0.000 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00222 (13484) covalent geometry : angle 0.65905 (18236) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.02991 ( 592) hydrogen bonds : angle 3.13960 ( 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 146 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 96 time to evaluate : 0.506 Fit side-chains REVERT: A 62 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8083 (mm) REVERT: A 77 LEU cc_start: 0.7457 (OUTLIER) cc_final: 0.7082 (mt) REVERT: A 221 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9066 (tt) REVERT: A 334 MET cc_start: 0.7880 (ttm) cc_final: 0.7638 (tpp) REVERT: A 388 ASP cc_start: 0.8456 (m-30) cc_final: 0.8199 (t0) REVERT: B 77 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7087 (mt) REVERT: B 171 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8822 (tp) REVERT: B 221 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9054 (tt) REVERT: B 334 MET cc_start: 0.7860 (ttm) cc_final: 0.7484 (tpt) REVERT: B 369 MET cc_start: 0.8630 (mmt) cc_final: 0.8375 (mmt) REVERT: B 388 ASP cc_start: 0.8454 (m-30) cc_final: 0.8192 (t0) REVERT: C 77 LEU cc_start: 0.7456 (OUTLIER) cc_final: 0.7066 (mt) REVERT: C 171 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8825 (tp) REVERT: C 221 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9070 (tt) REVERT: C 334 MET cc_start: 0.7936 (ttm) cc_final: 0.7503 (tpt) REVERT: C 388 ASP cc_start: 0.8456 (m-30) cc_final: 0.8219 (t0) REVERT: C 398 ASP cc_start: 0.8547 (m-30) cc_final: 0.8183 (t0) REVERT: D 60 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7440 (tt) REVERT: D 62 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8064 (mm) REVERT: D 77 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7101 (mt) REVERT: D 221 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9069 (tt) REVERT: D 334 MET cc_start: 0.7912 (ttm) cc_final: 0.7652 (tpp) REVERT: D 388 ASP cc_start: 0.8454 (m-30) cc_final: 0.8213 (t0) outliers start: 50 outliers final: 27 residues processed: 136 average time/residue: 0.1149 time to fit residues: 23.5344 Evaluate side-chains 127 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 87 time to evaluate : 0.583 ------------------------------------------------------------------------------- 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 314 ILE 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 171 LEU 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 D residue 19 ILE 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 314 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 143 optimal weight: 1.9990 chunk 129 optimal weight: 0.9980 chunk 116 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 43 optimal weight: 8.9990 chunk 147 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 153 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.091007 restraints weight = 24114.798| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 2.28 r_work: 0.2936 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13484 Z= 0.112 Angle : 0.641 12.073 18238 Z= 0.285 Chirality : 0.042 0.190 2124 Planarity : 0.004 0.024 2200 Dihedral : 16.456 179.982 2316 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.68 % Allowed : 16.03 % Favored : 80.29 % 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: 0.99 (0.23), residues: 1568 helix: 1.45 (0.18), residues: 948 sheet: -0.67 (0.55), residues: 92 loop : -0.45 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 382 TYR 0.016 0.001 TYR B 11 PHE 0.005 0.001 PHE D 40 TRP 0.011 0.001 TRP A 264 HIS 0.002 0.001 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00262 (13484) covalent geometry : angle 0.64144 (18236) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03086 ( 592) hydrogen bonds : angle 3.18617 ( 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 135 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 85 time to evaluate : 0.519 Fit side-chains REVERT: A 62 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8063 (mm) REVERT: A 77 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7140 (mt) REVERT: A 171 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8819 (tp) REVERT: A 221 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9053 (tt) REVERT: A 334 MET cc_start: 0.7929 (ttm) cc_final: 0.7690 (tpp) REVERT: A 388 ASP cc_start: 0.8462 (m-30) cc_final: 0.8179 (t0) REVERT: B 77 LEU cc_start: 0.7577 (OUTLIER) cc_final: 0.7117 (mt) REVERT: B 171 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8820 (tp) REVERT: B 221 LEU cc_start: 0.9330 (OUTLIER) cc_final: 0.9052 (tt) REVERT: B 369 MET cc_start: 0.8675 (mmt) cc_final: 0.8417 (mmt) REVERT: B 388 ASP cc_start: 0.8445 (m-30) cc_final: 0.8187 (t0) REVERT: C 77 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7088 (mt) REVERT: C 171 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8816 (tp) REVERT: C 221 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9069 (tt) REVERT: C 388 ASP cc_start: 0.8434 (m-30) cc_final: 0.8208 (t0) REVERT: C 398 ASP cc_start: 0.8533 (m-30) cc_final: 0.8174 (t0) REVERT: D 62 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.8050 (mm) REVERT: D 77 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7113 (mt) REVERT: D 221 LEU cc_start: 0.9349 (OUTLIER) cc_final: 0.9073 (tt) REVERT: D 303 LYS cc_start: 0.7365 (mptt) cc_final: 0.6653 (mmtt) REVERT: D 388 ASP cc_start: 0.8435 (m-30) cc_final: 0.8210 (t0) outliers start: 50 outliers final: 28 residues processed: 125 average time/residue: 0.1088 time to fit residues: 20.8717 Evaluate side-chains 122 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 81 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 314 ILE 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 171 LEU 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 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 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 314 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 151 optimal weight: 3.9990 chunk 129 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 67 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 122 optimal weight: 5.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.118714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.089929 restraints weight = 24029.524| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.28 r_work: 0.2925 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3531 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= 0.107 Angle : 0.674 11.980 18238 Z= 0.294 Chirality : 0.042 0.184 2124 Planarity : 0.004 0.024 2200 Dihedral : 16.166 179.503 2316 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.68 % Allowed : 16.32 % Favored : 80.00 % 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: 1.10 (0.23), residues: 1568 helix: 1.54 (0.18), residues: 948 sheet: -0.64 (0.56), residues: 92 loop : -0.42 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 374 TYR 0.034 0.001 TYR A 11 PHE 0.005 0.001 PHE D 40 TRP 0.011 0.001 TRP B 264 HIS 0.002 0.001 HIS C 232 Details of bonding type rmsd covalent geometry : bond 0.00247 (13484) covalent geometry : angle 0.67363 (18236) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03006 ( 592) hydrogen bonds : angle 3.15521 ( 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 141 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 91 time to evaluate : 0.543 Fit side-chains REVERT: A 62 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8064 (mm) REVERT: A 77 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7098 (mt) REVERT: A 221 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9086 (tt) REVERT: A 303 LYS cc_start: 0.7492 (mptt) cc_final: 0.6757 (mmtt) REVERT: A 334 MET cc_start: 0.7929 (ttm) cc_final: 0.7705 (tpp) REVERT: A 369 MET cc_start: 0.8476 (mmm) cc_final: 0.8221 (mmm) REVERT: A 388 ASP cc_start: 0.8449 (m-30) cc_final: 0.7950 (t0) REVERT: B 77 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7130 (mt) REVERT: B 221 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9086 (tt) REVERT: B 303 LYS cc_start: 0.7489 (mptt) cc_final: 0.6763 (mmtt) REVERT: B 369 MET cc_start: 0.8715 (mmt) cc_final: 0.8429 (mmt) REVERT: B 388 ASP cc_start: 0.8460 (m-30) cc_final: 0.7970 (t0) REVERT: C 77 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7107 (mt) REVERT: C 221 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9081 (tt) REVERT: C 303 LYS cc_start: 0.7468 (mptt) cc_final: 0.6740 (mmtt) REVERT: C 369 MET cc_start: 0.8438 (mmm) cc_final: 0.8144 (mmm) REVERT: C 388 ASP cc_start: 0.8424 (m-30) cc_final: 0.7974 (t0) REVERT: C 398 ASP cc_start: 0.8566 (m-30) cc_final: 0.8200 (t0) REVERT: D 62 LEU cc_start: 0.8315 (OUTLIER) cc_final: 0.7988 (mm) REVERT: D 77 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7098 (mt) REVERT: D 221 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9090 (tt) REVERT: D 303 LYS cc_start: 0.7484 (mptt) cc_final: 0.6740 (mmtt) REVERT: D 369 MET cc_start: 0.8424 (mmm) cc_final: 0.8159 (mmm) REVERT: D 388 ASP cc_start: 0.8431 (m-30) cc_final: 0.7972 (t0) outliers start: 50 outliers final: 36 residues processed: 130 average time/residue: 0.1102 time to fit residues: 22.0537 Evaluate side-chains 131 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 85 time to evaluate : 0.554 ------------------------------------------------------------------------------- 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 77 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 171 LEU 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 314 ILE 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: 0.2980 chunk 64 optimal weight: 4.9990 chunk 147 optimal weight: 0.3980 chunk 141 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 chunk 121 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.089706 restraints weight = 24190.606| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.25 r_work: 0.2948 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3642 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= 0.100 Angle : 0.670 11.821 18238 Z= 0.292 Chirality : 0.041 0.181 2124 Planarity : 0.003 0.024 2200 Dihedral : 15.876 179.325 2316 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.75 % Allowed : 16.54 % Favored : 79.71 % 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: 1.19 (0.23), residues: 1568 helix: 1.63 (0.18), residues: 944 sheet: -0.62 (0.56), residues: 92 loop : -0.41 (0.30), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 374 TYR 0.007 0.001 TYR B 128 PHE 0.004 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 covalent geometry : bond 0.00224 (13484) covalent geometry : angle 0.66970 (18236) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.02874 ( 592) hydrogen bonds : angle 3.10972 ( 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 144 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 93 time to evaluate : 0.586 Fit side-chains REVERT: A 62 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8003 (mm) REVERT: A 77 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7158 (mt) REVERT: A 221 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9096 (tt) REVERT: A 303 LYS cc_start: 0.7678 (mptt) cc_final: 0.6978 (mmtt) REVERT: A 369 MET cc_start: 0.8440 (mmm) cc_final: 0.8176 (mmm) REVERT: A 388 ASP cc_start: 0.8374 (m-30) cc_final: 0.8089 (t0) REVERT: B 62 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7922 (mm) REVERT: B 77 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7135 (mt) REVERT: B 221 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9095 (tt) REVERT: B 303 LYS cc_start: 0.7421 (mptt) cc_final: 0.6714 (mmtt) REVERT: B 369 MET cc_start: 0.8718 (mmt) cc_final: 0.8440 (mmt) REVERT: B 388 ASP cc_start: 0.8375 (m-30) cc_final: 0.8089 (t0) REVERT: C 62 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.7932 (mm) REVERT: C 77 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7142 (mt) REVERT: C 221 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9099 (tt) REVERT: C 303 LYS cc_start: 0.7441 (mptt) cc_final: 0.6747 (mmtt) REVERT: C 369 MET cc_start: 0.8468 (mmm) cc_final: 0.8155 (mmm) REVERT: C 388 ASP cc_start: 0.8340 (m-30) cc_final: 0.8104 (t0) REVERT: C 398 ASP cc_start: 0.8554 (m-30) cc_final: 0.8183 (t0) REVERT: D 62 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7950 (mm) REVERT: D 77 LEU cc_start: 0.7452 (OUTLIER) cc_final: 0.7107 (mt) REVERT: D 221 LEU cc_start: 0.9316 (OUTLIER) cc_final: 0.9100 (tt) REVERT: D 303 LYS cc_start: 0.7741 (mptt) cc_final: 0.7057 (mmtt) REVERT: D 369 MET cc_start: 0.8411 (mmm) cc_final: 0.8141 (mmm) REVERT: D 388 ASP cc_start: 0.8366 (m-30) cc_final: 0.8100 (t0) outliers start: 51 outliers final: 31 residues processed: 132 average time/residue: 0.1031 time to fit residues: 20.8288 Evaluate side-chains 134 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 91 time to evaluate : 0.534 ------------------------------------------------------------------------------- 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 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 171 LEU 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 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 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 80 optimal weight: 0.4980 chunk 116 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 110 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.117496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.087807 restraints weight = 24156.602| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.29 r_work: 0.2889 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13484 Z= 0.140 Angle : 0.708 12.702 18238 Z= 0.311 Chirality : 0.043 0.182 2124 Planarity : 0.004 0.026 2200 Dihedral : 16.040 179.738 2316 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 3.38 % Allowed : 16.76 % Favored : 79.85 % 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: 1.07 (0.23), residues: 1568 helix: 1.52 (0.18), residues: 952 sheet: -0.59 (0.56), residues: 92 loop : -0.48 (0.30), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 374 TYR 0.036 0.001 TYR C 11 PHE 0.005 0.001 PHE A 365 TRP 0.010 0.001 TRP B 264 HIS 0.002 0.001 HIS D 149 Details of bonding type rmsd covalent geometry : bond 0.00337 (13484) covalent geometry : angle 0.70808 (18236) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03378 ( 592) hydrogen bonds : angle 3.23453 ( 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 131 residues out of total 1360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 85 time to evaluate : 0.524 Fit side-chains REVERT: A 60 LEU cc_start: 0.7927 (OUTLIER) cc_final: 0.7440 (tt) REVERT: A 62 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8024 (mm) REVERT: A 77 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7034 (mt) REVERT: A 221 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9063 (tt) REVERT: A 303 LYS cc_start: 0.7694 (mptt) cc_final: 0.7126 (mmtt) REVERT: A 369 MET cc_start: 0.8445 (mmm) cc_final: 0.8166 (mmm) REVERT: A 388 ASP cc_start: 0.8596 (m-30) cc_final: 0.8108 (t0) REVERT: B 62 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7935 (mm) REVERT: B 77 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.7017 (mt) REVERT: B 221 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9060 (tt) REVERT: B 303 LYS cc_start: 0.7471 (mptt) cc_final: 0.6885 (mmtt) REVERT: B 388 ASP cc_start: 0.8589 (m-30) cc_final: 0.8113 (t0) REVERT: C 62 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7916 (mm) REVERT: C 77 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7021 (mt) REVERT: C 221 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9065 (tt) REVERT: C 303 LYS cc_start: 0.7443 (mptt) cc_final: 0.6835 (mmtt) REVERT: C 369 MET cc_start: 0.8462 (mmm) cc_final: 0.8149 (mmm) REVERT: C 388 ASP cc_start: 0.8556 (m-30) cc_final: 0.8132 (t0) REVERT: C 398 ASP cc_start: 0.8561 (m-30) cc_final: 0.8228 (t0) REVERT: D 60 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7442 (tt) REVERT: D 62 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7939 (mm) REVERT: D 77 LEU cc_start: 0.7467 (OUTLIER) cc_final: 0.7116 (mt) REVERT: D 221 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9068 (tt) REVERT: D 303 LYS cc_start: 0.7699 (mptt) cc_final: 0.7112 (mmtt) REVERT: D 369 MET cc_start: 0.8446 (mmm) cc_final: 0.8163 (mmm) REVERT: D 388 ASP cc_start: 0.8563 (m-30) cc_final: 0.8127 (t0) outliers start: 46 outliers final: 29 residues processed: 122 average time/residue: 0.1015 time to fit residues: 19.2659 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 : 0.478 ------------------------------------------------------------------------------- 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 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 171 LEU 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 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 389 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 156 random chunks: chunk 116 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 121 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 81 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 136 optimal weight: 0.7980 chunk 117 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 72 optimal weight: 8.9990 chunk 32 optimal weight: 7.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.116433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.089044 restraints weight = 24195.916| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.19 r_work: 0.2902 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3668 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= 0.133 Angle : 0.700 11.461 18238 Z= 0.306 Chirality : 0.042 0.186 2124 Planarity : 0.004 0.023 2200 Dihedral : 16.048 178.956 2316 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.46 % Allowed : 16.69 % Favored : 79.85 % 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: 1.13 (0.23), residues: 1568 helix: 1.70 (0.18), residues: 928 sheet: -0.64 (0.55), residues: 92 loop : -0.61 (0.29), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 374 TYR 0.010 0.001 TYR C 175 PHE 0.005 0.001 PHE D 366 TRP 0.012 0.001 TRP A 264 HIS 0.002 0.001 HIS C 149 Details of bonding type rmsd covalent geometry : bond 0.00321 (13484) covalent geometry : angle 0.69992 (18236) SS BOND : angle 0.00000 ( 2) hydrogen bonds : bond 0.03281 ( 592) hydrogen bonds : angle 3.22629 ( 1704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2599.72 seconds wall clock time: 45 minutes 28.30 seconds (2728.30 seconds total)