Starting phenix.real_space_refine on Wed Mar 4 08:57:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6n24_9322/03_2026/6n24_9322_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6n24_9322/03_2026/6n24_9322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6n24_9322/03_2026/6n24_9322.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6n24_9322/03_2026/6n24_9322.map" model { file = "/net/cci-nas-00/data/ceres_data/6n24_9322/03_2026/6n24_9322_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6n24_9322/03_2026/6n24_9322_neut.cif" } resolution = 3.0 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= 0.185 sd= 1.557 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: 4 Type Number sf(0) Gaussians S 65 5.16 5 C 8338 2.51 5 N 2060 2.21 5 O 2180 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12643 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2529 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "B" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2527 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2529 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2529 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2529 Classifications: {'peptide': 306} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 13, 'TRANS': 292} Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.63, per 1000 atoms: 0.21 Number of scatterers: 12643 At special positions: 0 Unit cell: (94.656, 94.656, 113.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 65 16.00 O 2180 8.00 N 2060 7.00 C 8338 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 135 " - pdb=" SG CYS A 185 " distance=2.04 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 185 " distance=2.04 Simple disulfide: pdb=" SG CYS C 135 " - pdb=" SG CYS C 185 " distance=2.04 Simple disulfide: pdb=" SG CYS D 135 " - pdb=" SG CYS D 185 " distance=2.04 Simple disulfide: pdb=" SG CYS E 135 " - pdb=" SG CYS E 185 " distance=2.04 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: 0.98 Conformation dependent library (CDL) restraints added in 538.0 milliseconds 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2940 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 0 sheets defined 74.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 34 through 53 removed outlier: 3.725A pdb=" N ILE A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 72 removed outlier: 3.584A pdb=" N LEU A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 64 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 65 " --> pdb=" O MET A 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 76 removed outlier: 3.626A pdb=" N ILE A 76 " --> pdb=" O ALA A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 73 through 76' Processing helix chain 'A' and resid 77 through 94 removed outlier: 3.717A pdb=" N GLY A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER A 87 " --> pdb=" O GLY A 83 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER A 91 " --> pdb=" O SER A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 97 No H-bonds generated for 'chain 'A' and resid 95 through 97' Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.757A pdb=" N ASN A 108 " --> pdb=" O ASP A 104 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS A 112 " --> pdb=" O ASN A 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 144 removed outlier: 3.680A pdb=" N ASN A 133 " --> pdb=" O MET A 129 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE A 139 " --> pdb=" O CYS A 135 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 151 Processing helix chain 'A' and resid 154 through 160 removed outlier: 3.534A pdb=" N VAL A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 172 removed outlier: 3.766A pdb=" N LYS A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A 170 " --> pdb=" O GLU A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 197 removed outlier: 3.972A pdb=" N SER A 189 " --> pdb=" O CYS A 185 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 230 removed outlier: 3.518A pdb=" N ILE A 210 " --> pdb=" O LEU A 206 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 213 " --> pdb=" O GLY A 209 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 216 " --> pdb=" O ASN A 212 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU A 224 " --> pdb=" O GLN A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 255 removed outlier: 4.070A pdb=" N VAL A 239 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL A 240 " --> pdb=" O TYR A 236 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR A 245 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG A 255 " --> pdb=" O CYS A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 285 Processing helix chain 'A' and resid 285 through 296 removed outlier: 4.358A pdb=" N ASN A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 319 removed outlier: 3.725A pdb=" N ASP A 312 " --> pdb=" O ASN A 308 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER A 318 " --> pdb=" O ASN A 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 53 removed outlier: 3.725A pdb=" N ILE B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 72 removed outlier: 3.585A pdb=" N LEU B 60 " --> pdb=" O GLU B 56 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET B 61 " --> pdb=" O SER B 57 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 64 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU B 65 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER B 71 " --> pdb=" O LEU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 76 removed outlier: 3.627A pdb=" N ILE B 76 " --> pdb=" O ALA B 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 73 through 76' Processing helix chain 'B' and resid 77 through 94 removed outlier: 3.718A pdb=" N GLY B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE B 84 " --> pdb=" O PHE B 80 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR B 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER B 87 " --> pdb=" O GLY B 83 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER B 91 " --> pdb=" O SER B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 97 No H-bonds generated for 'chain 'B' and resid 95 through 97' Processing helix chain 'B' and resid 103 through 114 removed outlier: 3.757A pdb=" N ASN B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS B 112 " --> pdb=" O ASN B 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 144 removed outlier: 3.680A pdb=" N ASN B 133 " --> pdb=" O MET B 129 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N ILE B 139 " --> pdb=" O CYS B 135 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 151 Processing helix chain 'B' and resid 154 through 160 removed outlier: 3.534A pdb=" N VAL B 158 " --> pdb=" O MET B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 172 removed outlier: 3.766A pdb=" N LYS B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 197 removed outlier: 3.973A pdb=" N SER B 189 " --> pdb=" O CYS B 185 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 230 removed outlier: 3.518A pdb=" N ILE B 210 " --> pdb=" O LEU B 206 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU B 213 " --> pdb=" O GLY B 209 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR B 216 " --> pdb=" O ASN B 212 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU B 217 " --> pdb=" O GLU B 213 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU B 224 " --> pdb=" O GLN B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 255 removed outlier: 4.070A pdb=" N VAL B 239 " --> pdb=" O VAL B 235 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL B 240 " --> pdb=" O TYR B 236 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL B 242 " --> pdb=" O GLN B 238 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR B 245 " --> pdb=" O THR B 241 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE B 247 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 255 " --> pdb=" O CYS B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 285 Processing helix chain 'B' and resid 285 through 296 removed outlier: 4.357A pdb=" N ASN B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 319 removed outlier: 3.724A pdb=" N ASP B 312 " --> pdb=" O ASN B 308 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN B 316 " --> pdb=" O ASP B 312 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER B 318 " --> pdb=" O ASN B 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 53 removed outlier: 3.725A pdb=" N ILE C 46 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 72 removed outlier: 3.584A pdb=" N LEU C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET C 61 " --> pdb=" O SER C 57 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS C 64 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU C 65 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER C 71 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 76 removed outlier: 3.626A pdb=" N ILE C 76 " --> pdb=" O ALA C 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 73 through 76' Processing helix chain 'C' and resid 77 through 94 removed outlier: 3.718A pdb=" N GLY C 83 " --> pdb=" O SER C 79 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR C 85 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER C 87 " --> pdb=" O GLY C 83 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER C 91 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 97 No H-bonds generated for 'chain 'C' and resid 95 through 97' Processing helix chain 'C' and resid 103 through 114 removed outlier: 3.757A pdb=" N ASN C 108 " --> pdb=" O ASP C 104 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N CYS C 112 " --> pdb=" O ASN C 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL C 114 " --> pdb=" O VAL C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 144 removed outlier: 3.680A pdb=" N ASN C 133 " --> pdb=" O MET C 129 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE C 139 " --> pdb=" O CYS C 135 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER C 142 " --> pdb=" O LEU C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 151 Processing helix chain 'C' and resid 154 through 160 removed outlier: 3.534A pdb=" N VAL C 158 " --> pdb=" O MET C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 172 removed outlier: 3.766A pdb=" N LYS C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS C 170 " --> pdb=" O GLU C 166 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 197 removed outlier: 3.972A pdb=" N SER C 189 " --> pdb=" O CYS C 185 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 230 removed outlier: 3.519A pdb=" N ILE C 210 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU C 213 " --> pdb=" O GLY C 209 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR C 216 " --> pdb=" O ASN C 212 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU C 217 " --> pdb=" O GLU C 213 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU C 224 " --> pdb=" O GLN C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 255 removed outlier: 4.071A pdb=" N VAL C 239 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL C 240 " --> pdb=" O TYR C 236 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL C 242 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 245 " --> pdb=" O THR C 241 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE C 247 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C 255 " --> pdb=" O CYS C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 285 Processing helix chain 'C' and resid 285 through 296 removed outlier: 4.358A pdb=" N ASN C 296 " --> pdb=" O GLU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 319 removed outlier: 3.725A pdb=" N ASP C 312 " --> pdb=" O ASN C 308 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN C 316 " --> pdb=" O ASP C 312 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N SER C 318 " --> pdb=" O ASN C 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 53 removed outlier: 3.725A pdb=" N ILE D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 72 removed outlier: 3.585A pdb=" N LEU D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET D 61 " --> pdb=" O SER D 57 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS D 64 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU D 65 " --> pdb=" O MET D 61 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER D 71 " --> pdb=" O LEU D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 removed outlier: 3.626A pdb=" N ILE D 76 " --> pdb=" O ALA D 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 73 through 76' Processing helix chain 'D' and resid 77 through 94 removed outlier: 3.717A pdb=" N GLY D 83 " --> pdb=" O SER D 79 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE D 84 " --> pdb=" O PHE D 80 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR D 85 " --> pdb=" O VAL D 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER D 87 " --> pdb=" O GLY D 83 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER D 91 " --> pdb=" O SER D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 97 No H-bonds generated for 'chain 'D' and resid 95 through 97' Processing helix chain 'D' and resid 103 through 114 removed outlier: 3.757A pdb=" N ASN D 108 " --> pdb=" O ASP D 104 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS D 112 " --> pdb=" O ASN D 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL D 114 " --> pdb=" O VAL D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 144 removed outlier: 3.679A pdb=" N ASN D 133 " --> pdb=" O MET D 129 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE D 139 " --> pdb=" O CYS D 135 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N SER D 142 " --> pdb=" O LEU D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 151 Processing helix chain 'D' and resid 154 through 160 removed outlier: 3.534A pdb=" N VAL D 158 " --> pdb=" O MET D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 172 removed outlier: 3.765A pdb=" N LYS D 169 " --> pdb=" O PRO D 165 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS D 170 " --> pdb=" O GLU D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 197 removed outlier: 3.973A pdb=" N SER D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N VAL D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 230 removed outlier: 3.519A pdb=" N ILE D 210 " --> pdb=" O LEU D 206 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU D 213 " --> pdb=" O GLY D 209 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR D 216 " --> pdb=" O ASN D 212 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU D 217 " --> pdb=" O GLU D 213 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU D 224 " --> pdb=" O GLN D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 255 removed outlier: 4.071A pdb=" N VAL D 239 " --> pdb=" O VAL D 235 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL D 240 " --> pdb=" O TYR D 236 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL D 242 " --> pdb=" O GLN D 238 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL D 244 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR D 245 " --> pdb=" O THR D 241 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N PHE D 247 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG D 255 " --> pdb=" O CYS D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 274 through 285 Processing helix chain 'D' and resid 285 through 296 removed outlier: 4.358A pdb=" N ASN D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 319 removed outlier: 3.724A pdb=" N ASP D 312 " --> pdb=" O ASN D 308 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN D 316 " --> pdb=" O ASP D 312 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER D 318 " --> pdb=" O ASN D 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 34 through 53 removed outlier: 3.725A pdb=" N ILE E 46 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 72 removed outlier: 3.584A pdb=" N LEU E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET E 61 " --> pdb=" O SER E 57 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS E 64 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU E 65 " --> pdb=" O MET E 61 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER E 71 " --> pdb=" O LEU E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 76 removed outlier: 3.627A pdb=" N ILE E 76 " --> pdb=" O ALA E 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 73 through 76' Processing helix chain 'E' and resid 77 through 94 removed outlier: 3.718A pdb=" N GLY E 83 " --> pdb=" O SER E 79 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N PHE E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR E 85 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N SER E 87 " --> pdb=" O GLY E 83 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N SER E 91 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 97 No H-bonds generated for 'chain 'E' and resid 95 through 97' Processing helix chain 'E' and resid 103 through 114 removed outlier: 3.757A pdb=" N ASN E 108 " --> pdb=" O ASP E 104 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS E 112 " --> pdb=" O ASN E 108 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL E 114 " --> pdb=" O VAL E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 144 removed outlier: 3.680A pdb=" N ASN E 133 " --> pdb=" O MET E 129 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N SER E 136 " --> pdb=" O SER E 132 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ILE E 139 " --> pdb=" O CYS E 135 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N SER E 142 " --> pdb=" O LEU E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 144 through 151 Processing helix chain 'E' and resid 154 through 160 removed outlier: 3.534A pdb=" N VAL E 158 " --> pdb=" O MET E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 172 removed outlier: 3.766A pdb=" N LYS E 169 " --> pdb=" O PRO E 165 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 197 removed outlier: 3.972A pdb=" N SER E 189 " --> pdb=" O CYS E 185 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL E 193 " --> pdb=" O SER E 189 " (cutoff:3.500A) Processing helix chain 'E' and resid 203 through 230 removed outlier: 3.518A pdb=" N ILE E 210 " --> pdb=" O LEU E 206 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU E 213 " --> pdb=" O GLY E 209 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR E 216 " --> pdb=" O ASN E 212 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 217 " --> pdb=" O GLU E 213 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 224 " --> pdb=" O GLN E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 255 removed outlier: 4.071A pdb=" N VAL E 239 " --> pdb=" O VAL E 235 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N VAL E 240 " --> pdb=" O TYR E 236 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL E 242 " --> pdb=" O GLN E 238 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL E 244 " --> pdb=" O VAL E 240 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR E 245 " --> pdb=" O THR E 241 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE E 247 " --> pdb=" O ALA E 243 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ARG E 255 " --> pdb=" O CYS E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 274 through 285 Processing helix chain 'E' and resid 285 through 296 removed outlier: 4.356A pdb=" N ASN E 296 " --> pdb=" O GLU E 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 319 removed outlier: 3.724A pdb=" N ASP E 312 " --> pdb=" O ASN E 308 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN E 316 " --> pdb=" O ASP E 312 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER E 318 " --> pdb=" O ASN E 314 " (cutoff:3.500A) 615 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.75 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3884 1.34 - 1.46: 3433 1.46 - 1.58: 5580 1.58 - 1.70: 0 1.70 - 1.82: 100 Bond restraints: 12997 Sorted by residual: bond pdb=" CB TRP D 229 " pdb=" CG TRP D 229 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.76e+00 bond pdb=" CB TRP B 229 " pdb=" CG TRP B 229 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.73e+00 bond pdb=" CB TRP E 229 " pdb=" CG TRP E 229 " ideal model delta sigma weight residual 1.498 1.457 0.041 3.10e-02 1.04e+03 1.72e+00 bond pdb=" CB TRP A 229 " pdb=" CG TRP A 229 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.70e+00 bond pdb=" CB TRP C 229 " pdb=" CG TRP C 229 " ideal model delta sigma weight residual 1.498 1.458 0.040 3.10e-02 1.04e+03 1.68e+00 ... (remaining 12992 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 16907 1.73 - 3.46: 659 3.46 - 5.18: 74 5.18 - 6.91: 20 6.91 - 8.64: 5 Bond angle restraints: 17665 Sorted by residual: angle pdb=" C LEU C 271 " pdb=" N PHE C 272 " pdb=" CA PHE C 272 " ideal model delta sigma weight residual 121.54 127.63 -6.09 1.91e+00 2.74e-01 1.02e+01 angle pdb=" C LEU A 271 " pdb=" N PHE A 272 " pdb=" CA PHE A 272 " ideal model delta sigma weight residual 121.54 127.62 -6.08 1.91e+00 2.74e-01 1.01e+01 angle pdb=" C LEU D 271 " pdb=" N PHE D 272 " pdb=" CA PHE D 272 " ideal model delta sigma weight residual 121.54 127.60 -6.06 1.91e+00 2.74e-01 1.01e+01 angle pdb=" C LEU E 271 " pdb=" N PHE E 272 " pdb=" CA PHE E 272 " ideal model delta sigma weight residual 121.54 127.59 -6.05 1.91e+00 2.74e-01 1.00e+01 angle pdb=" C LEU B 271 " pdb=" N PHE B 272 " pdb=" CA PHE B 272 " ideal model delta sigma weight residual 121.54 127.58 -6.04 1.91e+00 2.74e-01 9.99e+00 ... (remaining 17660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.48: 6516 8.48 - 16.95: 852 16.95 - 25.43: 139 25.43 - 33.91: 55 33.91 - 42.38: 65 Dihedral angle restraints: 7627 sinusoidal: 3077 harmonic: 4550 Sorted by residual: dihedral pdb=" CA TYR A 97 " pdb=" C TYR A 97 " pdb=" N GLU A 98 " pdb=" CA GLU A 98 " ideal model delta harmonic sigma weight residual 180.00 154.05 25.95 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA TYR C 97 " pdb=" C TYR C 97 " pdb=" N GLU C 98 " pdb=" CA GLU C 98 " ideal model delta harmonic sigma weight residual 180.00 154.07 25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA TYR B 97 " pdb=" C TYR B 97 " pdb=" N GLU B 98 " pdb=" CA GLU B 98 " ideal model delta harmonic sigma weight residual 180.00 154.07 25.93 0 5.00e+00 4.00e-02 2.69e+01 ... (remaining 7624 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 853 0.034 - 0.069: 767 0.069 - 0.103: 252 0.103 - 0.138: 60 0.138 - 0.172: 18 Chirality restraints: 1950 Sorted by residual: chirality pdb=" CG LEU C 258 " pdb=" CB LEU C 258 " pdb=" CD1 LEU C 258 " pdb=" CD2 LEU C 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.40e-01 chirality pdb=" CG LEU B 258 " pdb=" CB LEU B 258 " pdb=" CD1 LEU B 258 " pdb=" CD2 LEU B 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CG LEU D 258 " pdb=" CB LEU D 258 " pdb=" CD1 LEU D 258 " pdb=" CD2 LEU D 258 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 7.25e-01 ... (remaining 1947 not shown) Planarity restraints: 2194 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 227 " -0.010 2.00e-02 2.50e+03 1.34e-02 3.61e+00 pdb=" CG TYR A 227 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR A 227 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 227 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 227 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 227 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 227 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 227 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 227 " 0.010 2.00e-02 2.50e+03 1.33e-02 3.54e+00 pdb=" CG TYR D 227 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR D 227 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR D 227 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR D 227 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR D 227 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR D 227 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 227 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 227 " -0.010 2.00e-02 2.50e+03 1.33e-02 3.54e+00 pdb=" CG TYR B 227 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR B 227 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 227 " -0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR B 227 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 227 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 227 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 227 " 0.000 2.00e-02 2.50e+03 ... (remaining 2191 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 4220 2.85 - 3.36: 11420 3.36 - 3.87: 20563 3.87 - 4.39: 24194 4.39 - 4.90: 40721 Nonbonded interactions: 101118 Sorted by model distance: nonbonded pdb=" OD2 ASP D 104 " pdb=" NH2 ARG E 218 " model vdw 2.332 3.120 nonbonded pdb=" OD2 ASP C 104 " pdb=" NH2 ARG D 218 " model vdw 2.338 3.120 nonbonded pdb=" OE1 GLU B 63 " pdb=" OH TYR B 264 " model vdw 2.344 3.040 nonbonded pdb=" OE1 GLU D 63 " pdb=" OH TYR D 264 " model vdw 2.345 3.040 nonbonded pdb=" OE1 GLU A 63 " pdb=" OH TYR A 264 " model vdw 2.345 3.040 ... (remaining 101113 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 28 through 176 or (resid 177 and (name N or name CA or nam \ e C or name O or name CB )) or resid 178 through 339)) selection = chain 'B' selection = (chain 'C' and (resid 28 through 176 or (resid 177 and (name N or name CA or nam \ e C or name O or name CB )) or resid 178 through 339)) selection = (chain 'D' and (resid 28 through 176 or (resid 177 and (name N or name CA or nam \ e C or name O or name CB )) or resid 178 through 339)) selection = (chain 'E' and (resid 28 through 176 or (resid 177 and (name N or name CA or nam \ e C or name O or name CB )) or resid 178 through 339)) } 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: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.270 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 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 : 0.007 0.057 13002 Z= 0.305 Angle : 0.780 8.639 17675 Z= 0.425 Chirality : 0.052 0.172 1950 Planarity : 0.006 0.041 2194 Dihedral : 9.044 42.382 4672 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.29 % Allowed : 1.87 % Favored : 97.84 % 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: -6.07 (0.13), residues: 1510 helix: -4.24 (0.07), residues: 1070 sheet: None (None), residues: 0 loop : -2.69 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 125 TYR 0.032 0.003 TYR A 227 PHE 0.019 0.002 PHE D 181 TRP 0.024 0.003 TRP A 309 HIS 0.009 0.003 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00713 (12997) covalent geometry : angle 0.77818 (17665) SS BOND : bond 0.01113 ( 5) SS BOND : angle 2.28892 ( 10) hydrogen bonds : bond 0.29357 ( 615) hydrogen bonds : angle 8.96505 ( 1845) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 315 time to evaluate : 0.508 Fit side-chains revert: symmetry clash REVERT: A 29 TYR cc_start: 0.7772 (m-80) cc_final: 0.7349 (p90) REVERT: A 41 SER cc_start: 0.9494 (m) cc_final: 0.9277 (p) REVERT: A 61 MET cc_start: 0.8042 (ttm) cc_final: 0.6989 (tpt) REVERT: A 94 TRP cc_start: 0.7886 (t-100) cc_final: 0.6633 (m100) REVERT: A 259 ASP cc_start: 0.8548 (t0) cc_final: 0.8328 (t0) REVERT: A 312 ASP cc_start: 0.8233 (m-30) cc_final: 0.7799 (m-30) REVERT: A 316 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8487 (tm-30) REVERT: A 328 ASP cc_start: 0.7487 (t70) cc_final: 0.7213 (t70) REVERT: B 29 TYR cc_start: 0.7789 (m-80) cc_final: 0.7119 (p90) REVERT: B 41 SER cc_start: 0.9506 (m) cc_final: 0.9302 (p) REVERT: B 61 MET cc_start: 0.7949 (ttm) cc_final: 0.7724 (ttm) REVERT: B 94 TRP cc_start: 0.7796 (t-100) cc_final: 0.6605 (m100) REVERT: B 220 GLN cc_start: 0.8557 (mt0) cc_final: 0.8309 (mt0) REVERT: B 259 ASP cc_start: 0.8635 (t0) cc_final: 0.8115 (t0) REVERT: B 293 GLN cc_start: 0.8504 (tt0) cc_final: 0.7939 (mt0) REVERT: B 316 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8491 (tm-30) REVERT: B 328 ASP cc_start: 0.7324 (t70) cc_final: 0.7096 (t70) REVERT: C 29 TYR cc_start: 0.7696 (m-80) cc_final: 0.7249 (p90) REVERT: C 41 SER cc_start: 0.9440 (m) cc_final: 0.9201 (p) REVERT: C 60 LEU cc_start: 0.9159 (tt) cc_final: 0.8949 (mt) REVERT: C 61 MET cc_start: 0.7859 (ttm) cc_final: 0.6846 (tpt) REVERT: C 94 TRP cc_start: 0.7734 (t-100) cc_final: 0.6636 (m100) REVERT: C 259 ASP cc_start: 0.8622 (t0) cc_final: 0.8332 (t0) REVERT: C 316 GLN cc_start: 0.8697 (tm-30) cc_final: 0.8357 (tm-30) REVERT: C 328 ASP cc_start: 0.7453 (t70) cc_final: 0.7121 (t70) REVERT: D 29 TYR cc_start: 0.7812 (m-80) cc_final: 0.7132 (p90) REVERT: D 61 MET cc_start: 0.8044 (ttm) cc_final: 0.7090 (tpt) REVERT: D 94 TRP cc_start: 0.7839 (t-100) cc_final: 0.6525 (m100) REVERT: D 259 ASP cc_start: 0.8606 (t0) cc_final: 0.8063 (t0) REVERT: D 293 GLN cc_start: 0.8413 (tt0) cc_final: 0.8135 (tt0) REVERT: D 312 ASP cc_start: 0.8306 (m-30) cc_final: 0.7904 (m-30) REVERT: D 328 ASP cc_start: 0.7296 (t70) cc_final: 0.6984 (t0) REVERT: E 29 TYR cc_start: 0.7740 (m-80) cc_final: 0.7113 (p90) REVERT: E 30 LYS cc_start: 0.8313 (ttmt) cc_final: 0.8086 (mttp) REVERT: E 41 SER cc_start: 0.9479 (m) cc_final: 0.9269 (p) REVERT: E 61 MET cc_start: 0.8051 (ttm) cc_final: 0.7116 (tpt) REVERT: E 64 LYS cc_start: 0.9061 (mttt) cc_final: 0.8802 (mttm) REVERT: E 94 TRP cc_start: 0.7850 (t-100) cc_final: 0.6508 (m100) REVERT: E 259 ASP cc_start: 0.8594 (t0) cc_final: 0.8096 (t0) REVERT: E 293 GLN cc_start: 0.8317 (tt0) cc_final: 0.7887 (mt0) REVERT: E 312 ASP cc_start: 0.8166 (m-30) cc_final: 0.7832 (m-30) REVERT: E 316 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8506 (tm-30) REVERT: E 328 ASP cc_start: 0.7595 (t70) cc_final: 0.7325 (t0) outliers start: 4 outliers final: 2 residues processed: 318 average time/residue: 0.5979 time to fit residues: 205.8723 Evaluate side-chains 133 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 ILE Chi-restraints excluded: chain E residue 230 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 0.8980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 7.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN A 296 ASN C 58 GLN C 293 GLN C 296 ASN D 58 GLN D 296 ASN E 238 GLN E 296 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.088346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.063481 restraints weight = 25630.218| |-----------------------------------------------------------------------------| r_work (start): 0.2763 rms_B_bonded: 3.61 r_work: 0.2582 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7190 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13002 Z= 0.168 Angle : 0.619 8.032 17675 Z= 0.327 Chirality : 0.044 0.157 1950 Planarity : 0.005 0.034 2194 Dihedral : 4.726 24.998 1704 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.81 % Allowed : 11.09 % Favored : 86.11 % 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: -3.50 (0.18), residues: 1510 helix: -2.00 (0.13), residues: 1090 sheet: None (None), residues: 0 loop : -2.71 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 255 TYR 0.012 0.001 TYR E 43 PHE 0.022 0.002 PHE B 272 TRP 0.011 0.001 TRP E 94 HIS 0.002 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00382 (12997) covalent geometry : angle 0.61847 (17665) SS BOND : bond 0.00267 ( 5) SS BOND : angle 1.24784 ( 10) hydrogen bonds : bond 0.05167 ( 615) hydrogen bonds : angle 4.50464 ( 1845) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 170 time to evaluate : 0.494 Fit side-chains REVERT: A 29 TYR cc_start: 0.8079 (m-80) cc_final: 0.7185 (t80) REVERT: A 61 MET cc_start: 0.8119 (ttm) cc_final: 0.6998 (tpt) REVERT: A 94 TRP cc_start: 0.7463 (t-100) cc_final: 0.6803 (m100) REVERT: A 230 ILE cc_start: 0.6020 (mm) cc_final: 0.5565 (pt) REVERT: A 316 GLN cc_start: 0.8362 (tm-30) cc_final: 0.7836 (tm-30) REVERT: A 320 MET cc_start: 0.8152 (ttt) cc_final: 0.7923 (ttm) REVERT: B 29 TYR cc_start: 0.8000 (m-80) cc_final: 0.6999 (t80) REVERT: B 61 MET cc_start: 0.8228 (ttm) cc_final: 0.7383 (tpt) REVERT: B 94 TRP cc_start: 0.7323 (t-100) cc_final: 0.6557 (m100) REVERT: B 289 LYS cc_start: 0.7222 (mmmt) cc_final: 0.6755 (mmpt) REVERT: B 292 GLU cc_start: 0.7819 (pp20) cc_final: 0.7531 (pp20) REVERT: B 293 GLN cc_start: 0.7865 (tt0) cc_final: 0.7454 (mt0) REVERT: B 316 GLN cc_start: 0.8499 (tm-30) cc_final: 0.8054 (tm-30) REVERT: B 320 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.8042 (ttm) REVERT: C 29 TYR cc_start: 0.7984 (m-80) cc_final: 0.7273 (p90) REVERT: C 30 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7949 (mttt) REVERT: C 61 MET cc_start: 0.8030 (ttm) cc_final: 0.7020 (tpt) REVERT: C 94 TRP cc_start: 0.7366 (t-100) cc_final: 0.6838 (m100) REVERT: C 316 GLN cc_start: 0.8344 (tm-30) cc_final: 0.7955 (tm-30) REVERT: D 29 TYR cc_start: 0.8074 (m-80) cc_final: 0.7181 (p90) REVERT: D 30 LYS cc_start: 0.8310 (ttmt) cc_final: 0.8062 (mptt) REVERT: D 61 MET cc_start: 0.8174 (ttm) cc_final: 0.7895 (ttm) REVERT: D 94 TRP cc_start: 0.7395 (t-100) cc_final: 0.6789 (m100) REVERT: D 293 GLN cc_start: 0.7782 (tt0) cc_final: 0.7409 (mt0) REVERT: D 316 GLN cc_start: 0.7977 (tm-30) cc_final: 0.7716 (tm-30) REVERT: E 61 MET cc_start: 0.8298 (ttm) cc_final: 0.7318 (tpt) REVERT: E 64 LYS cc_start: 0.8478 (mttt) cc_final: 0.8272 (mttm) REVERT: E 94 TRP cc_start: 0.7328 (t-100) cc_final: 0.6572 (m100) REVERT: E 293 GLN cc_start: 0.7584 (tt0) cc_final: 0.7261 (mt0) REVERT: E 316 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8154 (tm-30) outliers start: 39 outliers final: 7 residues processed: 202 average time/residue: 0.5475 time to fit residues: 120.8673 Evaluate side-chains 145 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 37 LEU Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 61 optimal weight: 4.9990 chunk 120 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 130 optimal weight: 4.9990 chunk 138 optimal weight: 8.9990 chunk 98 optimal weight: 0.2980 chunk 90 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 125 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.087669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.062945 restraints weight = 25843.580| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.56 r_work: 0.2565 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 13002 Z= 0.157 Angle : 0.558 9.430 17675 Z= 0.285 Chirality : 0.042 0.159 1950 Planarity : 0.004 0.031 2194 Dihedral : 4.304 24.208 1700 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.38 % Allowed : 11.66 % Favored : 84.95 % 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: -2.14 (0.21), residues: 1510 helix: -0.86 (0.15), residues: 1095 sheet: None (None), residues: 0 loop : -2.66 (0.29), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 223 TYR 0.009 0.001 TYR C 43 PHE 0.015 0.001 PHE B 272 TRP 0.020 0.001 TRP B 229 HIS 0.002 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00365 (12997) covalent geometry : angle 0.55765 (17665) SS BOND : bond 0.00214 ( 5) SS BOND : angle 0.93235 ( 10) hydrogen bonds : bond 0.04209 ( 615) hydrogen bonds : angle 4.01485 ( 1845) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 148 time to evaluate : 0.446 Fit side-chains REVERT: A 61 MET cc_start: 0.8126 (ttm) cc_final: 0.6999 (tpt) REVERT: A 94 TRP cc_start: 0.7508 (t-100) cc_final: 0.6876 (m100) REVERT: A 316 GLN cc_start: 0.8253 (tm-30) cc_final: 0.7812 (tm-30) REVERT: A 320 MET cc_start: 0.8224 (ttt) cc_final: 0.7950 (ttm) REVERT: B 29 TYR cc_start: 0.8005 (m-80) cc_final: 0.6926 (t80) REVERT: B 54 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8862 (mm) REVERT: B 61 MET cc_start: 0.8197 (ttm) cc_final: 0.7299 (tpt) REVERT: B 94 TRP cc_start: 0.7432 (t-100) cc_final: 0.6663 (m100) REVERT: B 230 ILE cc_start: 0.5806 (mm) cc_final: 0.5403 (pt) REVERT: B 293 GLN cc_start: 0.7647 (tt0) cc_final: 0.7387 (mt0) REVERT: B 316 GLN cc_start: 0.8492 (tm-30) cc_final: 0.8042 (tm-30) REVERT: C 29 TYR cc_start: 0.8020 (m-80) cc_final: 0.7244 (p90) REVERT: C 54 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8833 (mm) REVERT: C 58 GLN cc_start: 0.8392 (tt0) cc_final: 0.8085 (mt0) REVERT: C 61 MET cc_start: 0.8081 (ttm) cc_final: 0.7084 (tpt) REVERT: C 94 TRP cc_start: 0.7369 (t-100) cc_final: 0.6776 (m100) REVERT: C 316 GLN cc_start: 0.8283 (tm-30) cc_final: 0.7821 (tm-30) REVERT: D 29 TYR cc_start: 0.8136 (m-80) cc_final: 0.7194 (p90) REVERT: D 30 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7982 (mttt) REVERT: D 58 GLN cc_start: 0.8444 (tt0) cc_final: 0.8041 (mt0) REVERT: D 61 MET cc_start: 0.8139 (ttm) cc_final: 0.7893 (ttm) REVERT: D 94 TRP cc_start: 0.7588 (t-100) cc_final: 0.6917 (m100) REVERT: D 293 GLN cc_start: 0.7691 (tt0) cc_final: 0.7363 (mt0) REVERT: E 54 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8641 (mm) REVERT: E 61 MET cc_start: 0.8313 (ttm) cc_final: 0.7344 (tpt) REVERT: E 92 ARG cc_start: 0.6984 (ttp80) cc_final: 0.6783 (ttt180) REVERT: E 94 TRP cc_start: 0.7293 (t-100) cc_final: 0.6679 (m100) REVERT: E 230 ILE cc_start: 0.6436 (mm) cc_final: 0.5981 (pt) REVERT: E 293 GLN cc_start: 0.7567 (tt0) cc_final: 0.7245 (mt0) REVERT: E 316 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8135 (tm-30) outliers start: 47 outliers final: 11 residues processed: 182 average time/residue: 0.5428 time to fit residues: 107.8660 Evaluate side-chains 145 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 44 optimal weight: 5.9990 chunk 96 optimal weight: 9.9990 chunk 103 optimal weight: 8.9990 chunk 128 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 123 optimal weight: 5.9990 chunk 53 optimal weight: 0.7980 chunk 54 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 114 optimal weight: 6.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 296 ASN B 256 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.093738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.069462 restraints weight = 25255.668| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 3.35 r_work: 0.2715 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7196 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13002 Z= 0.216 Angle : 0.589 9.664 17675 Z= 0.298 Chirality : 0.044 0.179 1950 Planarity : 0.004 0.052 2194 Dihedral : 4.244 23.573 1700 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 2.95 % Allowed : 12.81 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.53 (0.21), residues: 1510 helix: -0.41 (0.16), residues: 1105 sheet: None (None), residues: 0 loop : -2.47 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 59 TYR 0.029 0.001 TYR B 43 PHE 0.014 0.002 PHE A 248 TRP 0.020 0.001 TRP B 229 HIS 0.003 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00509 (12997) covalent geometry : angle 0.58852 (17665) SS BOND : bond 0.00283 ( 5) SS BOND : angle 1.10388 ( 10) hydrogen bonds : bond 0.04181 ( 615) hydrogen bonds : angle 3.98492 ( 1845) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 134 time to evaluate : 0.388 Fit side-chains REVERT: A 29 TYR cc_start: 0.8287 (m-80) cc_final: 0.8082 (m-80) REVERT: A 61 MET cc_start: 0.8106 (ttm) cc_final: 0.6964 (tpt) REVERT: A 94 TRP cc_start: 0.7407 (t-100) cc_final: 0.6859 (m100) REVERT: A 180 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7666 (mttp) REVERT: B 61 MET cc_start: 0.8197 (ttm) cc_final: 0.7292 (tpt) REVERT: B 94 TRP cc_start: 0.7461 (t-100) cc_final: 0.6740 (m100) REVERT: B 154 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8519 (mmp) REVERT: B 293 GLN cc_start: 0.7649 (tt0) cc_final: 0.7390 (mt0) REVERT: B 316 GLN cc_start: 0.8512 (tm-30) cc_final: 0.8239 (tm-30) REVERT: C 54 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8876 (mm) REVERT: C 58 GLN cc_start: 0.8422 (tt0) cc_final: 0.8001 (mt0) REVERT: C 61 MET cc_start: 0.8102 (ttm) cc_final: 0.7012 (tpt) REVERT: C 94 TRP cc_start: 0.7305 (t-100) cc_final: 0.6775 (m100) REVERT: C 316 GLN cc_start: 0.8278 (tm-30) cc_final: 0.7965 (tm-30) REVERT: D 29 TYR cc_start: 0.8241 (m-80) cc_final: 0.7228 (p90) REVERT: D 30 LYS cc_start: 0.8267 (ttmt) cc_final: 0.8042 (mptt) REVERT: D 58 GLN cc_start: 0.8498 (tt0) cc_final: 0.8078 (mt0) REVERT: D 61 MET cc_start: 0.8190 (ttm) cc_final: 0.7149 (tpt) REVERT: D 94 TRP cc_start: 0.7577 (t-100) cc_final: 0.6907 (m100) REVERT: D 293 GLN cc_start: 0.7747 (tt0) cc_final: 0.7412 (mt0) REVERT: E 54 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8633 (mm) REVERT: E 61 MET cc_start: 0.8265 (ttm) cc_final: 0.7285 (tpt) REVERT: E 94 TRP cc_start: 0.7357 (t-100) cc_final: 0.6685 (m100) REVERT: E 293 GLN cc_start: 0.7589 (tt0) cc_final: 0.7276 (mt0) REVERT: E 316 GLN cc_start: 0.8436 (tm-30) cc_final: 0.8132 (tm-30) outliers start: 41 outliers final: 13 residues processed: 166 average time/residue: 0.5476 time to fit residues: 99.3699 Evaluate side-chains 138 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 180 LYS Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 72 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 29 optimal weight: 8.9990 chunk 142 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 178 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.092623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.068002 restraints weight = 25443.642| |-----------------------------------------------------------------------------| r_work (start): 0.2892 rms_B_bonded: 3.47 r_work: 0.2714 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13002 Z= 0.187 Angle : 0.559 9.629 17675 Z= 0.282 Chirality : 0.043 0.142 1950 Planarity : 0.004 0.053 2194 Dihedral : 4.185 22.271 1700 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.17 % Allowed : 13.32 % Favored : 83.51 % 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: -1.08 (0.22), residues: 1510 helix: -0.04 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -2.39 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 223 TYR 0.022 0.001 TYR B 43 PHE 0.014 0.001 PHE A 248 TRP 0.020 0.001 TRP C 229 HIS 0.002 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00443 (12997) covalent geometry : angle 0.55882 (17665) SS BOND : bond 0.00271 ( 5) SS BOND : angle 0.99108 ( 10) hydrogen bonds : bond 0.03915 ( 615) hydrogen bonds : angle 3.90242 ( 1845) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 129 time to evaluate : 0.541 Fit side-chains REVERT: A 61 MET cc_start: 0.8070 (ttm) cc_final: 0.6942 (tpt) REVERT: A 94 TRP cc_start: 0.7478 (t-100) cc_final: 0.6867 (m100) REVERT: A 229 TRP cc_start: 0.7297 (t60) cc_final: 0.6963 (p-90) REVERT: B 61 MET cc_start: 0.8222 (ttm) cc_final: 0.7323 (tpt) REVERT: B 94 TRP cc_start: 0.7353 (t-100) cc_final: 0.6666 (t60) REVERT: B 154 MET cc_start: 0.8764 (OUTLIER) cc_final: 0.8538 (mmp) REVERT: B 293 GLN cc_start: 0.7641 (tt0) cc_final: 0.7382 (mt0) REVERT: B 316 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8276 (tm-30) REVERT: C 54 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8868 (mm) REVERT: C 58 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.7974 (mt0) REVERT: C 61 MET cc_start: 0.8089 (ttm) cc_final: 0.7016 (tpt) REVERT: C 94 TRP cc_start: 0.7327 (t-100) cc_final: 0.6752 (m100) REVERT: D 29 TYR cc_start: 0.8207 (m-80) cc_final: 0.7234 (p90) REVERT: D 30 LYS cc_start: 0.8310 (ttmt) cc_final: 0.8037 (mttt) REVERT: D 58 GLN cc_start: 0.8485 (tt0) cc_final: 0.8164 (mt0) REVERT: D 61 MET cc_start: 0.8191 (ttm) cc_final: 0.7155 (tpt) REVERT: D 94 TRP cc_start: 0.7607 (t-100) cc_final: 0.6960 (m100) REVERT: D 293 GLN cc_start: 0.7755 (tt0) cc_final: 0.7412 (mt0) REVERT: E 54 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8719 (mm) REVERT: E 58 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8127 (mt0) REVERT: E 61 MET cc_start: 0.8242 (ttm) cc_final: 0.7244 (tpt) REVERT: E 94 TRP cc_start: 0.7407 (t-100) cc_final: 0.6660 (m100) REVERT: E 293 GLN cc_start: 0.7510 (tt0) cc_final: 0.7205 (mt0) REVERT: E 316 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8188 (tm-30) outliers start: 44 outliers final: 11 residues processed: 166 average time/residue: 0.5622 time to fit residues: 101.6067 Evaluate side-chains 138 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 236 TYR Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 102 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 chunk 66 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 50 optimal weight: 10.0000 chunk 8 optimal weight: 0.0770 chunk 113 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 overall best weight: 1.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 238 GLN C 267 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.095656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.071136 restraints weight = 24894.610| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 3.44 r_work: 0.2766 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 13002 Z= 0.099 Angle : 0.529 10.939 17675 Z= 0.258 Chirality : 0.040 0.161 1950 Planarity : 0.003 0.036 2194 Dihedral : 3.986 20.748 1700 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.66 % Allowed : 15.91 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.61 (0.22), residues: 1510 helix: 0.34 (0.16), residues: 1085 sheet: None (None), residues: 0 loop : -2.27 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 223 TYR 0.015 0.001 TYR B 43 PHE 0.011 0.001 PHE C 248 TRP 0.025 0.001 TRP C 229 HIS 0.002 0.000 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00226 (12997) covalent geometry : angle 0.52860 (17665) SS BOND : bond 0.00114 ( 5) SS BOND : angle 0.48809 ( 10) hydrogen bonds : bond 0.03266 ( 615) hydrogen bonds : angle 3.65747 ( 1845) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.480 Fit side-chains revert: symmetry clash REVERT: A 43 TYR cc_start: 0.7885 (t80) cc_final: 0.7673 (t80) REVERT: A 61 MET cc_start: 0.8078 (ttm) cc_final: 0.6928 (tpt) REVERT: A 94 TRP cc_start: 0.7451 (t-100) cc_final: 0.6800 (m100) REVERT: A 100 ILE cc_start: 0.7849 (mm) cc_final: 0.7169 (pt) REVERT: A 316 GLN cc_start: 0.8122 (tm-30) cc_final: 0.7915 (tm-30) REVERT: B 61 MET cc_start: 0.8227 (ttm) cc_final: 0.7327 (tpt) REVERT: B 94 TRP cc_start: 0.7297 (t-100) cc_final: 0.6522 (m100) REVERT: B 293 GLN cc_start: 0.7609 (tt0) cc_final: 0.7386 (mt0) REVERT: C 54 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8848 (mm) REVERT: C 58 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: C 94 TRP cc_start: 0.7378 (t-100) cc_final: 0.6803 (m100) REVERT: C 316 GLN cc_start: 0.7666 (tm-30) cc_final: 0.7283 (tm-30) REVERT: D 29 TYR cc_start: 0.8165 (m-80) cc_final: 0.7170 (p90) REVERT: D 30 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7943 (mttp) REVERT: D 58 GLN cc_start: 0.8516 (tt0) cc_final: 0.8170 (mt0) REVERT: D 61 MET cc_start: 0.8176 (ttm) cc_final: 0.7122 (tpt) REVERT: D 94 TRP cc_start: 0.7331 (t-100) cc_final: 0.6615 (m100) REVERT: D 256 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8877 (mm110) REVERT: D 293 GLN cc_start: 0.7785 (tt0) cc_final: 0.7425 (mt0) REVERT: E 54 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8699 (mm) REVERT: E 58 GLN cc_start: 0.8443 (tt0) cc_final: 0.8025 (mt0) REVERT: E 61 MET cc_start: 0.8208 (ttm) cc_final: 0.7216 (tpt) REVERT: E 94 TRP cc_start: 0.7382 (t-100) cc_final: 0.6743 (m100) REVERT: E 293 GLN cc_start: 0.7461 (tt0) cc_final: 0.7167 (mt0) REVERT: E 316 GLN cc_start: 0.8370 (tm-30) cc_final: 0.8110 (tm-30) outliers start: 23 outliers final: 7 residues processed: 158 average time/residue: 0.5358 time to fit residues: 92.5295 Evaluate side-chains 135 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 30 optimal weight: 20.0000 chunk 39 optimal weight: 5.9990 chunk 90 optimal weight: 20.0000 chunk 101 optimal weight: 0.9990 chunk 37 optimal weight: 4.9990 chunk 53 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 51 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3376 r_free = 0.3376 target = 0.094375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.069766 restraints weight = 25043.175| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 3.46 r_work: 0.2746 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13002 Z= 0.143 Angle : 0.538 11.078 17675 Z= 0.266 Chirality : 0.042 0.141 1950 Planarity : 0.004 0.044 2194 Dihedral : 3.983 20.281 1700 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.80 % Allowed : 16.27 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.22), residues: 1510 helix: 0.40 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -2.13 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 92 TYR 0.014 0.001 TYR B 43 PHE 0.013 0.001 PHE A 248 TRP 0.027 0.001 TRP B 229 HIS 0.002 0.001 HIS D 326 Details of bonding type rmsd covalent geometry : bond 0.00343 (12997) covalent geometry : angle 0.53770 (17665) SS BOND : bond 0.00243 ( 5) SS BOND : angle 0.84517 ( 10) hydrogen bonds : bond 0.03482 ( 615) hydrogen bonds : angle 3.67082 ( 1845) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.490 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8070 (ttm) cc_final: 0.6910 (tpt) REVERT: A 94 TRP cc_start: 0.7450 (t-100) cc_final: 0.6753 (m100) REVERT: A 100 ILE cc_start: 0.7904 (mm) cc_final: 0.7217 (pt) REVERT: A 229 TRP cc_start: 0.7290 (t60) cc_final: 0.6992 (p-90) REVERT: B 61 MET cc_start: 0.8237 (ttm) cc_final: 0.7341 (tpt) REVERT: B 94 TRP cc_start: 0.7389 (t-100) cc_final: 0.6769 (t60) REVERT: B 293 GLN cc_start: 0.7629 (tt0) cc_final: 0.7409 (mt0) REVERT: C 54 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8841 (mm) REVERT: C 58 GLN cc_start: 0.8354 (OUTLIER) cc_final: 0.7936 (mt0) REVERT: C 94 TRP cc_start: 0.7332 (t-100) cc_final: 0.6692 (m100) REVERT: C 316 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7427 (tm-30) REVERT: D 29 TYR cc_start: 0.8221 (m-80) cc_final: 0.7166 (p90) REVERT: D 30 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7981 (mttp) REVERT: D 58 GLN cc_start: 0.8534 (tt0) cc_final: 0.8031 (mt0) REVERT: D 61 MET cc_start: 0.8188 (ttm) cc_final: 0.7136 (tpt) REVERT: D 94 TRP cc_start: 0.7452 (t-100) cc_final: 0.6643 (m100) REVERT: D 107 MET cc_start: 0.7676 (OUTLIER) cc_final: 0.7429 (ptp) REVERT: D 293 GLN cc_start: 0.7759 (tt0) cc_final: 0.7439 (mt0) REVERT: E 54 LEU cc_start: 0.9028 (OUTLIER) cc_final: 0.8711 (mm) REVERT: E 58 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: E 61 MET cc_start: 0.8214 (ttm) cc_final: 0.7227 (tpt) REVERT: E 94 TRP cc_start: 0.7353 (t-100) cc_final: 0.6708 (t60) REVERT: E 293 GLN cc_start: 0.7486 (tt0) cc_final: 0.7195 (mt0) REVERT: E 316 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8094 (tm-30) outliers start: 25 outliers final: 8 residues processed: 146 average time/residue: 0.5404 time to fit residues: 86.3857 Evaluate side-chains 136 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 2 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 126 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 57 optimal weight: 10.0000 chunk 52 optimal weight: 0.0970 chunk 122 optimal weight: 10.0000 chunk 117 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 98 optimal weight: 4.9990 chunk 106 optimal weight: 0.9980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.092266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.066845 restraints weight = 24743.542| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 3.42 r_work: 0.2760 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13002 Z= 0.124 Angle : 0.538 11.567 17675 Z= 0.263 Chirality : 0.041 0.140 1950 Planarity : 0.003 0.040 2194 Dihedral : 3.933 19.304 1700 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.51 % Allowed : 16.92 % Favored : 81.57 % 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: -0.17 (0.22), residues: 1510 helix: 0.58 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -2.01 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 223 TYR 0.030 0.001 TYR A 43 PHE 0.011 0.001 PHE D 248 TRP 0.032 0.001 TRP B 229 HIS 0.002 0.000 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00295 (12997) covalent geometry : angle 0.53764 (17665) SS BOND : bond 0.00186 ( 5) SS BOND : angle 0.68527 ( 10) hydrogen bonds : bond 0.03370 ( 615) hydrogen bonds : angle 3.62903 ( 1845) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 132 time to evaluate : 0.514 Fit side-chains REVERT: A 61 MET cc_start: 0.8095 (ttm) cc_final: 0.6941 (tpt) REVERT: A 94 TRP cc_start: 0.7441 (t-100) cc_final: 0.6755 (m100) REVERT: A 100 ILE cc_start: 0.7901 (mm) cc_final: 0.7215 (pt) REVERT: A 229 TRP cc_start: 0.7352 (t60) cc_final: 0.7067 (p-90) REVERT: B 61 MET cc_start: 0.8225 (ttm) cc_final: 0.7331 (tpt) REVERT: B 94 TRP cc_start: 0.7336 (t-100) cc_final: 0.6761 (t60) REVERT: B 293 GLN cc_start: 0.7575 (tt0) cc_final: 0.7352 (mt0) REVERT: C 54 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8832 (mm) REVERT: C 58 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: C 94 TRP cc_start: 0.7318 (t-100) cc_final: 0.6686 (m100) REVERT: C 316 GLN cc_start: 0.7685 (tm-30) cc_final: 0.7393 (tm-30) REVERT: D 29 TYR cc_start: 0.8269 (m-80) cc_final: 0.7182 (p90) REVERT: D 30 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7983 (mttp) REVERT: D 58 GLN cc_start: 0.8511 (tt0) cc_final: 0.8021 (mt0) REVERT: D 61 MET cc_start: 0.8178 (ttm) cc_final: 0.7129 (tpt) REVERT: D 94 TRP cc_start: 0.7454 (t-100) cc_final: 0.6638 (m100) REVERT: D 107 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.7325 (ptp) REVERT: D 293 GLN cc_start: 0.7736 (tt0) cc_final: 0.7413 (mt0) REVERT: E 54 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8701 (mm) REVERT: E 58 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8012 (mt0) REVERT: E 61 MET cc_start: 0.8059 (ttm) cc_final: 0.7062 (tpt) REVERT: E 94 TRP cc_start: 0.7366 (t-100) cc_final: 0.6698 (t60) REVERT: E 293 GLN cc_start: 0.7480 (tt0) cc_final: 0.7190 (mt0) REVERT: E 316 GLN cc_start: 0.8370 (tm-30) cc_final: 0.8054 (tm-30) outliers start: 21 outliers final: 8 residues processed: 145 average time/residue: 0.4895 time to fit residues: 78.4636 Evaluate side-chains 137 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 124 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain C residue 294 LEU Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 249 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 14 optimal weight: 7.9990 chunk 26 optimal weight: 8.9990 chunk 138 optimal weight: 0.0370 chunk 106 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 0.3980 chunk 30 optimal weight: 20.0000 chunk 91 optimal weight: 6.9990 chunk 45 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 1.4462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 293 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 = 0.3339 r_free = 0.3339 target = 0.093284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.067976 restraints weight = 24961.253| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.43 r_work: 0.2777 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13002 Z= 0.098 Angle : 0.519 11.182 17675 Z= 0.255 Chirality : 0.040 0.163 1950 Planarity : 0.003 0.041 2194 Dihedral : 3.810 18.134 1700 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.44 % Allowed : 17.06 % Favored : 81.50 % 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: 0.08 (0.22), residues: 1510 helix: 0.81 (0.16), residues: 1110 sheet: None (None), residues: 0 loop : -2.03 (0.29), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 223 TYR 0.013 0.001 TYR B 43 PHE 0.011 0.001 PHE A 248 TRP 0.035 0.001 TRP B 229 HIS 0.002 0.000 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00230 (12997) covalent geometry : angle 0.51853 (17665) SS BOND : bond 0.00157 ( 5) SS BOND : angle 0.53873 ( 10) hydrogen bonds : bond 0.03141 ( 615) hydrogen bonds : angle 3.51555 ( 1845) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8087 (ttm) cc_final: 0.6970 (tpt) REVERT: A 94 TRP cc_start: 0.7388 (t-100) cc_final: 0.6763 (m100) REVERT: A 100 ILE cc_start: 0.7864 (mm) cc_final: 0.7179 (pt) REVERT: A 229 TRP cc_start: 0.7301 (t60) cc_final: 0.7082 (p-90) REVERT: B 61 MET cc_start: 0.8212 (ttm) cc_final: 0.7313 (tpt) REVERT: B 94 TRP cc_start: 0.7345 (t-100) cc_final: 0.6770 (t60) REVERT: C 54 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8799 (mm) REVERT: C 58 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7900 (mt0) REVERT: C 94 TRP cc_start: 0.7281 (t-100) cc_final: 0.6650 (m100) REVERT: C 316 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7407 (tm-30) REVERT: D 29 TYR cc_start: 0.8280 (m-80) cc_final: 0.7181 (p90) REVERT: D 30 LYS cc_start: 0.8268 (ttmt) cc_final: 0.7970 (mttp) REVERT: D 58 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7949 (mt0) REVERT: D 61 MET cc_start: 0.8152 (ttm) cc_final: 0.7140 (tpt) REVERT: D 94 TRP cc_start: 0.7408 (t-100) cc_final: 0.6608 (m100) REVERT: D 107 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7285 (ptp) REVERT: D 229 TRP cc_start: 0.7031 (t60) cc_final: 0.6828 (p-90) REVERT: D 293 GLN cc_start: 0.7739 (tt0) cc_final: 0.7407 (mt0) REVERT: E 54 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8663 (mm) REVERT: E 58 GLN cc_start: 0.8425 (OUTLIER) cc_final: 0.8003 (mt0) REVERT: E 61 MET cc_start: 0.8139 (ttm) cc_final: 0.7159 (tpt) REVERT: E 94 TRP cc_start: 0.7321 (t-100) cc_final: 0.6710 (t60) REVERT: E 293 GLN cc_start: 0.7484 (tt0) cc_final: 0.7200 (mt0) REVERT: E 316 GLN cc_start: 0.8352 (tm-30) cc_final: 0.8037 (tm-30) outliers start: 20 outliers final: 8 residues processed: 152 average time/residue: 0.4453 time to fit residues: 75.1385 Evaluate side-chains 147 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 107 MET Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 249 LEU Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 72 optimal weight: 7.9990 chunk 21 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 14 optimal weight: 7.9990 chunk 84 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.8980 chunk 96 optimal weight: 20.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 238 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.094682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.069199 restraints weight = 25024.844| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.45 r_work: 0.2807 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13002 Z= 0.090 Angle : 0.529 12.734 17675 Z= 0.256 Chirality : 0.040 0.154 1950 Planarity : 0.003 0.034 2194 Dihedral : 3.682 17.214 1700 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.37 % Allowed : 17.49 % Favored : 81.14 % 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: 0.31 (0.23), residues: 1510 helix: 0.92 (0.16), residues: 1120 sheet: None (None), residues: 0 loop : -1.82 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 126 TYR 0.010 0.001 TYR B 43 PHE 0.010 0.001 PHE E 188 TRP 0.038 0.001 TRP B 229 HIS 0.002 0.000 HIS C 326 Details of bonding type rmsd covalent geometry : bond 0.00208 (12997) covalent geometry : angle 0.52942 (17665) SS BOND : bond 0.00112 ( 5) SS BOND : angle 0.46769 ( 10) hydrogen bonds : bond 0.02981 ( 615) hydrogen bonds : angle 3.44221 ( 1845) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3020 Ramachandran restraints generated. 1510 Oldfield, 0 Emsley, 1510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 61 MET cc_start: 0.8061 (ttm) cc_final: 0.6947 (tpt) REVERT: A 94 TRP cc_start: 0.7425 (t-100) cc_final: 0.6824 (m100) REVERT: A 100 ILE cc_start: 0.7807 (mm) cc_final: 0.7126 (pt) REVERT: A 229 TRP cc_start: 0.7309 (t60) cc_final: 0.7106 (p-90) REVERT: B 61 MET cc_start: 0.8198 (ttm) cc_final: 0.7255 (tpt) REVERT: B 94 TRP cc_start: 0.7354 (t-100) cc_final: 0.6512 (m100) REVERT: B 229 TRP cc_start: 0.6857 (t60) cc_final: 0.6598 (p-90) REVERT: C 54 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8802 (mm) REVERT: C 58 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.7917 (mt0) REVERT: C 94 TRP cc_start: 0.7276 (t-100) cc_final: 0.6684 (m100) REVERT: C 316 GLN cc_start: 0.7717 (tm-30) cc_final: 0.7498 (tm-30) REVERT: D 29 TYR cc_start: 0.8267 (m-80) cc_final: 0.7185 (p90) REVERT: D 30 LYS cc_start: 0.8216 (ttmt) cc_final: 0.7920 (mttp) REVERT: D 58 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.7910 (mt0) REVERT: D 61 MET cc_start: 0.8129 (ttm) cc_final: 0.7121 (tpt) REVERT: D 94 TRP cc_start: 0.7410 (t-100) cc_final: 0.6625 (m100) REVERT: D 107 MET cc_start: 0.7524 (OUTLIER) cc_final: 0.7226 (ptp) REVERT: D 293 GLN cc_start: 0.7723 (tt0) cc_final: 0.7363 (mt0) REVERT: E 54 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8659 (mm) REVERT: E 58 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7997 (mt0) REVERT: E 61 MET cc_start: 0.8072 (ttm) cc_final: 0.7110 (tpt) REVERT: E 94 TRP cc_start: 0.7338 (t-100) cc_final: 0.6690 (t60) REVERT: E 293 GLN cc_start: 0.7475 (tt0) cc_final: 0.7206 (mt0) REVERT: E 316 GLN cc_start: 0.8341 (tm-30) cc_final: 0.8029 (tm-30) outliers start: 19 outliers final: 8 residues processed: 155 average time/residue: 0.4354 time to fit residues: 75.0971 Evaluate side-chains 146 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 294 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain C residue 58 GLN Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 58 GLN Chi-restraints excluded: chain D residue 107 MET Chi-restraints excluded: chain D residue 249 LEU Chi-restraints excluded: chain E residue 54 LEU Chi-restraints excluded: chain E residue 58 GLN Chi-restraints excluded: chain E residue 294 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 34 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 33 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 69 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 56 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 293 GLN ** C 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.085984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.061102 restraints weight = 25586.495| |-----------------------------------------------------------------------------| r_work (start): 0.2716 rms_B_bonded: 3.56 r_work: 0.2529 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.3757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13002 Z= 0.232 Angle : 0.621 12.104 17675 Z= 0.304 Chirality : 0.045 0.191 1950 Planarity : 0.004 0.061 2194 Dihedral : 3.965 17.016 1700 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.73 % Allowed : 17.57 % Favored : 80.71 % 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: 0.06 (0.22), residues: 1510 helix: 0.83 (0.16), residues: 1095 sheet: None (None), residues: 0 loop : -2.06 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 223 TYR 0.011 0.001 TYR E 227 PHE 0.014 0.002 PHE A 248 TRP 0.034 0.001 TRP B 229 HIS 0.003 0.001 HIS B 178 Details of bonding type rmsd covalent geometry : bond 0.00554 (12997) covalent geometry : angle 0.62050 (17665) SS BOND : bond 0.00335 ( 5) SS BOND : angle 1.33770 ( 10) hydrogen bonds : bond 0.04031 ( 615) hydrogen bonds : angle 3.78499 ( 1845) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3381.33 seconds wall clock time: 58 minutes 29.04 seconds (3509.04 seconds total)