Starting phenix.real_space_refine on Tue Nov 18 12:25:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ebl_9025/11_2025/6ebl_9025_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ebl_9025/11_2025/6ebl_9025.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 { model { file = "/net/cci-nas-00/data/ceres_data/6ebl_9025/11_2025/6ebl_9025_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ebl_9025/11_2025/6ebl_9025_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6ebl_9025/11_2025/6ebl_9025.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ebl_9025/11_2025/6ebl_9025.map" } 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= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 12 5.49 5 S 84 5.16 5 C 8764 2.51 5 N 2388 2.21 5 O 2704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13952 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "B" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 860 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "D" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 860 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "F" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 860 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2548 Classifications: {'peptide': 325} Link IDs: {'PTRANS': 12, 'TRANS': 312} Chain: "H" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 860 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NAP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "D" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Time building chain proxies: 3.19, per 1000 atoms: 0.23 Number of scatterers: 13952 At special positions: 0 Unit cell: (132.765, 132.765, 99.365, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 84 16.00 P 12 15.00 O 2704 8.00 N 2388 7.00 C 8764 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.09 Conformation dependent library (CDL) restraints added in 605.0 milliseconds 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3144 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 12 sheets defined 51.9% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 65 through 78 Processing helix chain 'A' and resid 89 through 92 removed outlier: 3.543A pdb=" N ALA A 92 " --> pdb=" O VAL A 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 89 through 92' Processing helix chain 'A' and resid 93 through 107 removed outlier: 3.793A pdb=" N VAL A 97 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS A 104 " --> pdb=" O GLY A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 Processing helix chain 'A' and resid 125 through 129 removed outlier: 3.866A pdb=" N ARG A 129 " --> pdb=" O GLU A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 147 removed outlier: 3.680A pdb=" N GLU A 145 " --> pdb=" O LYS A 141 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 146 " --> pdb=" O ALA A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 179 Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.501A pdb=" N ALA A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 227 through 236 removed outlier: 4.140A pdb=" N GLU A 231 " --> pdb=" O VAL A 227 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU A 232 " --> pdb=" O GLN A 228 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS A 234 " --> pdb=" O PRO A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.724A pdb=" N ASP A 256 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER A 257 " --> pdb=" O LYS A 254 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 258 " --> pdb=" O TYR A 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 258' Processing helix chain 'A' and resid 263 through 267 Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.514A pdb=" N LYS A 274 " --> pdb=" O TYR A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 299 removed outlier: 3.520A pdb=" N GLN A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN A 286 " --> pdb=" O GLY A 282 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU A 291 " --> pdb=" O ALA A 287 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ILE A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 326 through 335 Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.675A pdb=" N VAL A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 52 Processing helix chain 'B' and resid 64 through 67 removed outlier: 3.974A pdb=" N ARG B 67 " --> pdb=" O LYS B 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 64 through 67' Processing helix chain 'B' and resid 84 through 95 removed outlier: 3.844A pdb=" N TYR B 92 " --> pdb=" O ILE B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 114 removed outlier: 3.644A pdb=" N GLU B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG B 114 " --> pdb=" O SER B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 131 removed outlier: 3.821A pdb=" N GLU B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N MET B 125 " --> pdb=" O GLU B 121 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP B 129 " --> pdb=" O MET B 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 78 Processing helix chain 'C' and resid 89 through 92 removed outlier: 3.544A pdb=" N ALA C 92 " --> pdb=" O VAL C 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 89 through 92' Processing helix chain 'C' and resid 93 through 107 removed outlier: 3.789A pdb=" N VAL C 97 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE C 103 " --> pdb=" O LEU C 99 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS C 104 " --> pdb=" O GLY C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 113 Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.866A pdb=" N ARG C 129 " --> pdb=" O GLU C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 147 removed outlier: 3.681A pdb=" N GLU C 145 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG C 146 " --> pdb=" O ALA C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 179 Processing helix chain 'C' and resid 191 through 205 removed outlier: 3.501A pdb=" N ALA C 202 " --> pdb=" O ALA C 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 227 Processing helix chain 'C' and resid 227 through 236 removed outlier: 4.009A pdb=" N GLU C 231 " --> pdb=" O VAL C 227 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU C 232 " --> pdb=" O GLN C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.727A pdb=" N ASP C 256 " --> pdb=" O GLY C 253 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER C 257 " --> pdb=" O LYS C 254 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY C 258 " --> pdb=" O TYR C 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 253 through 258' Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.533A pdb=" N LYS C 274 " --> pdb=" O TYR C 270 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER C 279 " --> pdb=" O ASP C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 299 removed outlier: 3.560A pdb=" N GLN C 285 " --> pdb=" O GLU C 281 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLN C 286 " --> pdb=" O GLY C 282 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA C 287 " --> pdb=" O ARG C 283 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU C 291 " --> pdb=" O ALA C 287 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ALA C 294 " --> pdb=" O LYS C 290 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ILE C 295 " --> pdb=" O GLU C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 310 Processing helix chain 'C' and resid 326 through 335 Processing helix chain 'C' and resid 344 through 356 removed outlier: 3.661A pdb=" N VAL C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 48 through 52 Processing helix chain 'D' and resid 64 through 67 removed outlier: 3.967A pdb=" N ARG D 67 " --> pdb=" O LYS D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 64 through 67' Processing helix chain 'D' and resid 84 through 95 removed outlier: 3.846A pdb=" N TYR D 92 " --> pdb=" O ILE D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 114 removed outlier: 3.640A pdb=" N GLU D 111 " --> pdb=" O ASP D 107 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 131 removed outlier: 3.814A pdb=" N GLU D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N MET D 125 " --> pdb=" O GLU D 121 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP D 129 " --> pdb=" O MET D 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 65 through 78 Processing helix chain 'E' and resid 89 through 92 removed outlier: 3.543A pdb=" N ALA E 92 " --> pdb=" O VAL E 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 89 through 92' Processing helix chain 'E' and resid 93 through 107 removed outlier: 3.789A pdb=" N VAL E 97 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LYS E 104 " --> pdb=" O GLY E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 113 Processing helix chain 'E' and resid 125 through 129 removed outlier: 3.866A pdb=" N ARG E 129 " --> pdb=" O GLU E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 147 removed outlier: 3.681A pdb=" N GLU E 145 " --> pdb=" O LYS E 141 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG E 146 " --> pdb=" O ALA E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 179 Processing helix chain 'E' and resid 191 through 205 Processing helix chain 'E' and resid 222 through 227 Processing helix chain 'E' and resid 227 through 236 removed outlier: 4.054A pdb=" N GLU E 231 " --> pdb=" O VAL E 227 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LEU E 232 " --> pdb=" O GLN E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 253 through 258 removed outlier: 3.728A pdb=" N ASP E 256 " --> pdb=" O GLY E 253 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER E 257 " --> pdb=" O LYS E 254 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY E 258 " --> pdb=" O TYR E 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 253 through 258' Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 270 through 279 removed outlier: 3.532A pdb=" N LYS E 274 " --> pdb=" O TYR E 270 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER E 279 " --> pdb=" O ASP E 275 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 299 removed outlier: 3.561A pdb=" N GLN E 285 " --> pdb=" O GLU E 281 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLN E 286 " --> pdb=" O GLY E 282 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA E 287 " --> pdb=" O ARG E 283 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU E 291 " --> pdb=" O ALA E 287 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA E 294 " --> pdb=" O LYS E 290 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE E 295 " --> pdb=" O GLU E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 310 Processing helix chain 'E' and resid 326 through 335 Processing helix chain 'E' and resid 344 through 356 removed outlier: 3.660A pdb=" N VAL E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 52 Processing helix chain 'F' and resid 64 through 67 removed outlier: 3.969A pdb=" N ARG F 67 " --> pdb=" O LYS F 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 64 through 67' Processing helix chain 'F' and resid 84 through 95 removed outlier: 3.845A pdb=" N TYR F 92 " --> pdb=" O ILE F 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 114 removed outlier: 3.637A pdb=" N GLU F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG F 114 " --> pdb=" O SER F 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 120 through 131 removed outlier: 3.767A pdb=" N GLU F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N MET F 125 " --> pdb=" O GLU F 121 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP F 129 " --> pdb=" O MET F 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 78 Processing helix chain 'G' and resid 89 through 92 removed outlier: 3.544A pdb=" N ALA G 92 " --> pdb=" O VAL G 89 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 89 through 92' Processing helix chain 'G' and resid 93 through 106 removed outlier: 3.791A pdb=" N VAL G 97 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LYS G 104 " --> pdb=" O GLY G 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 109 through 113 Processing helix chain 'G' and resid 125 through 129 removed outlier: 3.865A pdb=" N ARG G 129 " --> pdb=" O GLU G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 147 removed outlier: 3.681A pdb=" N GLU G 145 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG G 146 " --> pdb=" O ALA G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 165 through 179 Processing helix chain 'G' and resid 191 through 205 removed outlier: 3.501A pdb=" N ALA G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 227 Processing helix chain 'G' and resid 227 through 236 removed outlier: 4.011A pdb=" N GLU G 231 " --> pdb=" O VAL G 227 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU G 232 " --> pdb=" O GLN G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 253 through 258 removed outlier: 3.722A pdb=" N ASP G 256 " --> pdb=" O GLY G 253 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER G 257 " --> pdb=" O LYS G 254 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLY G 258 " --> pdb=" O TYR G 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 253 through 258' Processing helix chain 'G' and resid 263 through 267 Processing helix chain 'G' and resid 270 through 279 removed outlier: 3.534A pdb=" N LYS G 274 " --> pdb=" O TYR G 270 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER G 279 " --> pdb=" O ASP G 275 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 299 removed outlier: 3.521A pdb=" N GLN G 285 " --> pdb=" O GLU G 281 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLN G 286 " --> pdb=" O GLY G 282 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ALA G 287 " --> pdb=" O ARG G 283 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU G 291 " --> pdb=" O ALA G 287 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA G 294 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE G 295 " --> pdb=" O GLU G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 302 through 310 Processing helix chain 'G' and resid 326 through 335 Processing helix chain 'G' and resid 344 through 356 removed outlier: 3.662A pdb=" N VAL G 348 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 52 Processing helix chain 'H' and resid 64 through 67 removed outlier: 3.970A pdb=" N ARG H 67 " --> pdb=" O LYS H 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 64 through 67' Processing helix chain 'H' and resid 84 through 95 removed outlier: 3.844A pdb=" N TYR H 92 " --> pdb=" O ILE H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 114 removed outlier: 3.638A pdb=" N GLU H 111 " --> pdb=" O ASP H 107 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG H 114 " --> pdb=" O SER H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 131 removed outlier: 3.799A pdb=" N GLU H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET H 125 " --> pdb=" O GLU H 121 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ASP H 129 " --> pdb=" O MET H 125 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA2, first strand: chain 'A' and resid 212 through 214 removed outlier: 10.213A pdb=" N CYS A 212 " --> pdb=" O MET A 183 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N TRP A 185 " --> pdb=" O CYS A 212 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N GLN A 214 " --> pdb=" O TRP A 185 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N THR A 187 " --> pdb=" O GLN A 214 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP A 153 " --> pdb=" O TYR A 184 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N GLY A 186 " --> pdb=" O ASP A 153 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N VAL A 155 " --> pdb=" O GLY A 186 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N SER A 188 " --> pdb=" O VAL A 155 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA A 157 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE A 115 " --> pdb=" O VAL A 154 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N PHE A 156 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR A 117 " --> pdb=" O PHE A 156 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LEU A 83 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N ALA A 240 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N VAL A 320 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR A 242 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LEU A 322 " --> pdb=" O THR A 242 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 42 through 47 removed outlier: 3.504A pdb=" N ILE B 37 " --> pdb=" O PHE B 44 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AA5, first strand: chain 'C' and resid 212 through 214 removed outlier: 10.209A pdb=" N CYS C 212 " --> pdb=" O MET C 183 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N TRP C 185 " --> pdb=" O CYS C 212 " (cutoff:3.500A) removed outlier: 8.976A pdb=" N GLN C 214 " --> pdb=" O TRP C 185 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N THR C 187 " --> pdb=" O GLN C 214 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASP C 153 " --> pdb=" O TYR C 184 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLY C 186 " --> pdb=" O ASP C 153 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N VAL C 155 " --> pdb=" O GLY C 186 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N SER C 188 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ALA C 157 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE C 115 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N PHE C 156 " --> pdb=" O ILE C 115 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N THR C 117 " --> pdb=" O PHE C 156 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU C 83 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N ALA C 240 " --> pdb=" O SER C 318 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL C 320 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR C 242 " --> pdb=" O VAL C 320 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU C 322 " --> pdb=" O THR C 242 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 42 through 47 Processing sheet with id=AA7, first strand: chain 'E' and resid 39 through 41 Processing sheet with id=AA8, first strand: chain 'E' and resid 212 through 214 removed outlier: 10.210A pdb=" N CYS E 212 " --> pdb=" O MET E 183 " (cutoff:3.500A) removed outlier: 7.806A pdb=" N TRP E 185 " --> pdb=" O CYS E 212 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N GLN E 214 " --> pdb=" O TRP E 185 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N THR E 187 " --> pdb=" O GLN E 214 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N ASP E 153 " --> pdb=" O TYR E 184 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N GLY E 186 " --> pdb=" O ASP E 153 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N VAL E 155 " --> pdb=" O GLY E 186 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N SER E 188 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA E 157 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE E 115 " --> pdb=" O ASP E 153 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL E 155 " --> pdb=" O ILE E 115 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N THR E 117 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N ALA E 157 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU E 83 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N ALA E 240 " --> pdb=" O SER E 318 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL E 320 " --> pdb=" O ALA E 240 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N THR E 242 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU E 322 " --> pdb=" O THR E 242 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 42 through 47 Processing sheet with id=AB1, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AB2, first strand: chain 'G' and resid 212 through 214 removed outlier: 10.209A pdb=" N CYS G 212 " --> pdb=" O MET G 183 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N TRP G 185 " --> pdb=" O CYS G 212 " (cutoff:3.500A) removed outlier: 8.977A pdb=" N GLN G 214 " --> pdb=" O TRP G 185 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N THR G 187 " --> pdb=" O GLN G 214 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASP G 153 " --> pdb=" O TYR G 184 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N GLY G 186 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N VAL G 155 " --> pdb=" O GLY G 186 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N SER G 188 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ALA G 157 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE G 115 " --> pdb=" O ASP G 153 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL G 155 " --> pdb=" O ILE G 115 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR G 117 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ALA G 157 " --> pdb=" O THR G 117 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU G 83 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ALA G 240 " --> pdb=" O SER G 318 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N VAL G 320 " --> pdb=" O ALA G 240 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR G 242 " --> pdb=" O VAL G 320 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LEU G 322 " --> pdb=" O THR G 242 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 42 through 47 526 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 1.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2858 1.32 - 1.45: 3316 1.45 - 1.57: 7782 1.57 - 1.69: 28 1.69 - 1.81: 144 Bond restraints: 14128 Sorted by residual: bond pdb=" O2B NAP A1001 " pdb=" P2B NAP A1001 " ideal model delta sigma weight residual 1.736 1.613 0.123 2.00e-02 2.50e+03 3.80e+01 bond pdb=" O2B NAP E1001 " pdb=" P2B NAP E1001 " ideal model delta sigma weight residual 1.736 1.613 0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" O2B NAP C1001 " pdb=" P2B NAP C1001 " ideal model delta sigma weight residual 1.736 1.614 0.122 2.00e-02 2.50e+03 3.74e+01 bond pdb=" O2B NAP G1001 " pdb=" P2B NAP G1001 " ideal model delta sigma weight residual 1.736 1.614 0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" O3 NAP A1001 " pdb=" PN NAP A1001 " ideal model delta sigma weight residual 1.643 1.745 -0.102 2.00e-02 2.50e+03 2.59e+01 ... (remaining 14123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.12: 19007 7.12 - 14.24: 76 14.24 - 21.36: 13 21.36 - 28.47: 4 28.47 - 35.59: 4 Bond angle restraints: 19104 Sorted by residual: angle pdb=" O1A NAP G1001 " pdb=" PA NAP G1001 " pdb=" O3 NAP G1001 " ideal model delta sigma weight residual 111.13 75.54 35.59 3.00e+00 1.11e-01 1.41e+02 angle pdb=" O1A NAP A1001 " pdb=" PA NAP A1001 " pdb=" O3 NAP A1001 " ideal model delta sigma weight residual 111.13 75.55 35.58 3.00e+00 1.11e-01 1.41e+02 angle pdb=" O1A NAP C1001 " pdb=" PA NAP C1001 " pdb=" O3 NAP C1001 " ideal model delta sigma weight residual 111.13 75.61 35.52 3.00e+00 1.11e-01 1.40e+02 angle pdb=" O1A NAP E1001 " pdb=" PA NAP E1001 " pdb=" O3 NAP E1001 " ideal model delta sigma weight residual 111.13 75.65 35.48 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N ILE A 119 " pdb=" CA ILE A 119 " pdb=" C ILE A 119 " ideal model delta sigma weight residual 112.17 122.69 -10.52 9.50e-01 1.11e+00 1.23e+02 ... (remaining 19099 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.90: 8016 14.90 - 29.79: 458 29.79 - 44.69: 138 44.69 - 59.58: 36 59.58 - 74.48: 16 Dihedral angle restraints: 8664 sinusoidal: 3752 harmonic: 4912 Sorted by residual: dihedral pdb=" N PHE A 120 " pdb=" C PHE A 120 " pdb=" CA PHE A 120 " pdb=" CB PHE A 120 " ideal model delta harmonic sigma weight residual 122.80 133.54 -10.74 0 2.50e+00 1.60e-01 1.84e+01 dihedral pdb=" C PHE A 120 " pdb=" N PHE A 120 " pdb=" CA PHE A 120 " pdb=" CB PHE A 120 " ideal model delta harmonic sigma weight residual -122.60 -132.74 10.14 0 2.50e+00 1.60e-01 1.64e+01 dihedral pdb=" N VAL E 58 " pdb=" C VAL E 58 " pdb=" CA VAL E 58 " pdb=" CB VAL E 58 " ideal model delta harmonic sigma weight residual 123.40 133.07 -9.67 0 2.50e+00 1.60e-01 1.49e+01 ... (remaining 8661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 1992 0.154 - 0.307: 40 0.307 - 0.461: 15 0.461 - 0.614: 1 0.614 - 0.768: 4 Chirality restraints: 2052 Sorted by residual: chirality pdb=" C2B NAP E1001 " pdb=" C1B NAP E1001 " pdb=" C3B NAP E1001 " pdb=" O2B NAP E1001 " both_signs ideal model delta sigma weight residual False -2.75 -1.99 -0.77 2.00e-01 2.50e+01 1.47e+01 chirality pdb=" C2B NAP A1001 " pdb=" C1B NAP A1001 " pdb=" C3B NAP A1001 " pdb=" O2B NAP A1001 " both_signs ideal model delta sigma weight residual False -2.75 -1.99 -0.76 2.00e-01 2.50e+01 1.45e+01 chirality pdb=" C2B NAP C1001 " pdb=" C1B NAP C1001 " pdb=" C3B NAP C1001 " pdb=" O2B NAP C1001 " both_signs ideal model delta sigma weight residual False -2.75 -1.99 -0.76 2.00e-01 2.50e+01 1.45e+01 ... (remaining 2049 not shown) Planarity restraints: 2436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE G 103 " -0.019 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C ILE G 103 " 0.065 2.00e-02 2.50e+03 pdb=" O ILE G 103 " -0.025 2.00e-02 2.50e+03 pdb=" N LYS G 104 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 136 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C ILE C 136 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE C 136 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE C 137 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 340 " 0.045 5.00e-02 4.00e+02 6.81e-02 7.41e+00 pdb=" N PRO E 341 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 341 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 341 " 0.039 5.00e-02 4.00e+02 ... (remaining 2433 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 164 2.61 - 3.18: 11514 3.18 - 3.75: 21529 3.75 - 4.33: 33158 4.33 - 4.90: 53006 Nonbonded interactions: 119371 Sorted by model distance: nonbonded pdb=" OH TYR E 199 " pdb=" O PRO F 71 " model vdw 2.034 3.040 nonbonded pdb=" ND2 ASN D 81 " pdb=" OG SER D 84 " model vdw 2.126 3.120 nonbonded pdb=" OH TYR G 199 " pdb=" O PRO H 71 " model vdw 2.195 3.040 nonbonded pdb=" OH TYR C 199 " pdb=" O PRO D 71 " model vdw 2.196 3.040 nonbonded pdb=" OG SER C 191 " pdb=" O HOH C1101 " model vdw 2.198 3.040 ... (remaining 119366 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' } 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: 5.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 13.890 Find NCS groups from input model: 0.240 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:8.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 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 : 0.011 0.123 14128 Z= 0.510 Angle : 1.409 35.593 19104 Z= 0.678 Chirality : 0.077 0.768 2052 Planarity : 0.007 0.068 2436 Dihedral : 11.599 74.476 5520 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.21 % Allowed : 1.65 % Favored : 98.15 % 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: -4.53 (0.15), residues: 1692 helix: -4.14 (0.09), residues: 808 sheet: -0.54 (0.38), residues: 176 loop : -1.99 (0.18), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG F 80 TYR 0.045 0.004 TYR D 116 PHE 0.031 0.004 PHE E 84 TRP 0.036 0.004 TRP G 185 HIS 0.008 0.003 HIS C 71 Details of bonding type rmsd covalent geometry : bond 0.01142 (14128) covalent geometry : angle 1.40888 (19104) hydrogen bonds : bond 0.31043 ( 526) hydrogen bonds : angle 9.61830 ( 1494) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 394 time to evaluate : 0.572 Fit side-chains revert: symmetry clash REVERT: A 75 LEU cc_start: 0.8575 (tp) cc_final: 0.8149 (mt) REVERT: A 148 GLN cc_start: 0.8616 (mt0) cc_final: 0.8203 (mt0) REVERT: A 301 CYS cc_start: 0.7705 (p) cc_final: 0.7393 (p) REVERT: B 97 ARG cc_start: 0.7999 (mtm180) cc_final: 0.7116 (ttt90) REVERT: C 75 LEU cc_start: 0.8587 (tp) cc_final: 0.8164 (mt) REVERT: C 148 GLN cc_start: 0.8588 (mt0) cc_final: 0.8132 (mt0) REVERT: C 301 CYS cc_start: 0.7685 (p) cc_final: 0.7391 (p) REVERT: D 97 ARG cc_start: 0.7972 (mtm180) cc_final: 0.7081 (ttt90) REVERT: E 75 LEU cc_start: 0.8594 (tp) cc_final: 0.8173 (mt) REVERT: E 148 GLN cc_start: 0.8622 (mt0) cc_final: 0.8165 (mt0) REVERT: E 301 CYS cc_start: 0.7666 (p) cc_final: 0.7364 (p) REVERT: F 97 ARG cc_start: 0.7992 (mtm180) cc_final: 0.7096 (ttt90) REVERT: G 75 LEU cc_start: 0.8590 (tp) cc_final: 0.8172 (mt) REVERT: G 148 GLN cc_start: 0.8635 (mt0) cc_final: 0.8165 (mt0) REVERT: H 97 ARG cc_start: 0.7978 (mtm180) cc_final: 0.7098 (ttt90) outliers start: 3 outliers final: 1 residues processed: 397 average time/residue: 0.8975 time to fit residues: 378.5996 Evaluate side-chains 280 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 279 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.0670 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 0.5980 chunk 149 optimal weight: 0.6980 overall best weight: 0.4318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN A 135 HIS A 333 ASN C 135 HIS C 175 HIS ** D 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 135 HIS E 175 HIS F 81 ASN G 135 HIS G 204 GLN H 81 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.138148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.114840 restraints weight = 16509.193| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.64 r_work: 0.3043 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14128 Z= 0.136 Angle : 0.669 8.341 19104 Z= 0.330 Chirality : 0.045 0.289 2052 Planarity : 0.005 0.033 2436 Dihedral : 10.796 64.505 2153 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.85 % Allowed : 9.89 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.44 (0.17), residues: 1692 helix: -1.99 (0.14), residues: 816 sheet: -0.49 (0.36), residues: 176 loop : -1.22 (0.21), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 43 TYR 0.012 0.001 TYR B 116 PHE 0.017 0.002 PHE A 120 TRP 0.014 0.001 TRP A 185 HIS 0.005 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00295 (14128) covalent geometry : angle 0.66928 (19104) hydrogen bonds : bond 0.05232 ( 526) hydrogen bonds : angle 4.78725 ( 1494) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 310 time to evaluate : 0.625 Fit side-chains REVERT: A 148 GLN cc_start: 0.8803 (mt0) cc_final: 0.8229 (mt0) REVERT: A 150 GLU cc_start: 0.8211 (pm20) cc_final: 0.7988 (pm20) REVERT: A 193 MET cc_start: 0.8056 (ttt) cc_final: 0.7839 (ttm) REVERT: B 33 GLU cc_start: 0.7478 (tt0) cc_final: 0.6779 (tt0) REVERT: B 67 ARG cc_start: 0.8361 (ptp-110) cc_final: 0.7875 (ptm160) REVERT: B 97 ARG cc_start: 0.8045 (mtm180) cc_final: 0.6764 (ttt90) REVERT: C 94 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7259 (ttmt) REVERT: C 148 GLN cc_start: 0.8755 (mt0) cc_final: 0.8205 (mt0) REVERT: D 43 ARG cc_start: 0.8164 (mtp-110) cc_final: 0.7557 (mtt90) REVERT: D 47 GLN cc_start: 0.8438 (OUTLIER) cc_final: 0.7666 (mt0) REVERT: D 97 ARG cc_start: 0.8052 (mtm180) cc_final: 0.6744 (ttt90) REVERT: D 111 GLU cc_start: 0.7360 (tp30) cc_final: 0.7032 (mm-30) REVERT: D 123 MET cc_start: 0.6644 (tpt) cc_final: 0.6433 (tpt) REVERT: E 94 LYS cc_start: 0.7712 (OUTLIER) cc_final: 0.7171 (ttmt) REVERT: E 126 GLU cc_start: 0.7939 (mm-30) cc_final: 0.7733 (mm-30) REVERT: E 148 GLN cc_start: 0.8757 (mt0) cc_final: 0.8219 (mt0) REVERT: E 315 GLU cc_start: 0.7356 (pt0) cc_final: 0.7002 (pt0) REVERT: F 43 ARG cc_start: 0.8153 (mtp-110) cc_final: 0.7522 (mtt90) REVERT: F 47 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7643 (mt0) REVERT: F 97 ARG cc_start: 0.8070 (mtm180) cc_final: 0.6771 (ttt90) REVERT: F 111 GLU cc_start: 0.7333 (tp30) cc_final: 0.7022 (mm-30) REVERT: G 94 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.7195 (ttmt) REVERT: G 126 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7765 (mm-30) REVERT: G 148 GLN cc_start: 0.8760 (mt0) cc_final: 0.8169 (mt0) REVERT: H 43 ARG cc_start: 0.8129 (mtp-110) cc_final: 0.7537 (mtt90) REVERT: H 47 GLN cc_start: 0.8453 (OUTLIER) cc_final: 0.7676 (mt0) REVERT: H 97 ARG cc_start: 0.8042 (mtm180) cc_final: 0.6752 (ttt90) REVERT: H 127 ARG cc_start: 0.6931 (mmm-85) cc_final: 0.6328 (mtt-85) outliers start: 27 outliers final: 8 residues processed: 319 average time/residue: 0.8104 time to fit residues: 276.5602 Evaluate side-chains 285 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 271 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 66 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN B 93 GLN C 204 GLN C 326 ASN C 333 ASN D 81 ASN D 93 GLN E 333 ASN F 81 ASN F 93 GLN G 333 ASN H 81 ASN H 93 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.134627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.109915 restraints weight = 16765.920| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 1.68 r_work: 0.3079 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 14128 Z= 0.241 Angle : 0.682 8.988 19104 Z= 0.332 Chirality : 0.047 0.316 2052 Planarity : 0.004 0.038 2436 Dihedral : 10.546 61.045 2152 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.30 % Allowed : 12.23 % Favored : 84.48 % 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: -1.46 (0.18), residues: 1692 helix: -0.94 (0.16), residues: 812 sheet: -0.48 (0.36), residues: 176 loop : -0.93 (0.21), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 298 TYR 0.026 0.002 TYR F 116 PHE 0.018 0.002 PHE B 85 TRP 0.020 0.002 TRP A 185 HIS 0.007 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00573 (14128) covalent geometry : angle 0.68233 (19104) hydrogen bonds : bond 0.04812 ( 526) hydrogen bonds : angle 4.33514 ( 1494) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 268 time to evaluate : 0.571 Fit side-chains REVERT: A 148 GLN cc_start: 0.8966 (mt0) cc_final: 0.8566 (mt0) REVERT: A 314 ASN cc_start: 0.8130 (m-40) cc_final: 0.7574 (p0) REVERT: A 350 GLU cc_start: 0.7826 (tp30) cc_final: 0.7559 (tp30) REVERT: B 97 ARG cc_start: 0.8242 (mtm180) cc_final: 0.7195 (tpt170) REVERT: C 94 LYS cc_start: 0.8239 (OUTLIER) cc_final: 0.7820 (ttmt) REVERT: C 148 GLN cc_start: 0.8969 (mt0) cc_final: 0.8513 (mt0) REVERT: C 193 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.8122 (mtt) REVERT: C 314 ASN cc_start: 0.8133 (m-40) cc_final: 0.7593 (p0) REVERT: D 43 ARG cc_start: 0.8201 (mtp-110) cc_final: 0.7941 (mtt90) REVERT: D 47 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7997 (mt0) REVERT: D 97 ARG cc_start: 0.8231 (mtm180) cc_final: 0.7170 (tpt170) REVERT: E 75 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8580 (tp) REVERT: E 94 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7771 (ttmt) REVERT: E 126 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7799 (mm-30) REVERT: E 148 GLN cc_start: 0.8959 (mt0) cc_final: 0.8465 (mt0) REVERT: E 314 ASN cc_start: 0.8143 (m-40) cc_final: 0.7598 (p0) REVERT: F 43 ARG cc_start: 0.8204 (mtp-110) cc_final: 0.7935 (mtt90) REVERT: F 47 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8000 (mt0) REVERT: F 97 ARG cc_start: 0.8244 (mtm180) cc_final: 0.7191 (tpt170) REVERT: G 94 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7787 (ttmt) REVERT: G 126 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7790 (mm-30) REVERT: G 148 GLN cc_start: 0.8980 (mt0) cc_final: 0.8482 (mt0) REVERT: G 350 GLU cc_start: 0.7829 (tp30) cc_final: 0.7556 (tp30) REVERT: H 43 ARG cc_start: 0.8227 (mtp-110) cc_final: 0.7955 (mtt90) REVERT: H 47 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7984 (mt0) REVERT: H 97 ARG cc_start: 0.8258 (mtm180) cc_final: 0.7191 (tpt170) outliers start: 48 outliers final: 10 residues processed: 290 average time/residue: 0.8528 time to fit residues: 263.8057 Evaluate side-chains 263 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 245 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 94 LYS Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 106 LYS Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 50 THR Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 57 optimal weight: 0.4980 chunk 78 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN F 81 ASN H 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.137947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.113583 restraints weight = 16531.234| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.67 r_work: 0.3123 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14128 Z= 0.130 Angle : 0.576 8.447 19104 Z= 0.280 Chirality : 0.042 0.241 2052 Planarity : 0.003 0.029 2436 Dihedral : 8.996 58.551 2152 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.34 % Allowed : 14.35 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.72 (0.19), residues: 1692 helix: -0.11 (0.17), residues: 812 sheet: -1.06 (0.41), residues: 136 loop : -0.62 (0.21), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 284 TYR 0.013 0.001 TYR C 199 PHE 0.009 0.001 PHE H 85 TRP 0.012 0.001 TRP A 185 HIS 0.005 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00302 (14128) covalent geometry : angle 0.57640 (19104) hydrogen bonds : bond 0.03593 ( 526) hydrogen bonds : angle 4.01528 ( 1494) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 259 time to evaluate : 0.504 Fit side-chains REVERT: A 75 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8565 (tp) REVERT: A 148 GLN cc_start: 0.8939 (mt0) cc_final: 0.8470 (mt0) REVERT: A 314 ASN cc_start: 0.8098 (m-40) cc_final: 0.7540 (OUTLIER) REVERT: A 331 MET cc_start: 0.8059 (mmm) cc_final: 0.7859 (mmm) REVERT: B 99 ARG cc_start: 0.8626 (ptm160) cc_final: 0.8163 (ptp-170) REVERT: C 75 LEU cc_start: 0.8851 (OUTLIER) cc_final: 0.8627 (tp) REVERT: C 148 GLN cc_start: 0.8932 (mt0) cc_final: 0.8391 (mt0) REVERT: C 314 ASN cc_start: 0.8104 (m-40) cc_final: 0.7582 (OUTLIER) REVERT: D 99 ARG cc_start: 0.8704 (ptm160) cc_final: 0.8225 (ptp-170) REVERT: E 94 LYS cc_start: 0.8114 (OUTLIER) cc_final: 0.7670 (ttmt) REVERT: E 126 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7769 (mm-30) REVERT: E 148 GLN cc_start: 0.8934 (mt0) cc_final: 0.8427 (mt0) REVERT: E 314 ASN cc_start: 0.8133 (m-40) cc_final: 0.7588 (OUTLIER) REVERT: F 43 ARG cc_start: 0.8142 (mtp-110) cc_final: 0.7892 (mtt90) REVERT: F 99 ARG cc_start: 0.8652 (ptm160) cc_final: 0.8214 (ptp-170) REVERT: F 123 MET cc_start: 0.6886 (tpt) cc_final: 0.6680 (tpt) REVERT: G 75 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8536 (tp) REVERT: G 94 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7667 (ttmt) REVERT: G 105 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8299 (ptmm) REVERT: G 126 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7725 (mm-30) REVERT: G 148 GLN cc_start: 0.8975 (mt0) cc_final: 0.8454 (mt0) REVERT: G 314 ASN cc_start: 0.8079 (m-40) cc_final: 0.7528 (OUTLIER) REVERT: G 331 MET cc_start: 0.8080 (mmm) cc_final: 0.7857 (mmm) REVERT: H 99 ARG cc_start: 0.8686 (ptm160) cc_final: 0.8207 (ptp-170) outliers start: 34 outliers final: 9 residues processed: 271 average time/residue: 0.8317 time to fit residues: 240.7895 Evaluate side-chains 255 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 244 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 106 LYS Chi-restraints excluded: chain G residue 302 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 41 optimal weight: 0.4980 chunk 81 optimal weight: 0.4980 chunk 107 optimal weight: 5.9990 chunk 160 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 154 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 142 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN F 81 ASN H 81 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.141547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.118761 restraints weight = 16504.749| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 1.53 r_work: 0.3020 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.3106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14128 Z= 0.146 Angle : 0.584 8.540 19104 Z= 0.285 Chirality : 0.043 0.262 2052 Planarity : 0.003 0.030 2436 Dihedral : 7.846 54.880 2152 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.40 % Allowed : 15.32 % Favored : 82.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.22 (0.20), residues: 1692 helix: 0.41 (0.18), residues: 804 sheet: -1.03 (0.42), residues: 136 loop : -0.45 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 284 TYR 0.013 0.001 TYR B 116 PHE 0.016 0.001 PHE A 205 TRP 0.016 0.001 TRP A 185 HIS 0.006 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00344 (14128) covalent geometry : angle 0.58398 (19104) hydrogen bonds : bond 0.03636 ( 526) hydrogen bonds : angle 3.89711 ( 1494) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 261 time to evaluate : 0.569 Fit side-chains REVERT: A 148 GLN cc_start: 0.8806 (mt0) cc_final: 0.8238 (mt0) REVERT: A 193 MET cc_start: 0.8173 (OUTLIER) cc_final: 0.7158 (mpp) REVERT: A 314 ASN cc_start: 0.8199 (m-40) cc_final: 0.7476 (OUTLIER) REVERT: A 350 GLU cc_start: 0.7904 (tp30) cc_final: 0.7694 (tp30) REVERT: B 47 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8028 (mt0) REVERT: B 99 ARG cc_start: 0.8603 (ptm160) cc_final: 0.8033 (ptp-170) REVERT: C 148 GLN cc_start: 0.8803 (mt0) cc_final: 0.8183 (mt0) REVERT: C 314 ASN cc_start: 0.8201 (m-40) cc_final: 0.7501 (OUTLIER) REVERT: D 47 GLN cc_start: 0.8544 (OUTLIER) cc_final: 0.7725 (mt0) REVERT: D 99 ARG cc_start: 0.8638 (ptm160) cc_final: 0.8036 (ptp-170) REVERT: E 94 LYS cc_start: 0.7896 (OUTLIER) cc_final: 0.7385 (ttmt) REVERT: E 148 GLN cc_start: 0.8854 (mt0) cc_final: 0.8275 (mt0) REVERT: E 193 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7171 (mpp) REVERT: E 314 ASN cc_start: 0.8205 (m-40) cc_final: 0.7501 (OUTLIER) REVERT: E 350 GLU cc_start: 0.7745 (tp30) cc_final: 0.7418 (tp30) REVERT: F 43 ARG cc_start: 0.8221 (mtp-110) cc_final: 0.7710 (mtt90) REVERT: F 73 ARG cc_start: 0.7945 (mtt180) cc_final: 0.7718 (mtm-85) REVERT: F 99 ARG cc_start: 0.8631 (ptm160) cc_final: 0.8014 (ptp-170) REVERT: G 94 LYS cc_start: 0.7870 (OUTLIER) cc_final: 0.7355 (ttmt) REVERT: G 105 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.8084 (ptmm) REVERT: G 148 GLN cc_start: 0.8848 (mt0) cc_final: 0.8245 (mt0) REVERT: G 193 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7173 (mpp) REVERT: G 314 ASN cc_start: 0.8181 (m-40) cc_final: 0.7446 (OUTLIER) REVERT: H 99 ARG cc_start: 0.8622 (ptm160) cc_final: 0.8023 (ptp-170) outliers start: 35 outliers final: 16 residues processed: 278 average time/residue: 0.8319 time to fit residues: 247.0584 Evaluate side-chains 266 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 246 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 315 GLU Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 154 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 95 optimal weight: 0.0670 chunk 147 optimal weight: 2.9990 chunk 167 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.2922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN D 81 ASN F 81 ASN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.140022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.117225 restraints weight = 16404.141| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.52 r_work: 0.2991 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 14128 Z= 0.182 Angle : 0.612 8.652 19104 Z= 0.298 Chirality : 0.044 0.272 2052 Planarity : 0.004 0.039 2436 Dihedral : 7.459 52.638 2152 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.16 % Allowed : 15.66 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.20), residues: 1692 helix: 0.51 (0.18), residues: 804 sheet: -1.02 (0.42), residues: 136 loop : -0.39 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 43 TYR 0.016 0.002 TYR H 116 PHE 0.015 0.002 PHE B 85 TRP 0.018 0.001 TRP A 185 HIS 0.007 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00436 (14128) covalent geometry : angle 0.61154 (19104) hydrogen bonds : bond 0.03806 ( 526) hydrogen bonds : angle 3.92927 ( 1494) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 263 time to evaluate : 0.602 Fit side-chains REVERT: A 75 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8289 (tp) REVERT: A 148 GLN cc_start: 0.8831 (mt0) cc_final: 0.8252 (mt0) REVERT: A 193 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7156 (mpp) REVERT: A 314 ASN cc_start: 0.8221 (m-40) cc_final: 0.7460 (OUTLIER) REVERT: A 331 MET cc_start: 0.7979 (mmm) cc_final: 0.7743 (mmm) REVERT: A 350 GLU cc_start: 0.7899 (tp30) cc_final: 0.7571 (tp30) REVERT: B 99 ARG cc_start: 0.8628 (ptm160) cc_final: 0.8027 (ptp-170) REVERT: C 75 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8319 (tp) REVERT: C 148 GLN cc_start: 0.8781 (mt0) cc_final: 0.8165 (mt0) REVERT: C 314 ASN cc_start: 0.8314 (m-40) cc_final: 0.7473 (OUTLIER) REVERT: C 350 GLU cc_start: 0.7877 (tp30) cc_final: 0.7596 (tp30) REVERT: D 47 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8286 (mp10) REVERT: D 99 ARG cc_start: 0.8640 (ptm160) cc_final: 0.7999 (ptp-170) REVERT: E 75 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8238 (tt) REVERT: E 94 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7345 (ttmt) REVERT: E 148 GLN cc_start: 0.8793 (mt0) cc_final: 0.8200 (mt0) REVERT: E 314 ASN cc_start: 0.8313 (m-40) cc_final: 0.7471 (OUTLIER) REVERT: E 350 GLU cc_start: 0.7732 (tp30) cc_final: 0.7413 (tp30) REVERT: F 43 ARG cc_start: 0.8222 (mtp-110) cc_final: 0.7690 (mtt90) REVERT: F 73 ARG cc_start: 0.7957 (mtt180) cc_final: 0.7660 (mtm-85) REVERT: F 99 ARG cc_start: 0.8636 (ptm160) cc_final: 0.7990 (ptp-170) REVERT: G 75 LEU cc_start: 0.8657 (OUTLIER) cc_final: 0.8320 (tp) REVERT: G 94 LYS cc_start: 0.7861 (OUTLIER) cc_final: 0.7339 (ttmt) REVERT: G 105 LYS cc_start: 0.8326 (OUTLIER) cc_final: 0.8046 (ptmm) REVERT: G 148 GLN cc_start: 0.8798 (mt0) cc_final: 0.8190 (mt0) REVERT: G 193 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7148 (mpp) REVERT: G 223 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7533 (tm-30) REVERT: G 314 ASN cc_start: 0.8209 (m-40) cc_final: 0.7459 (OUTLIER) REVERT: G 331 MET cc_start: 0.7985 (mmm) cc_final: 0.7742 (mmm) REVERT: H 99 ARG cc_start: 0.8631 (ptm160) cc_final: 0.7994 (ptp-170) outliers start: 46 outliers final: 16 residues processed: 281 average time/residue: 0.7839 time to fit residues: 236.1517 Evaluate side-chains 266 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 244 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 75 LEU Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 47 GLN Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 94 LYS Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 75 LEU Chi-restraints excluded: chain G residue 94 LYS Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 315 GLU Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 77 optimal weight: 0.0570 chunk 37 optimal weight: 0.9980 chunk 130 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 74 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN D 81 ASN F 81 ASN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.136784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.113455 restraints weight = 16523.854| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 1.58 r_work: 0.2987 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14128 Z= 0.166 Angle : 0.605 8.521 19104 Z= 0.295 Chirality : 0.043 0.261 2052 Planarity : 0.004 0.027 2436 Dihedral : 7.384 52.562 2152 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.68 % Allowed : 17.03 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.20), residues: 1692 helix: 0.64 (0.18), residues: 804 sheet: -1.00 (0.42), residues: 136 loop : -0.35 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 43 TYR 0.013 0.001 TYR H 116 PHE 0.018 0.002 PHE H 54 TRP 0.016 0.001 TRP A 185 HIS 0.006 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00396 (14128) covalent geometry : angle 0.60515 (19104) hydrogen bonds : bond 0.03643 ( 526) hydrogen bonds : angle 3.89843 ( 1494) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 253 time to evaluate : 0.469 Fit side-chains REVERT: A 148 GLN cc_start: 0.8800 (mt0) cc_final: 0.8219 (mt0) REVERT: A 193 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7455 (mpp) REVERT: A 314 ASN cc_start: 0.8220 (m-40) cc_final: 0.7466 (OUTLIER) REVERT: B 33 GLU cc_start: 0.7430 (tt0) cc_final: 0.7192 (mp0) REVERT: B 47 GLN cc_start: 0.8521 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: B 99 ARG cc_start: 0.8651 (ptm160) cc_final: 0.8073 (ptp-170) REVERT: B 111 GLU cc_start: 0.7305 (tp30) cc_final: 0.7102 (mm-30) REVERT: C 148 GLN cc_start: 0.8810 (mt0) cc_final: 0.8183 (mt0) REVERT: C 193 MET cc_start: 0.8337 (mtt) cc_final: 0.7489 (mpp) REVERT: C 314 ASN cc_start: 0.8314 (m-40) cc_final: 0.7475 (OUTLIER) REVERT: C 350 GLU cc_start: 0.7862 (tp30) cc_final: 0.7552 (tp30) REVERT: D 33 GLU cc_start: 0.7798 (pm20) cc_final: 0.7444 (pt0) REVERT: D 99 ARG cc_start: 0.8647 (ptm160) cc_final: 0.8016 (ptp-170) REVERT: E 75 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8399 (tm) REVERT: E 148 GLN cc_start: 0.8832 (mt0) cc_final: 0.8233 (mt0) REVERT: E 314 ASN cc_start: 0.8296 (m-40) cc_final: 0.7460 (OUTLIER) REVERT: E 331 MET cc_start: 0.7987 (mmm) cc_final: 0.7765 (mmm) REVERT: E 350 GLU cc_start: 0.7732 (tp30) cc_final: 0.7433 (tp30) REVERT: F 43 ARG cc_start: 0.8209 (mtp-110) cc_final: 0.7703 (mtt90) REVERT: F 47 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7788 (mt0) REVERT: F 73 ARG cc_start: 0.7947 (mtt180) cc_final: 0.7689 (mtm-85) REVERT: F 99 ARG cc_start: 0.8648 (ptm160) cc_final: 0.8003 (ptp-170) REVERT: G 105 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8055 (ptmm) REVERT: G 148 GLN cc_start: 0.8780 (mt0) cc_final: 0.8173 (mt0) REVERT: G 193 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7160 (mpp) REVERT: G 223 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7537 (tm-30) REVERT: G 314 ASN cc_start: 0.8207 (m-40) cc_final: 0.7461 (OUTLIER) REVERT: H 47 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7771 (mt0) outliers start: 39 outliers final: 20 residues processed: 269 average time/residue: 0.7763 time to fit residues: 224.0330 Evaluate side-chains 260 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 237 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 315 GLU Chi-restraints excluded: chain B residue 40 SER Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 68 MET Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain E residue 75 LEU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain F residue 40 SER Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 105 LYS Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain G residue 315 GLU Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 47 GLN Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 100 optimal weight: 0.9980 chunk 64 optimal weight: 0.0470 chunk 84 optimal weight: 4.9990 chunk 124 optimal weight: 0.9990 chunk 148 optimal weight: 0.0570 chunk 141 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN B 81 ASN D 81 ASN F 81 ASN H 81 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.140745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.116284 restraints weight = 16518.948| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.65 r_work: 0.3177 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14128 Z= 0.113 Angle : 0.574 9.077 19104 Z= 0.278 Chirality : 0.041 0.220 2052 Planarity : 0.003 0.026 2436 Dihedral : 7.012 54.735 2152 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.51 % Allowed : 19.02 % Favored : 79.46 % 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: 0.32 (0.20), residues: 1692 helix: 0.94 (0.19), residues: 804 sheet: -0.95 (0.43), residues: 136 loop : -0.24 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 43 TYR 0.015 0.001 TYR G 199 PHE 0.018 0.001 PHE D 54 TRP 0.012 0.001 TRP A 185 HIS 0.005 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00263 (14128) covalent geometry : angle 0.57377 (19104) hydrogen bonds : bond 0.03139 ( 526) hydrogen bonds : angle 3.78412 ( 1494) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 260 time to evaluate : 0.420 Fit side-chains REVERT: A 148 GLN cc_start: 0.8905 (mt0) cc_final: 0.8419 (mt0) REVERT: A 193 MET cc_start: 0.8382 (OUTLIER) cc_final: 0.7524 (mpp) REVERT: A 314 ASN cc_start: 0.8133 (m-40) cc_final: 0.7582 (OUTLIER) REVERT: B 47 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: B 99 ARG cc_start: 0.8705 (ptm160) cc_final: 0.8300 (ptp-170) REVERT: C 148 GLN cc_start: 0.8915 (mt0) cc_final: 0.8383 (mt0) REVERT: C 193 MET cc_start: 0.8535 (mtt) cc_final: 0.7879 (mpp) REVERT: C 314 ASN cc_start: 0.8222 (m-40) cc_final: 0.7610 (OUTLIER) REVERT: D 33 GLU cc_start: 0.7883 (pm20) cc_final: 0.7551 (pt0) REVERT: D 97 ARG cc_start: 0.8274 (ptp-170) cc_final: 0.7894 (mtm-85) REVERT: E 75 LEU cc_start: 0.8872 (tt) cc_final: 0.8669 (tm) REVERT: E 148 GLN cc_start: 0.8917 (mt0) cc_final: 0.8413 (mt0) REVERT: E 314 ASN cc_start: 0.8207 (m-40) cc_final: 0.7595 (OUTLIER) REVERT: E 350 GLU cc_start: 0.7741 (tp30) cc_final: 0.7513 (tp30) REVERT: F 43 ARG cc_start: 0.8186 (mtp-110) cc_final: 0.7927 (mtt90) REVERT: F 47 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.7958 (mt0) REVERT: F 99 ARG cc_start: 0.8741 (ptm160) cc_final: 0.8288 (ptp-170) REVERT: G 148 GLN cc_start: 0.8916 (mt0) cc_final: 0.8408 (mt0) REVERT: G 193 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7762 (mpp) REVERT: G 314 ASN cc_start: 0.8117 (m-40) cc_final: 0.7564 (OUTLIER) REVERT: H 47 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7944 (mt0) REVERT: H 48 LEU cc_start: 0.8597 (tp) cc_final: 0.8320 (mt) outliers start: 22 outliers final: 8 residues processed: 265 average time/residue: 0.7868 time to fit residues: 223.5462 Evaluate side-chains 252 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 243 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain H residue 47 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 62 optimal weight: 0.9980 chunk 126 optimal weight: 1.9990 chunk 166 optimal weight: 0.6980 chunk 85 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 133 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 153 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 ASN B 81 ASN C 79 ASN D 81 ASN E 79 ASN F 81 ASN G 79 ASN H 81 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.132247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.105546 restraints weight = 16895.293| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.94 r_work: 0.2976 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14128 Z= 0.139 Angle : 0.596 9.505 19104 Z= 0.288 Chirality : 0.042 0.232 2052 Planarity : 0.003 0.030 2436 Dihedral : 7.002 53.860 2152 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.24 % Allowed : 19.71 % Favored : 79.05 % 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: 0.36 (0.20), residues: 1692 helix: 0.98 (0.19), residues: 804 sheet: -0.98 (0.42), residues: 136 loop : -0.21 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 43 TYR 0.011 0.001 TYR F 92 PHE 0.011 0.001 PHE B 85 TRP 0.015 0.001 TRP A 185 HIS 0.006 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00330 (14128) covalent geometry : angle 0.59598 (19104) hydrogen bonds : bond 0.03348 ( 526) hydrogen bonds : angle 3.80243 ( 1494) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 240 time to evaluate : 0.413 Fit side-chains REVERT: A 148 GLN cc_start: 0.8879 (mt0) cc_final: 0.8345 (mt0) REVERT: A 193 MET cc_start: 0.8363 (OUTLIER) cc_final: 0.7647 (mpp) REVERT: A 223 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7678 (tm-30) REVERT: A 314 ASN cc_start: 0.8305 (m-40) cc_final: 0.7511 (OUTLIER) REVERT: B 33 GLU cc_start: 0.7606 (tt0) cc_final: 0.7297 (mp0) REVERT: B 47 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8206 (mt0) REVERT: B 97 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7825 (ptp-170) REVERT: B 99 ARG cc_start: 0.8710 (ptm160) cc_final: 0.8189 (ptp-170) REVERT: C 148 GLN cc_start: 0.8870 (mt0) cc_final: 0.8292 (mt0) REVERT: C 193 MET cc_start: 0.8574 (mtt) cc_final: 0.7743 (mpp) REVERT: C 314 ASN cc_start: 0.8295 (m-40) cc_final: 0.7545 (OUTLIER) REVERT: D 33 GLU cc_start: 0.7899 (pm20) cc_final: 0.7612 (pt0) REVERT: E 148 GLN cc_start: 0.8876 (mt0) cc_final: 0.8324 (mt0) REVERT: E 223 GLU cc_start: 0.7896 (mm-30) cc_final: 0.7684 (tm-30) REVERT: E 314 ASN cc_start: 0.8308 (m-40) cc_final: 0.7537 (OUTLIER) REVERT: E 350 GLU cc_start: 0.7759 (tp30) cc_final: 0.7491 (tp30) REVERT: F 47 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.7943 (mt0) REVERT: F 73 ARG cc_start: 0.7908 (mtm-85) cc_final: 0.7634 (mtp-110) REVERT: F 99 ARG cc_start: 0.8806 (ptm160) cc_final: 0.8216 (ptp-170) REVERT: G 148 GLN cc_start: 0.8894 (mt0) cc_final: 0.8342 (mt0) REVERT: G 193 MET cc_start: 0.8699 (OUTLIER) cc_final: 0.7724 (mpp) REVERT: G 314 ASN cc_start: 0.8214 (m-40) cc_final: 0.7521 (OUTLIER) outliers start: 18 outliers final: 12 residues processed: 245 average time/residue: 0.7784 time to fit residues: 204.9569 Evaluate side-chains 250 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 237 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain D residue 98 LEU Chi-restraints excluded: chain D residue 112 GLU Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain F residue 47 GLN Chi-restraints excluded: chain G residue 153 ASP Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 302 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 94 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 144 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 165 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 131 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 81 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN D 81 ASN F 81 ASN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.132224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.105697 restraints weight = 16722.395| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.92 r_work: 0.2982 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14128 Z= 0.138 Angle : 0.605 10.862 19104 Z= 0.292 Chirality : 0.042 0.219 2052 Planarity : 0.003 0.031 2436 Dihedral : 6.945 53.745 2152 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.10 % Allowed : 19.99 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.20), residues: 1692 helix: 1.01 (0.19), residues: 804 sheet: -1.00 (0.42), residues: 136 loop : -0.20 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 43 TYR 0.017 0.001 TYR C 199 PHE 0.011 0.001 PHE E 205 TRP 0.014 0.001 TRP A 185 HIS 0.006 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00329 (14128) covalent geometry : angle 0.60476 (19104) hydrogen bonds : bond 0.03341 ( 526) hydrogen bonds : angle 3.80969 ( 1494) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3384 Ramachandran restraints generated. 1692 Oldfield, 0 Emsley, 1692 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 248 time to evaluate : 0.579 Fit side-chains REVERT: A 148 GLN cc_start: 0.8874 (mt0) cc_final: 0.8344 (mt0) REVERT: A 193 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7368 (mpp) REVERT: A 223 GLU cc_start: 0.7910 (mm-30) cc_final: 0.7675 (tm-30) REVERT: A 314 ASN cc_start: 0.8297 (m-40) cc_final: 0.7511 (OUTLIER) REVERT: B 47 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8153 (mt0) REVERT: B 97 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7746 (ptp-170) REVERT: B 99 ARG cc_start: 0.8711 (ptm160) cc_final: 0.8206 (ptp-170) REVERT: C 148 GLN cc_start: 0.8863 (mt0) cc_final: 0.8286 (mt0) REVERT: C 193 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.7782 (mpp) REVERT: C 314 ASN cc_start: 0.8293 (m-40) cc_final: 0.7544 (OUTLIER) REVERT: D 33 GLU cc_start: 0.7892 (pm20) cc_final: 0.7640 (pt0) REVERT: E 148 GLN cc_start: 0.8884 (mt0) cc_final: 0.8336 (mt0) REVERT: E 193 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7675 (mpp) REVERT: E 223 GLU cc_start: 0.7915 (mm-30) cc_final: 0.7699 (tm-30) REVERT: E 314 ASN cc_start: 0.8318 (m-40) cc_final: 0.7538 (OUTLIER) REVERT: E 350 GLU cc_start: 0.7798 (tp30) cc_final: 0.7495 (tp30) REVERT: F 73 ARG cc_start: 0.7894 (mtm-85) cc_final: 0.7609 (mtp-110) REVERT: F 99 ARG cc_start: 0.8780 (ptm160) cc_final: 0.8217 (ptp-170) REVERT: G 148 GLN cc_start: 0.8881 (mt0) cc_final: 0.8323 (mt0) REVERT: G 193 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.7695 (mpp) REVERT: G 314 ASN cc_start: 0.8207 (m-40) cc_final: 0.7522 (OUTLIER) REVERT: G 350 GLU cc_start: 0.7906 (tp30) cc_final: 0.7548 (tp30) REVERT: H 111 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7296 (tm-30) outliers start: 16 outliers final: 12 residues processed: 252 average time/residue: 0.7643 time to fit residues: 207.2718 Evaluate side-chains 253 residues out of total 1460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 239 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 MET Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain B residue 47 GLN Chi-restraints excluded: chain B residue 97 ARG Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain C residue 153 ASP Chi-restraints excluded: chain C residue 193 MET Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain E residue 193 MET Chi-restraints excluded: chain E residue 302 THR Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain G residue 193 MET Chi-restraints excluded: chain G residue 302 THR Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 82 optimal weight: 1.9990 chunk 152 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 ASN D 81 ASN F 81 ASN H 81 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.133075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.106549 restraints weight = 16823.518| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 1.93 r_work: 0.2997 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14128 Z= 0.126 Angle : 0.600 11.307 19104 Z= 0.289 Chirality : 0.041 0.197 2052 Planarity : 0.003 0.030 2436 Dihedral : 6.817 54.405 2152 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.03 % Allowed : 20.33 % Favored : 78.64 % 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: 0.48 (0.20), residues: 1692 helix: 1.06 (0.18), residues: 820 sheet: -1.04 (0.42), residues: 136 loop : -0.14 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 284 TYR 0.011 0.001 TYR H 92 PHE 0.010 0.001 PHE B 85 TRP 0.014 0.001 TRP A 185 HIS 0.005 0.001 HIS C 135 Details of bonding type rmsd covalent geometry : bond 0.00299 (14128) covalent geometry : angle 0.59971 (19104) hydrogen bonds : bond 0.03244 ( 526) hydrogen bonds : angle 3.77735 ( 1494) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5948.23 seconds wall clock time: 101 minutes 58.04 seconds (6118.04 seconds total)