Starting phenix.real_space_refine on Wed Mar 4 21:07:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6u5r_20653/03_2026/6u5r_20653.cif Found real_map, /net/cci-nas-00/data/ceres_data/6u5r_20653/03_2026/6u5r_20653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6u5r_20653/03_2026/6u5r_20653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6u5r_20653/03_2026/6u5r_20653.map" model { file = "/net/cci-nas-00/data/ceres_data/6u5r_20653/03_2026/6u5r_20653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6u5r_20653/03_2026/6u5r_20653.cif" } resolution = 3.6 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 Ca 8 9.91 5 S 68 5.16 5 C 10436 2.51 5 N 2820 2.21 5 O 3184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16516 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2445 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "C" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2445 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "D" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "E" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2445 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "F" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "G" Number of atoms: 2445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2445 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 9, 'TRANS': 307} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "H" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 55 Unresolved non-hydrogen dihedrals: 35 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 2, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 38 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.91, per 1000 atoms: 0.24 Number of scatterers: 16516 At special positions: 0 Unit cell: (150.152, 150.152, 117.272, 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) Ca 8 19.99 S 68 16.00 O 3184 8.00 N 2820 7.00 C 10436 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: 1.37 Conformation dependent library (CDL) restraints added in 729.1 milliseconds 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3952 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 16 sheets defined 46.8% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain 'A' and resid 21 through 42 removed outlier: 3.920A pdb=" N LEU A 25 " --> pdb=" O THR A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 69 through 105 removed outlier: 4.076A pdb=" N VAL A 77 " --> pdb=" O MET A 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 129 Processing helix chain 'A' and resid 146 through 156 removed outlier: 3.530A pdb=" N LYS A 150 " --> pdb=" O GLU A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 170 Processing helix chain 'A' and resid 187 through 202 removed outlier: 3.755A pdb=" N THR A 191 " --> pdb=" O SER A 187 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE A 201 " --> pdb=" O GLY A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 216 through 223 Processing helix chain 'A' and resid 230 through 240 removed outlier: 3.604A pdb=" N ILE A 234 " --> pdb=" O SER A 230 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER A 240 " --> pdb=" O GLY A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 257 removed outlier: 4.044A pdb=" N MET A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE A 251 " --> pdb=" O TYR A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 284 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 323 through 335 removed outlier: 3.692A pdb=" N SER A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 131 Processing helix chain 'B' and resid 146 through 156 removed outlier: 4.359A pdb=" N LYS B 150 " --> pdb=" O GLU B 146 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS B 151 " --> pdb=" O ASN B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 202 Processing helix chain 'B' and resid 216 through 224 removed outlier: 3.578A pdb=" N GLY B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 240 removed outlier: 3.662A pdb=" N ILE B 234 " --> pdb=" O SER B 230 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER B 240 " --> pdb=" O GLY B 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 247 through 256 removed outlier: 3.709A pdb=" N PHE B 251 " --> pdb=" O TYR B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 323 through 334 removed outlier: 3.924A pdb=" N GLU B 328 " --> pdb=" O PRO B 324 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 329 " --> pdb=" O GLU B 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 42 removed outlier: 3.920A pdb=" N LEU C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 57 Processing helix chain 'C' and resid 69 through 105 removed outlier: 4.076A pdb=" N VAL C 77 " --> pdb=" O MET C 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 78 " --> pdb=" O TYR C 74 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL C 91 " --> pdb=" O PHE C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 146 through 156 removed outlier: 3.530A pdb=" N LYS C 150 " --> pdb=" O GLU C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 170 Processing helix chain 'C' and resid 187 through 202 removed outlier: 3.755A pdb=" N THR C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LYS C 200 " --> pdb=" O LEU C 196 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE C 201 " --> pdb=" O GLY C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 215 No H-bonds generated for 'chain 'C' and resid 213 through 215' Processing helix chain 'C' and resid 216 through 223 Processing helix chain 'C' and resid 230 through 240 removed outlier: 3.604A pdb=" N ILE C 234 " --> pdb=" O SER C 230 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER C 240 " --> pdb=" O GLY C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 246 through 257 removed outlier: 4.044A pdb=" N MET C 250 " --> pdb=" O GLY C 246 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE C 251 " --> pdb=" O TYR C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 284 Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 323 through 335 removed outlier: 3.692A pdb=" N SER C 335 " --> pdb=" O LYS C 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 131 Processing helix chain 'D' and resid 146 through 156 removed outlier: 4.360A pdb=" N LYS D 150 " --> pdb=" O GLU D 146 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS D 151 " --> pdb=" O ASN D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 202 Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.578A pdb=" N GLY D 224 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 230 through 240 removed outlier: 3.662A pdb=" N ILE D 234 " --> pdb=" O SER D 230 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER D 240 " --> pdb=" O GLY D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 247 through 256 removed outlier: 3.709A pdb=" N PHE D 251 " --> pdb=" O TYR D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 289 Processing helix chain 'D' and resid 323 through 334 removed outlier: 3.924A pdb=" N GLU D 328 " --> pdb=" O PRO D 324 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG D 329 " --> pdb=" O GLU D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 42 removed outlier: 3.920A pdb=" N LEU E 25 " --> pdb=" O THR E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 57 Processing helix chain 'E' and resid 69 through 105 removed outlier: 4.076A pdb=" N VAL E 77 " --> pdb=" O MET E 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR E 78 " --> pdb=" O TYR E 74 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL E 91 " --> pdb=" O PHE E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 124 through 129 Processing helix chain 'E' and resid 146 through 156 removed outlier: 3.530A pdb=" N LYS E 150 " --> pdb=" O GLU E 146 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 170 Processing helix chain 'E' and resid 187 through 202 removed outlier: 3.754A pdb=" N THR E 191 " --> pdb=" O SER E 187 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS E 200 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ILE E 201 " --> pdb=" O GLY E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 216 through 223 Processing helix chain 'E' and resid 230 through 240 removed outlier: 3.604A pdb=" N ILE E 234 " --> pdb=" O SER E 230 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N SER E 240 " --> pdb=" O GLY E 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 257 removed outlier: 4.043A pdb=" N MET E 250 " --> pdb=" O GLY E 246 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE E 251 " --> pdb=" O TYR E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 284 Processing helix chain 'E' and resid 284 through 289 Processing helix chain 'E' and resid 323 through 335 removed outlier: 3.691A pdb=" N SER E 335 " --> pdb=" O LYS E 331 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 131 Processing helix chain 'F' and resid 146 through 156 removed outlier: 4.359A pdb=" N LYS F 150 " --> pdb=" O GLU F 146 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS F 151 " --> pdb=" O ASN F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 202 Processing helix chain 'F' and resid 216 through 224 removed outlier: 3.579A pdb=" N GLY F 224 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 240 removed outlier: 3.661A pdb=" N ILE F 234 " --> pdb=" O SER F 230 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N SER F 240 " --> pdb=" O GLY F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 256 removed outlier: 3.710A pdb=" N PHE F 251 " --> pdb=" O TYR F 247 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 289 Processing helix chain 'F' and resid 323 through 334 removed outlier: 3.924A pdb=" N GLU F 328 " --> pdb=" O PRO F 324 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG F 329 " --> pdb=" O GLU F 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 42 removed outlier: 3.920A pdb=" N LEU G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 57 Processing helix chain 'G' and resid 69 through 105 removed outlier: 4.077A pdb=" N VAL G 77 " --> pdb=" O MET G 73 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR G 78 " --> pdb=" O TYR G 74 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL G 91 " --> pdb=" O PHE G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 129 Processing helix chain 'G' and resid 146 through 156 removed outlier: 3.530A pdb=" N LYS G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 170 Processing helix chain 'G' and resid 187 through 202 removed outlier: 3.755A pdb=" N THR G 191 " --> pdb=" O SER G 187 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS G 200 " --> pdb=" O LEU G 196 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE G 201 " --> pdb=" O GLY G 197 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 215 No H-bonds generated for 'chain 'G' and resid 213 through 215' Processing helix chain 'G' and resid 216 through 223 Processing helix chain 'G' and resid 230 through 240 removed outlier: 3.604A pdb=" N ILE G 234 " --> pdb=" O SER G 230 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER G 240 " --> pdb=" O GLY G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 257 removed outlier: 4.043A pdb=" N MET G 250 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE G 251 " --> pdb=" O TYR G 247 " (cutoff:3.500A) Processing helix chain 'G' and resid 279 through 284 Processing helix chain 'G' and resid 284 through 289 Processing helix chain 'G' and resid 323 through 335 removed outlier: 3.692A pdb=" N SER G 335 " --> pdb=" O LYS G 331 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 131 Processing helix chain 'H' and resid 146 through 156 removed outlier: 4.359A pdb=" N LYS H 150 " --> pdb=" O GLU H 146 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS H 151 " --> pdb=" O ASN H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 187 through 202 Processing helix chain 'H' and resid 216 through 224 removed outlier: 3.577A pdb=" N GLY H 224 " --> pdb=" O LEU H 220 " (cutoff:3.500A) Processing helix chain 'H' and resid 230 through 240 removed outlier: 3.662A pdb=" N ILE H 234 " --> pdb=" O SER H 230 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER H 240 " --> pdb=" O GLY H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 247 through 256 removed outlier: 3.710A pdb=" N PHE H 251 " --> pdb=" O TYR H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 284 through 289 Processing helix chain 'H' and resid 323 through 334 removed outlier: 3.925A pdb=" N GLU H 328 " --> pdb=" O PRO H 324 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG H 329 " --> pdb=" O GLU H 325 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 161 removed outlier: 6.493A pdb=" N VAL A 118 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU A 142 " --> pdb=" O VAL A 118 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE A 120 " --> pdb=" O LEU A 142 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL A 119 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE A 207 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE A 229 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA A 209 " --> pdb=" O ILE A 229 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 268 removed outlier: 6.296A pdb=" N ILE A 317 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL A 296 " --> pdb=" O ILE A 317 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 319 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 296 " --> pdb=" O ILE A 303 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 160 through 161 removed outlier: 7.221A pdb=" N VAL B 160 " --> pdb=" O VAL B 139 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL B 141 " --> pdb=" O VAL B 160 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL B 118 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU B 142 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE B 120 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE B 229 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 263 through 268 removed outlier: 3.554A pdb=" N GLY B 295 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE B 321 " --> pdb=" O ILE B 293 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE B 293 " --> pdb=" O ILE B 321 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 158 through 161 removed outlier: 6.493A pdb=" N VAL C 118 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N LEU C 142 " --> pdb=" O VAL C 118 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE C 120 " --> pdb=" O LEU C 142 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL C 119 " --> pdb=" O ILE C 182 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE C 207 " --> pdb=" O GLN C 227 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE C 229 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA C 209 " --> pdb=" O ILE C 229 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 263 through 268 removed outlier: 6.296A pdb=" N ILE C 317 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL C 296 " --> pdb=" O ILE C 317 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU C 319 " --> pdb=" O ILE C 294 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 296 " --> pdb=" O ILE C 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 160 through 161 removed outlier: 7.221A pdb=" N VAL D 160 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL D 141 " --> pdb=" O VAL D 160 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL D 118 " --> pdb=" O PHE D 140 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU D 142 " --> pdb=" O VAL D 118 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE D 120 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE D 229 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 263 through 268 removed outlier: 3.554A pdb=" N GLY D 295 " --> pdb=" O LEU D 319 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE D 321 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N ILE D 293 " --> pdb=" O ILE D 321 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 158 through 161 removed outlier: 6.492A pdb=" N VAL E 118 " --> pdb=" O PHE E 140 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU E 142 " --> pdb=" O VAL E 118 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE E 120 " --> pdb=" O LEU E 142 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL E 119 " --> pdb=" O ILE E 182 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ILE E 207 " --> pdb=" O GLN E 227 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N ILE E 229 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA E 209 " --> pdb=" O ILE E 229 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 263 through 268 removed outlier: 6.296A pdb=" N ILE E 317 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL E 296 " --> pdb=" O ILE E 317 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU E 319 " --> pdb=" O ILE E 294 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL E 296 " --> pdb=" O ILE E 303 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 160 through 161 removed outlier: 7.221A pdb=" N VAL F 160 " --> pdb=" O VAL F 139 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL F 141 " --> pdb=" O VAL F 160 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL F 118 " --> pdb=" O PHE F 140 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU F 142 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ILE F 120 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE F 229 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 263 through 268 removed outlier: 3.554A pdb=" N GLY F 295 " --> pdb=" O LEU F 319 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE F 321 " --> pdb=" O ILE F 293 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE F 293 " --> pdb=" O ILE F 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 158 through 161 removed outlier: 6.494A pdb=" N VAL G 118 " --> pdb=" O PHE G 140 " (cutoff:3.500A) removed outlier: 7.319A pdb=" N LEU G 142 " --> pdb=" O VAL G 118 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE G 120 " --> pdb=" O LEU G 142 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL G 119 " --> pdb=" O ILE G 182 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE G 207 " --> pdb=" O GLN G 227 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE G 229 " --> pdb=" O ILE G 207 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA G 209 " --> pdb=" O ILE G 229 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 263 through 268 removed outlier: 6.297A pdb=" N ILE G 317 " --> pdb=" O VAL G 296 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N VAL G 296 " --> pdb=" O ILE G 317 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU G 319 " --> pdb=" O ILE G 294 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL G 296 " --> pdb=" O ILE G 303 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 160 through 161 removed outlier: 7.222A pdb=" N VAL H 160 " --> pdb=" O VAL H 139 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N VAL H 141 " --> pdb=" O VAL H 160 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N VAL H 118 " --> pdb=" O PHE H 140 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N LEU H 142 " --> pdb=" O VAL H 118 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ILE H 120 " --> pdb=" O LEU H 142 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE H 229 " --> pdb=" O ALA H 209 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 263 through 268 removed outlier: 3.554A pdb=" N GLY H 295 " --> pdb=" O LEU H 319 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE H 321 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ILE H 293 " --> pdb=" O ILE H 321 " (cutoff:3.500A) 724 hydrogen bonds defined for protein. 2064 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: 2.72 Time building geometry restraints manager: 1.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4147 1.33 - 1.45: 2871 1.45 - 1.57: 9610 1.57 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 16740 Sorted by residual: bond pdb=" CG1 ILE G 195 " pdb=" CD1 ILE G 195 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.35e+00 bond pdb=" CG1 ILE A 195 " pdb=" CD1 ILE A 195 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.35e+00 bond pdb=" CG1 ILE E 195 " pdb=" CD1 ILE E 195 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.35e+00 bond pdb=" CG1 ILE C 195 " pdb=" CD1 ILE C 195 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.35e+00 bond pdb=" CG LEU F 220 " pdb=" CD2 LEU F 220 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.15e+00 ... (remaining 16735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 21700 2.06 - 4.11: 864 4.11 - 6.17: 100 6.17 - 8.22: 12 8.22 - 10.28: 8 Bond angle restraints: 22684 Sorted by residual: angle pdb=" C GLY D 299 " pdb=" N ASP D 300 " pdb=" CA ASP D 300 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C GLY F 299 " pdb=" N ASP F 300 " pdb=" CA ASP F 300 " ideal model delta sigma weight residual 121.54 131.34 -9.80 1.91e+00 2.74e-01 2.63e+01 angle pdb=" C GLY B 299 " pdb=" N ASP B 300 " pdb=" CA ASP B 300 " ideal model delta sigma weight residual 121.54 131.32 -9.78 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C GLY H 299 " pdb=" N ASP H 300 " pdb=" CA ASP H 300 " ideal model delta sigma weight residual 121.54 131.29 -9.75 1.91e+00 2.74e-01 2.60e+01 angle pdb=" C GLY A 272 " pdb=" N SER A 273 " pdb=" CA SER A 273 " ideal model delta sigma weight residual 123.05 128.31 -5.26 1.57e+00 4.06e-01 1.12e+01 ... (remaining 22679 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.71: 8940 16.71 - 33.41: 924 33.41 - 50.12: 224 50.12 - 66.82: 24 66.82 - 83.53: 12 Dihedral angle restraints: 10124 sinusoidal: 3972 harmonic: 6152 Sorted by residual: dihedral pdb=" CA SER E 273 " pdb=" C SER E 273 " pdb=" N LYS E 274 " pdb=" CA LYS E 274 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA SER G 273 " pdb=" C SER G 273 " pdb=" N LYS G 274 " pdb=" CA LYS G 274 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 dihedral pdb=" CA SER A 273 " pdb=" C SER A 273 " pdb=" N LYS A 274 " pdb=" CA LYS A 274 " ideal model delta harmonic sigma weight residual 180.00 159.29 20.71 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 10121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1472 0.048 - 0.095: 926 0.095 - 0.143: 250 0.143 - 0.191: 28 0.191 - 0.238: 12 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CA ASP D 300 " pdb=" N ASP D 300 " pdb=" C ASP D 300 " pdb=" CB ASP D 300 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ASP F 300 " pdb=" N ASP F 300 " pdb=" C ASP F 300 " pdb=" CB ASP F 300 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ASP H 300 " pdb=" N ASP H 300 " pdb=" C ASP H 300 " pdb=" CB ASP H 300 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.40e+00 ... (remaining 2685 not shown) Planarity restraints: 2932 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 252 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C VAL G 252 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL G 252 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN G 253 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 252 " 0.010 2.00e-02 2.50e+03 1.90e-02 3.61e+00 pdb=" C VAL A 252 " -0.033 2.00e-02 2.50e+03 pdb=" O VAL A 252 " 0.012 2.00e-02 2.50e+03 pdb=" N GLN A 253 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 252 " -0.010 2.00e-02 2.50e+03 1.89e-02 3.59e+00 pdb=" C VAL C 252 " 0.033 2.00e-02 2.50e+03 pdb=" O VAL C 252 " -0.012 2.00e-02 2.50e+03 pdb=" N GLN C 253 " -0.011 2.00e-02 2.50e+03 ... (remaining 2929 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 51 2.39 - 3.02: 8640 3.02 - 3.65: 23709 3.65 - 4.27: 34898 4.27 - 4.90: 59912 Nonbonded interactions: 127210 Sorted by model distance: nonbonded pdb="CA CA H 401 " pdb=" O HOH H 501 " model vdw 1.768 2.510 nonbonded pdb="CA CA B 401 " pdb=" O HOH B 501 " model vdw 1.768 2.510 nonbonded pdb="CA CA F 401 " pdb=" O HOH F 501 " model vdw 1.768 2.510 nonbonded pdb="CA CA D 401 " pdb=" O HOH D 501 " model vdw 1.768 2.510 nonbonded pdb=" OD2 ASP H 184 " pdb=" OE1 GLU H 210 " model vdw 2.206 3.040 ... (remaining 127205 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.910 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 0.090 16740 Z= 0.447 Angle : 0.960 10.280 22684 Z= 0.550 Chirality : 0.061 0.238 2688 Planarity : 0.005 0.043 2932 Dihedral : 14.543 83.528 6172 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.23 % Allowed : 12.44 % Favored : 87.33 % 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: -4.18 (0.13), residues: 2140 helix: -3.07 (0.11), residues: 992 sheet: -0.44 (0.26), residues: 344 loop : -3.26 (0.15), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 116 TYR 0.013 0.002 TYR F 214 PHE 0.021 0.003 PHE B 232 TRP 0.007 0.002 TRP F 123 HIS 0.018 0.003 HIS E 117 Details of bonding type rmsd covalent geometry : bond 0.01063 (16740) covalent geometry : angle 0.95981 (22684) hydrogen bonds : bond 0.20269 ( 724) hydrogen bonds : angle 7.38660 ( 2064) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 466 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8612 (tmmt) cc_final: 0.8404 (tmmt) REVERT: A 200 LYS cc_start: 0.8564 (tptm) cc_final: 0.8266 (tppt) REVERT: A 218 GLU cc_start: 0.6602 (mm-30) cc_final: 0.6395 (mm-30) REVERT: A 264 MET cc_start: 0.8408 (ttm) cc_final: 0.8177 (ttt) REVERT: B 250 MET cc_start: 0.8711 (mtt) cc_final: 0.8454 (mtt) REVERT: B 301 GLU cc_start: 0.7097 (pp20) cc_final: 0.6338 (pp20) REVERT: C 105 LYS cc_start: 0.8614 (tmmt) cc_final: 0.8404 (tmmt) REVERT: C 200 LYS cc_start: 0.8574 (tptm) cc_final: 0.8318 (tptm) REVERT: C 218 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6386 (mm-30) REVERT: C 264 MET cc_start: 0.8421 (ttm) cc_final: 0.8182 (ttt) REVERT: D 250 MET cc_start: 0.8708 (mtt) cc_final: 0.8450 (mtt) REVERT: D 301 GLU cc_start: 0.7101 (pp20) cc_final: 0.6347 (pp20) REVERT: E 105 LYS cc_start: 0.8615 (tmmt) cc_final: 0.8405 (tmmt) REVERT: E 200 LYS cc_start: 0.8576 (tptm) cc_final: 0.8320 (tptm) REVERT: E 218 GLU cc_start: 0.6609 (mm-30) cc_final: 0.6398 (mm-30) REVERT: E 264 MET cc_start: 0.8408 (ttm) cc_final: 0.8183 (ttt) REVERT: F 250 MET cc_start: 0.8710 (mtt) cc_final: 0.8449 (mtt) REVERT: F 301 GLU cc_start: 0.7105 (pp20) cc_final: 0.6273 (pp20) REVERT: G 105 LYS cc_start: 0.8612 (tmmt) cc_final: 0.8400 (tmmt) REVERT: G 200 LYS cc_start: 0.8572 (tptm) cc_final: 0.8314 (tptm) REVERT: G 218 GLU cc_start: 0.6612 (mm-30) cc_final: 0.6406 (mm-30) REVERT: G 264 MET cc_start: 0.8406 (ttm) cc_final: 0.8176 (ttt) REVERT: H 250 MET cc_start: 0.8709 (mtt) cc_final: 0.8450 (mtt) REVERT: H 301 GLU cc_start: 0.7094 (pp20) cc_final: 0.6335 (pp20) outliers start: 4 outliers final: 4 residues processed: 470 average time/residue: 0.1874 time to fit residues: 120.4391 Evaluate side-chains 344 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 340 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain C residue 64 ASP Chi-restraints excluded: chain E residue 64 ASP Chi-restraints excluded: chain G residue 64 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 0.9980 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.4980 chunk 200 optimal weight: 0.5980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 219 GLN A 253 GLN C 103 GLN C 219 GLN C 253 GLN E 103 GLN E 219 GLN E 253 GLN G 103 GLN G 219 GLN G 253 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.154367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.118529 restraints weight = 23395.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.122040 restraints weight = 12606.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.124333 restraints weight = 8323.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.125772 restraints weight = 6305.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.126597 restraints weight = 5317.617| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 16740 Z= 0.113 Angle : 0.524 7.359 22684 Z= 0.280 Chirality : 0.045 0.156 2688 Planarity : 0.003 0.025 2932 Dihedral : 5.009 49.404 2364 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.15 % Allowed : 15.65 % Favored : 81.19 % 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: -2.47 (0.16), residues: 2140 helix: -1.11 (0.15), residues: 1008 sheet: -0.19 (0.26), residues: 336 loop : -2.93 (0.16), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 237 TYR 0.021 0.002 TYR E 333 PHE 0.010 0.001 PHE C 75 TRP 0.004 0.001 TRP C 52 HIS 0.004 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00249 (16740) covalent geometry : angle 0.52359 (22684) hydrogen bonds : bond 0.03660 ( 724) hydrogen bonds : angle 4.78910 ( 2064) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 408 time to evaluate : 0.688 Fit side-chains REVERT: A 105 LYS cc_start: 0.8560 (tmmt) cc_final: 0.8255 (tmmt) REVERT: A 174 ASN cc_start: 0.8847 (t0) cc_final: 0.8620 (t0) REVERT: A 203 GLU cc_start: 0.7676 (tm-30) cc_final: 0.7432 (tm-30) REVERT: B 179 ARG cc_start: 0.8031 (mtp180) cc_final: 0.7650 (tpt-90) REVERT: B 323 LYS cc_start: 0.8065 (mttp) cc_final: 0.7850 (mtpp) REVERT: C 105 LYS cc_start: 0.8563 (tmmt) cc_final: 0.8253 (tmmt) REVERT: C 174 ASN cc_start: 0.8843 (t0) cc_final: 0.8635 (t0) REVERT: C 203 GLU cc_start: 0.7678 (tm-30) cc_final: 0.7434 (tm-30) REVERT: D 179 ARG cc_start: 0.8027 (mtp180) cc_final: 0.7643 (tpt-90) REVERT: D 323 LYS cc_start: 0.8055 (mttp) cc_final: 0.7842 (mtpp) REVERT: E 105 LYS cc_start: 0.8567 (tmmt) cc_final: 0.8258 (tmmt) REVERT: E 174 ASN cc_start: 0.8842 (t0) cc_final: 0.8637 (t0) REVERT: E 203 GLU cc_start: 0.7658 (tm-30) cc_final: 0.7413 (tm-30) REVERT: F 179 ARG cc_start: 0.8024 (mtp180) cc_final: 0.7652 (tpt-90) REVERT: F 323 LYS cc_start: 0.8109 (mttp) cc_final: 0.7886 (mtpp) REVERT: G 105 LYS cc_start: 0.8560 (tmmt) cc_final: 0.8254 (tmmt) REVERT: G 174 ASN cc_start: 0.8844 (t0) cc_final: 0.8640 (t0) REVERT: G 203 GLU cc_start: 0.7672 (tm-30) cc_final: 0.7426 (tm-30) REVERT: H 179 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7646 (tpt-90) REVERT: H 323 LYS cc_start: 0.8060 (mttp) cc_final: 0.7850 (mtpp) outliers start: 56 outliers final: 20 residues processed: 452 average time/residue: 0.1659 time to fit residues: 106.0950 Evaluate side-chains 353 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 333 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 114 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 chunk 211 optimal weight: 3.9990 chunk 126 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.152417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.116577 restraints weight = 23871.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.120113 restraints weight = 12716.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.122339 restraints weight = 8358.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.123752 restraints weight = 6371.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.124619 restraints weight = 5363.431| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 16740 Z= 0.157 Angle : 0.550 8.682 22684 Z= 0.286 Chirality : 0.047 0.199 2688 Planarity : 0.004 0.068 2932 Dihedral : 4.701 48.866 2356 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.87 % Allowed : 21.06 % Favored : 76.07 % 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: -1.56 (0.17), residues: 2140 helix: -0.21 (0.16), residues: 1012 sheet: 0.21 (0.27), residues: 336 loop : -2.67 (0.17), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 135 TYR 0.015 0.001 TYR E 333 PHE 0.007 0.001 PHE A 75 TRP 0.002 0.001 TRP G 46 HIS 0.006 0.001 HIS C 117 Details of bonding type rmsd covalent geometry : bond 0.00373 (16740) covalent geometry : angle 0.55008 (22684) hydrogen bonds : bond 0.03522 ( 724) hydrogen bonds : angle 4.53166 ( 2064) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 423 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 372 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 174 ASN cc_start: 0.8894 (t0) cc_final: 0.8653 (t0) REVERT: A 203 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7504 (tm-30) REVERT: B 179 ARG cc_start: 0.8024 (mtp180) cc_final: 0.7645 (tpt-90) REVERT: B 323 LYS cc_start: 0.8144 (mttp) cc_final: 0.7858 (mtpp) REVERT: C 174 ASN cc_start: 0.8877 (t0) cc_final: 0.8621 (t0) REVERT: C 203 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7517 (tm-30) REVERT: D 179 ARG cc_start: 0.8021 (mtp180) cc_final: 0.7640 (tpt-90) REVERT: D 323 LYS cc_start: 0.8140 (mttp) cc_final: 0.7858 (mtpp) REVERT: E 174 ASN cc_start: 0.8873 (t0) cc_final: 0.8617 (t0) REVERT: E 203 GLU cc_start: 0.7776 (tm-30) cc_final: 0.7503 (tm-30) REVERT: F 179 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7660 (tpt-90) REVERT: F 323 LYS cc_start: 0.8146 (mttp) cc_final: 0.7817 (mtpp) REVERT: G 174 ASN cc_start: 0.8874 (t0) cc_final: 0.8622 (t0) REVERT: G 203 GLU cc_start: 0.7767 (tm-30) cc_final: 0.7490 (tm-30) REVERT: H 179 ARG cc_start: 0.8019 (mtp180) cc_final: 0.7639 (tpt-90) REVERT: H 323 LYS cc_start: 0.8148 (mttp) cc_final: 0.7865 (mtpp) outliers start: 51 outliers final: 39 residues processed: 402 average time/residue: 0.1706 time to fit residues: 96.2438 Evaluate side-chains 383 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 344 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 78 THR Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 226 ASP Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 226 ASP Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 78 THR Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 226 ASP Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain G residue 332 ASN Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 83 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 178 optimal weight: 3.9990 chunk 168 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 197 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 23 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 82 optimal weight: 9.9990 chunk 121 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN E 103 GLN G 103 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.152467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.116760 restraints weight = 23847.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.120217 restraints weight = 12690.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.122333 restraints weight = 8348.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.123826 restraints weight = 6390.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.124483 restraints weight = 5386.782| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16740 Z= 0.123 Angle : 0.497 7.352 22684 Z= 0.261 Chirality : 0.046 0.170 2688 Planarity : 0.003 0.050 2932 Dihedral : 4.415 47.690 2356 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.60 % Allowed : 22.35 % Favored : 74.04 % 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: -0.97 (0.17), residues: 2140 helix: 0.31 (0.17), residues: 1012 sheet: 0.55 (0.27), residues: 336 loop : -2.48 (0.18), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 135 TYR 0.009 0.001 TYR D 214 PHE 0.007 0.001 PHE A 75 TRP 0.003 0.001 TRP E 52 HIS 0.003 0.001 HIS H 117 Details of bonding type rmsd covalent geometry : bond 0.00284 (16740) covalent geometry : angle 0.49689 (22684) hydrogen bonds : bond 0.03097 ( 724) hydrogen bonds : angle 4.32510 ( 2064) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 416 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 352 time to evaluate : 0.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 TYR cc_start: 0.8786 (t80) cc_final: 0.8552 (t80) REVERT: B 135 ARG cc_start: 0.7416 (mtm-85) cc_final: 0.6923 (mpp80) REVERT: B 179 ARG cc_start: 0.7984 (mtp180) cc_final: 0.7640 (tpt-90) REVERT: B 323 LYS cc_start: 0.8068 (mttp) cc_final: 0.7802 (mtpp) REVERT: C 333 TYR cc_start: 0.8785 (t80) cc_final: 0.8561 (t80) REVERT: D 135 ARG cc_start: 0.7411 (mtm-85) cc_final: 0.6905 (mpp80) REVERT: D 179 ARG cc_start: 0.7986 (mtp180) cc_final: 0.7638 (tpt-90) REVERT: D 323 LYS cc_start: 0.8075 (mttp) cc_final: 0.7800 (mtpp) REVERT: E 333 TYR cc_start: 0.8773 (t80) cc_final: 0.8508 (t80) REVERT: F 179 ARG cc_start: 0.7993 (mtp180) cc_final: 0.7641 (tpt-90) REVERT: F 323 LYS cc_start: 0.8102 (mttp) cc_final: 0.7747 (mtpp) REVERT: G 333 TYR cc_start: 0.8781 (t80) cc_final: 0.8491 (t80) REVERT: H 135 ARG cc_start: 0.7413 (mtm-85) cc_final: 0.6923 (mpp80) REVERT: H 179 ARG cc_start: 0.7984 (mtp180) cc_final: 0.7637 (tpt-90) REVERT: H 323 LYS cc_start: 0.8076 (mttp) cc_final: 0.7806 (mtpp) outliers start: 64 outliers final: 40 residues processed: 393 average time/residue: 0.1635 time to fit residues: 91.5799 Evaluate side-chains 366 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 326 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain G residue 332 ASN Chi-restraints excluded: chain H residue 187 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 71 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 134 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 176 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN C 103 GLN E 103 GLN G 103 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.152616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.117045 restraints weight = 23894.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.120411 restraints weight = 12901.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.122551 restraints weight = 8555.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.123967 restraints weight = 6564.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.124695 restraints weight = 5552.781| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16740 Z= 0.154 Angle : 0.524 8.630 22684 Z= 0.272 Chirality : 0.047 0.148 2688 Planarity : 0.003 0.045 2932 Dihedral : 4.363 47.367 2356 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 4.11 % Allowed : 24.61 % Favored : 71.28 % 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: -0.71 (0.18), residues: 2140 helix: 0.57 (0.17), residues: 1016 sheet: 0.70 (0.28), residues: 336 loop : -2.44 (0.18), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 135 TYR 0.010 0.001 TYR F 214 PHE 0.008 0.001 PHE A 75 TRP 0.003 0.001 TRP E 52 HIS 0.004 0.001 HIS C 117 Details of bonding type rmsd covalent geometry : bond 0.00366 (16740) covalent geometry : angle 0.52431 (22684) hydrogen bonds : bond 0.03223 ( 724) hydrogen bonds : angle 4.31187 ( 2064) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 348 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8627 (tmmt) cc_final: 0.8259 (tmmt) REVERT: B 135 ARG cc_start: 0.7370 (mtm-85) cc_final: 0.6853 (mpp80) REVERT: B 179 ARG cc_start: 0.8023 (mtp180) cc_final: 0.7657 (tpt-90) REVERT: C 105 LYS cc_start: 0.8641 (tmmt) cc_final: 0.8268 (tmmt) REVERT: D 135 ARG cc_start: 0.7350 (mtm-85) cc_final: 0.6856 (mpp80) REVERT: D 179 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7658 (tpt-90) REVERT: E 105 LYS cc_start: 0.8649 (tmmt) cc_final: 0.8281 (tmmt) REVERT: F 179 ARG cc_start: 0.8055 (mtp180) cc_final: 0.7665 (tpt-90) REVERT: G 105 LYS cc_start: 0.8633 (tmmt) cc_final: 0.8260 (tmmt) REVERT: H 135 ARG cc_start: 0.7361 (mtm-85) cc_final: 0.6855 (mpp80) REVERT: H 179 ARG cc_start: 0.8024 (mtp180) cc_final: 0.7653 (tpt-90) outliers start: 73 outliers final: 50 residues processed: 389 average time/residue: 0.1731 time to fit residues: 94.2524 Evaluate side-chains 374 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 324 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 215 GLU Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 261 THR Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 215 GLU Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 261 THR Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 215 GLU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 261 THR Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 215 GLU Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain G residue 332 ASN Chi-restraints excluded: chain H residue 130 CYS Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 63 optimal weight: 0.9980 chunk 143 optimal weight: 4.9990 chunk 129 optimal weight: 0.1980 chunk 167 optimal weight: 3.9990 chunk 116 optimal weight: 0.0050 chunk 10 optimal weight: 0.0570 chunk 186 optimal weight: 0.9990 chunk 195 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 160 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.4514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 103 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.156176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.120571 restraints weight = 23708.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.124135 restraints weight = 12588.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.126423 restraints weight = 8232.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.127759 restraints weight = 6234.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.128651 restraints weight = 5271.917| |-----------------------------------------------------------------------------| r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16740 Z= 0.089 Angle : 0.481 8.484 22684 Z= 0.248 Chirality : 0.045 0.139 2688 Planarity : 0.003 0.040 2932 Dihedral : 4.030 42.634 2356 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.49 % Allowed : 24.38 % Favored : 72.13 % 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 (0.18), residues: 2140 helix: 0.87 (0.17), residues: 1012 sheet: 0.85 (0.29), residues: 332 loop : -2.31 (0.18), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 135 TYR 0.008 0.001 TYR D 310 PHE 0.009 0.001 PHE E 75 TRP 0.006 0.001 TRP E 52 HIS 0.002 0.001 HIS B 117 Details of bonding type rmsd covalent geometry : bond 0.00198 (16740) covalent geometry : angle 0.48100 (22684) hydrogen bonds : bond 0.02593 ( 724) hydrogen bonds : angle 4.09117 ( 2064) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 350 time to evaluate : 0.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 333 TYR cc_start: 0.8542 (t80) cc_final: 0.8267 (t80) REVERT: B 179 ARG cc_start: 0.7951 (mtp180) cc_final: 0.7590 (tpt-90) REVERT: B 237 ARG cc_start: 0.7403 (mtp-110) cc_final: 0.7001 (mtp-110) REVERT: C 333 TYR cc_start: 0.8540 (t80) cc_final: 0.8269 (t80) REVERT: D 179 ARG cc_start: 0.7957 (mtp180) cc_final: 0.7590 (tpt-90) REVERT: D 237 ARG cc_start: 0.7397 (mtp-110) cc_final: 0.6993 (mtp-110) REVERT: E 105 LYS cc_start: 0.8590 (tmmt) cc_final: 0.8206 (tmmt) REVERT: F 179 ARG cc_start: 0.7962 (mtp180) cc_final: 0.7603 (tpt-90) REVERT: G 200 LYS cc_start: 0.8332 (tppt) cc_final: 0.8056 (tptm) REVERT: G 333 TYR cc_start: 0.8534 (t80) cc_final: 0.8259 (t80) REVERT: H 179 ARG cc_start: 0.7951 (mtp180) cc_final: 0.7586 (tpt-90) REVERT: H 237 ARG cc_start: 0.7400 (mtp-110) cc_final: 0.6994 (mtp-110) outliers start: 62 outliers final: 50 residues processed: 389 average time/residue: 0.1812 time to fit residues: 97.9703 Evaluate side-chains 373 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 323 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 326 GLU Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 284 ASP Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 326 GLU Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain G residue 326 GLU Chi-restraints excluded: chain G residue 332 ASN Chi-restraints excluded: chain H residue 130 CYS Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 175 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 163 optimal weight: 0.5980 chunk 177 optimal weight: 1.9990 chunk 108 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 43 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.154107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.118507 restraints weight = 23680.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.121978 restraints weight = 12901.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.124151 restraints weight = 8536.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.125492 restraints weight = 6551.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.126254 restraints weight = 5542.016| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16740 Z= 0.138 Angle : 0.520 10.272 22684 Z= 0.264 Chirality : 0.047 0.151 2688 Planarity : 0.003 0.039 2932 Dihedral : 4.039 42.743 2356 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.55 % Allowed : 25.00 % Favored : 71.45 % 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 (0.18), residues: 2140 helix: 1.02 (0.17), residues: 1020 sheet: 0.94 (0.29), residues: 332 loop : -2.06 (0.19), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 313 TYR 0.008 0.001 TYR H 310 PHE 0.006 0.001 PHE E 75 TRP 0.003 0.001 TRP G 52 HIS 0.003 0.001 HIS F 117 Details of bonding type rmsd covalent geometry : bond 0.00335 (16740) covalent geometry : angle 0.52046 (22684) hydrogen bonds : bond 0.02892 ( 724) hydrogen bonds : angle 4.09143 ( 2064) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 337 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8610 (tmmt) cc_final: 0.8231 (tmmt) REVERT: A 333 TYR cc_start: 0.8547 (t80) cc_final: 0.8311 (t80) REVERT: C 105 LYS cc_start: 0.8613 (tmmt) cc_final: 0.8234 (tmmt) REVERT: C 333 TYR cc_start: 0.8543 (t80) cc_final: 0.8307 (t80) REVERT: E 105 LYS cc_start: 0.8627 (tmmt) cc_final: 0.8263 (tmmt) REVERT: G 105 LYS cc_start: 0.8616 (tmmt) cc_final: 0.8233 (tmmt) REVERT: G 200 LYS cc_start: 0.8335 (tppt) cc_final: 0.8039 (tptm) REVERT: G 333 TYR cc_start: 0.8539 (t80) cc_final: 0.8303 (t80) outliers start: 63 outliers final: 54 residues processed: 374 average time/residue: 0.1798 time to fit residues: 94.0087 Evaluate side-chains 381 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 327 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain G residue 332 ASN Chi-restraints excluded: chain H residue 130 CYS Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 115 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 172 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 178 optimal weight: 5.9990 chunk 128 optimal weight: 0.0570 chunk 52 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 123 optimal weight: 0.6980 chunk 174 optimal weight: 0.7980 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN A 216 ASN C 103 GLN C 216 ASN E 216 ASN G 103 GLN G 216 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.155533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.120084 restraints weight = 23694.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.123549 restraints weight = 12771.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.125762 restraints weight = 8445.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.127159 restraints weight = 6454.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.127872 restraints weight = 5440.070| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16740 Z= 0.107 Angle : 0.512 11.545 22684 Z= 0.254 Chirality : 0.046 0.171 2688 Planarity : 0.003 0.039 2932 Dihedral : 3.927 40.696 2356 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 3.60 % Allowed : 25.06 % Favored : 71.34 % 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: 0.09 (0.18), residues: 2140 helix: 1.18 (0.17), residues: 1024 sheet: 1.00 (0.29), residues: 332 loop : -1.94 (0.20), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 313 TYR 0.008 0.001 TYR H 310 PHE 0.007 0.001 PHE E 75 TRP 0.005 0.001 TRP G 52 HIS 0.003 0.001 HIS D 117 Details of bonding type rmsd covalent geometry : bond 0.00253 (16740) covalent geometry : angle 0.51211 (22684) hydrogen bonds : bond 0.02663 ( 724) hydrogen bonds : angle 3.99611 ( 2064) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 346 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8635 (tmmt) cc_final: 0.8257 (tmmt) REVERT: A 333 TYR cc_start: 0.8607 (t80) cc_final: 0.8371 (t80) REVERT: B 237 ARG cc_start: 0.7401 (mtp-110) cc_final: 0.7023 (mtp-110) REVERT: C 105 LYS cc_start: 0.8638 (tmmt) cc_final: 0.8253 (tmmt) REVERT: C 333 TYR cc_start: 0.8604 (t80) cc_final: 0.8368 (t80) REVERT: D 237 ARG cc_start: 0.7396 (mtp-110) cc_final: 0.7024 (mtp-110) REVERT: E 105 LYS cc_start: 0.8657 (tmmt) cc_final: 0.8294 (tmmt) REVERT: G 105 LYS cc_start: 0.8641 (tmmt) cc_final: 0.8252 (tmmt) REVERT: G 200 LYS cc_start: 0.8347 (tppt) cc_final: 0.8003 (tptm) REVERT: G 333 TYR cc_start: 0.8600 (t80) cc_final: 0.8364 (t80) REVERT: H 237 ARG cc_start: 0.7401 (mtp-110) cc_final: 0.7022 (mtp-110) outliers start: 64 outliers final: 56 residues processed: 384 average time/residue: 0.1671 time to fit residues: 90.4059 Evaluate side-chains 389 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 333 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 218 GLU Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 332 ASN Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 218 GLU Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain E residue 332 ASN Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 145 ASP Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 218 GLU Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain G residue 332 ASN Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 56 optimal weight: 3.9990 chunk 177 optimal weight: 0.6980 chunk 117 optimal weight: 0.0980 chunk 31 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 127 optimal weight: 1.9990 chunk 45 optimal weight: 0.0470 chunk 176 optimal weight: 0.6980 chunk 87 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 128 optimal weight: 1.9990 overall best weight: 0.5080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 GLN ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 103 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.157383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.121950 restraints weight = 23639.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.125442 restraints weight = 12762.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.127552 restraints weight = 8413.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.128994 restraints weight = 6455.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.129871 restraints weight = 5438.619| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16740 Z= 0.087 Angle : 0.496 12.707 22684 Z= 0.246 Chirality : 0.045 0.140 2688 Planarity : 0.003 0.038 2932 Dihedral : 3.704 35.733 2356 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.32 % Allowed : 25.34 % Favored : 71.34 % 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: 0.24 (0.19), residues: 2140 helix: 1.31 (0.17), residues: 1036 sheet: 1.10 (0.29), residues: 332 loop : -1.95 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.008 0.001 TYR B 310 PHE 0.006 0.001 PHE E 75 TRP 0.006 0.001 TRP G 52 HIS 0.002 0.000 HIS D 117 Details of bonding type rmsd covalent geometry : bond 0.00200 (16740) covalent geometry : angle 0.49620 (22684) hydrogen bonds : bond 0.02348 ( 724) hydrogen bonds : angle 3.86071 ( 2064) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 345 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8621 (tmmt) cc_final: 0.8258 (tmmt) REVERT: C 105 LYS cc_start: 0.8624 (tmmt) cc_final: 0.8258 (tmmt) REVERT: C 333 TYR cc_start: 0.8579 (t80) cc_final: 0.8348 (t80) REVERT: E 105 LYS cc_start: 0.8660 (tmmt) cc_final: 0.8334 (tmmt) REVERT: G 105 LYS cc_start: 0.8626 (tmmt) cc_final: 0.8253 (tmmt) REVERT: G 200 LYS cc_start: 0.8277 (tppt) cc_final: 0.7859 (tptm) REVERT: G 333 TYR cc_start: 0.8574 (t80) cc_final: 0.8344 (t80) outliers start: 59 outliers final: 52 residues processed: 376 average time/residue: 0.1563 time to fit residues: 82.9918 Evaluate side-chains 383 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 331 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 130 CYS Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 201 ILE Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 201 ILE Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 130 CYS Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain H residue 130 CYS Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 201 ILE Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 144 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 126 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 131 optimal weight: 10.0000 chunk 125 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.155217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.119947 restraints weight = 23810.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.123334 restraints weight = 13306.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.125422 restraints weight = 8898.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.126769 restraints weight = 6868.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.127481 restraints weight = 5850.154| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 16740 Z= 0.129 Angle : 0.522 13.131 22684 Z= 0.260 Chirality : 0.046 0.134 2688 Planarity : 0.003 0.040 2932 Dihedral : 3.777 36.100 2356 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.27 % Allowed : 25.45 % Favored : 71.28 % 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 (0.19), residues: 2140 helix: 1.29 (0.17), residues: 1036 sheet: 1.14 (0.29), residues: 332 loop : -1.98 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 241 TYR 0.015 0.001 TYR B 214 PHE 0.006 0.001 PHE C 75 TRP 0.005 0.001 TRP G 52 HIS 0.003 0.001 HIS F 117 Details of bonding type rmsd covalent geometry : bond 0.00308 (16740) covalent geometry : angle 0.52154 (22684) hydrogen bonds : bond 0.02712 ( 724) hydrogen bonds : angle 3.87182 ( 2064) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4280 Ramachandran restraints generated. 2140 Oldfield, 0 Emsley, 2140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 335 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 LYS cc_start: 0.8646 (tmmt) cc_final: 0.8277 (tmmt) REVERT: C 105 LYS cc_start: 0.8649 (tmmt) cc_final: 0.8276 (tmmt) REVERT: E 105 LYS cc_start: 0.8690 (tmmt) cc_final: 0.8356 (tmmt) REVERT: G 105 LYS cc_start: 0.8643 (tmmt) cc_final: 0.8266 (tmmt) REVERT: G 200 LYS cc_start: 0.8305 (tppt) cc_final: 0.7927 (tptm) outliers start: 58 outliers final: 49 residues processed: 368 average time/residue: 0.1512 time to fit residues: 78.9626 Evaluate side-chains 376 residues out of total 1836 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 327 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 PHE Chi-restraints excluded: chain A residue 87 PHE Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain B residue 130 CYS Chi-restraints excluded: chain B residue 187 SER Chi-restraints excluded: chain B residue 327 ILE Chi-restraints excluded: chain B residue 330 LEU Chi-restraints excluded: chain C residue 75 PHE Chi-restraints excluded: chain C residue 87 PHE Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain C residue 107 MET Chi-restraints excluded: chain C residue 284 ASP Chi-restraints excluded: chain C residue 291 VAL Chi-restraints excluded: chain C residue 300 ASP Chi-restraints excluded: chain C residue 332 ASN Chi-restraints excluded: chain D residue 130 CYS Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 327 ILE Chi-restraints excluded: chain D residue 330 LEU Chi-restraints excluded: chain E residue 75 PHE Chi-restraints excluded: chain E residue 87 PHE Chi-restraints excluded: chain E residue 91 VAL Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 291 VAL Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain F residue 130 CYS Chi-restraints excluded: chain F residue 187 SER Chi-restraints excluded: chain F residue 327 ILE Chi-restraints excluded: chain F residue 330 LEU Chi-restraints excluded: chain G residue 75 PHE Chi-restraints excluded: chain G residue 87 PHE Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 95 LEU Chi-restraints excluded: chain G residue 107 MET Chi-restraints excluded: chain G residue 284 ASP Chi-restraints excluded: chain G residue 291 VAL Chi-restraints excluded: chain G residue 300 ASP Chi-restraints excluded: chain G residue 332 ASN Chi-restraints excluded: chain H residue 130 CYS Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 261 THR Chi-restraints excluded: chain H residue 327 ILE Chi-restraints excluded: chain H residue 330 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 94 optimal weight: 0.6980 chunk 188 optimal weight: 0.6980 chunk 111 optimal weight: 8.9990 chunk 193 optimal weight: 6.9990 chunk 67 optimal weight: 3.9990 chunk 198 optimal weight: 0.7980 chunk 173 optimal weight: 3.9990 chunk 190 optimal weight: 0.0000 chunk 107 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 216 ASN C 216 ASN E 216 ASN G 216 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.156863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.121834 restraints weight = 23607.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.125079 restraints weight = 13003.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.127226 restraints weight = 8745.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.128443 restraints weight = 6743.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.129321 restraints weight = 5759.236| |-----------------------------------------------------------------------------| r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16740 Z= 0.094 Angle : 0.504 13.265 22684 Z= 0.250 Chirality : 0.045 0.136 2688 Planarity : 0.003 0.041 2932 Dihedral : 3.651 33.407 2356 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.93 % Allowed : 24.89 % Favored : 72.18 % 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: 0.33 (0.19), residues: 2140 helix: 1.41 (0.17), residues: 1036 sheet: 1.17 (0.29), residues: 332 loop : -1.96 (0.20), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 237 TYR 0.008 0.001 TYR H 310 PHE 0.007 0.001 PHE C 75 TRP 0.006 0.001 TRP C 52 HIS 0.002 0.001 HIS F 117 Details of bonding type rmsd covalent geometry : bond 0.00219 (16740) covalent geometry : angle 0.50365 (22684) hydrogen bonds : bond 0.02432 ( 724) hydrogen bonds : angle 3.81941 ( 2064) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3233.34 seconds wall clock time: 56 minutes 18.36 seconds (3378.36 seconds total)