Starting phenix.real_space_refine on Mon Aug 25 05:33:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vji_43282/08_2025/8vji_43282.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vji_43282/08_2025/8vji_43282.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vji_43282/08_2025/8vji_43282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vji_43282/08_2025/8vji_43282.map" model { file = "/net/cci-nas-00/data/ceres_data/8vji_43282/08_2025/8vji_43282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vji_43282/08_2025/8vji_43282.cif" } resolution = 3.3 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= 0.013 sd= 0.064 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 139 5.16 5 C 16355 2.51 5 N 4423 2.21 5 O 4810 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 120 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 25727 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2793 Classifications: {'peptide': 353} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 337} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2793 Classifications: {'peptide': 353} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 337} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2793 Classifications: {'peptide': 353} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 337} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2793 Classifications: {'peptide': 353} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 337} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2793 Classifications: {'peptide': 353} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 337} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2793 Classifications: {'peptide': 353} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 337} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2629 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 316} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "a" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 906 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "b" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 906 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 906 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "d" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 906 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "e" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 906 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 906 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "g" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 904 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 8, 'TRANS': 115} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 6.02, per 1000 atoms: 0.23 Number of scatterers: 25727 At special positions: 0 Unit cell: (187.915, 197.525, 170.832, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 139 16.00 O 4810 8.00 N 4423 7.00 C 16355 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: 2.13 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 953.7 nanoseconds 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6028 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 61 sheets defined 23.1% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 23 through 27 Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 105 through 140 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 174 through 193 Processing helix chain 'A' and resid 206 through 217 Processing helix chain 'A' and resid 293 through 296 Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.759A pdb=" N TYR A 311 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 23 through 28 Processing helix chain 'B' and resid 86 through 91 Processing helix chain 'B' and resid 105 through 140 Processing helix chain 'B' and resid 159 through 161 No H-bonds generated for 'chain 'B' and resid 159 through 161' Processing helix chain 'B' and resid 174 through 193 Processing helix chain 'B' and resid 206 through 217 Processing helix chain 'B' and resid 293 through 295 No H-bonds generated for 'chain 'B' and resid 293 through 295' Processing helix chain 'B' and resid 307 through 312 removed outlier: 3.716A pdb=" N TYR B 311 " --> pdb=" O GLY B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 345 No H-bonds generated for 'chain 'B' and resid 343 through 345' Processing helix chain 'C' and resid 23 through 28 Processing helix chain 'C' and resid 86 through 91 Processing helix chain 'C' and resid 105 through 140 Processing helix chain 'C' and resid 159 through 161 No H-bonds generated for 'chain 'C' and resid 159 through 161' Processing helix chain 'C' and resid 174 through 193 removed outlier: 3.720A pdb=" N GLY C 185 " --> pdb=" O ASP C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Processing helix chain 'C' and resid 293 through 296 Processing helix chain 'C' and resid 307 through 312 removed outlier: 3.639A pdb=" N TYR C 311 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 345 No H-bonds generated for 'chain 'C' and resid 343 through 345' Processing helix chain 'D' and resid 23 through 27 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 105 through 140 Processing helix chain 'D' and resid 159 through 161 No H-bonds generated for 'chain 'D' and resid 159 through 161' Processing helix chain 'D' and resid 174 through 193 Processing helix chain 'D' and resid 206 through 217 Processing helix chain 'D' and resid 292 through 296 Processing helix chain 'D' and resid 307 through 312 removed outlier: 3.714A pdb=" N TYR D 311 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 347 removed outlier: 4.056A pdb=" N SER D 347 " --> pdb=" O PRO D 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 28 Processing helix chain 'E' and resid 86 through 91 removed outlier: 3.804A pdb=" N ILE E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 140 Processing helix chain 'E' and resid 159 through 161 No H-bonds generated for 'chain 'E' and resid 159 through 161' Processing helix chain 'E' and resid 174 through 193 removed outlier: 3.539A pdb=" N GLY E 185 " --> pdb=" O ASP E 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 206 through 217 Processing helix chain 'E' and resid 293 through 296 Processing helix chain 'E' and resid 307 through 312 removed outlier: 3.647A pdb=" N TYR E 311 " --> pdb=" O GLY E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 345 No H-bonds generated for 'chain 'E' and resid 343 through 345' Processing helix chain 'F' and resid 23 through 28 Processing helix chain 'F' and resid 86 through 91 Processing helix chain 'F' and resid 105 through 140 Processing helix chain 'F' and resid 159 through 161 No H-bonds generated for 'chain 'F' and resid 159 through 161' Processing helix chain 'F' and resid 174 through 193 Processing helix chain 'F' and resid 206 through 217 Processing helix chain 'F' and resid 293 through 296 Processing helix chain 'F' and resid 307 through 312 removed outlier: 3.504A pdb=" N TYR F 311 " --> pdb=" O GLY F 308 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 28 Processing helix chain 'G' and resid 86 through 91 Processing helix chain 'G' and resid 105 through 140 Processing helix chain 'G' and resid 159 through 161 No H-bonds generated for 'chain 'G' and resid 159 through 161' Processing helix chain 'G' and resid 174 through 193 Processing helix chain 'G' and resid 205 through 216 Processing helix chain 'G' and resid 237 through 243 Processing helix chain 'G' and resid 293 through 296 Processing helix chain 'G' and resid 307 through 312 removed outlier: 3.555A pdb=" N GLY G 310 " --> pdb=" O LYS G 307 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR G 311 " --> pdb=" O GLY G 308 " (cutoff:3.500A) Processing helix chain 'a' and resid 80 through 84 removed outlier: 3.634A pdb=" N VAL a 84 " --> pdb=" O PRO a 81 " (cutoff:3.500A) Processing helix chain 'a' and resid 110 through 112 No H-bonds generated for 'chain 'a' and resid 110 through 112' Processing helix chain 'a' and resid 120 through 127 Processing helix chain 'b' and resid 80 through 84 Processing helix chain 'b' and resid 120 through 127 Processing helix chain 'c' and resid 80 through 84 removed outlier: 3.588A pdb=" N VAL c 84 " --> pdb=" O PRO c 81 " (cutoff:3.500A) Processing helix chain 'c' and resid 120 through 126 Processing helix chain 'c' and resid 127 through 129 No H-bonds generated for 'chain 'c' and resid 127 through 129' Processing helix chain 'd' and resid 80 through 84 removed outlier: 3.680A pdb=" N VAL d 84 " --> pdb=" O PRO d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 120 through 127 removed outlier: 3.526A pdb=" N ALA d 126 " --> pdb=" O ALA d 122 " (cutoff:3.500A) Processing helix chain 'e' and resid 80 through 84 removed outlier: 3.727A pdb=" N VAL e 84 " --> pdb=" O PRO e 81 " (cutoff:3.500A) Processing helix chain 'e' and resid 120 through 126 removed outlier: 3.885A pdb=" N ALA e 126 " --> pdb=" O ALA e 122 " (cutoff:3.500A) Processing helix chain 'f' and resid 80 through 84 removed outlier: 3.703A pdb=" N VAL f 84 " --> pdb=" O PRO f 81 " (cutoff:3.500A) Processing helix chain 'f' and resid 120 through 127 Processing helix chain 'g' and resid 80 through 83 Processing helix chain 'g' and resid 110 through 112 No H-bonds generated for 'chain 'g' and resid 110 through 112' Processing helix chain 'g' and resid 120 through 126 removed outlier: 3.693A pdb=" N ALA g 126 " --> pdb=" O ALA g 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 10 removed outlier: 6.039A pdb=" N GLN A 9 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASP B 42 " --> pdb=" O GLN A 9 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N GLN A 14 " --> pdb=" O VAL B 44 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N GLN B 46 " --> pdb=" O GLN A 14 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LYS A 16 " --> pdb=" O GLN B 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 8 through 10 removed outlier: 6.039A pdb=" N GLN A 9 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N ASP B 42 " --> pdb=" O GLN A 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 33 removed outlier: 6.693A pdb=" N ARG A 30 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N PHE A 301 " --> pdb=" O ARG A 30 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ILE A 32 " --> pdb=" O PHE A 301 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 74 removed outlier: 6.403A pdb=" N MET A 38 " --> pdb=" O TYR F 8 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU F 10 " --> pdb=" O MET A 38 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA A 40 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N GLU F 12 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ASP A 42 " --> pdb=" O GLU F 12 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 62 through 63 removed outlier: 5.453A pdb=" N ARG A 62 " --> pdb=" O LYS F 82 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VAL F 84 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLU F 329 " --> pdb=" O ILE F 85 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL F 328 " --> pdb=" O GLN F 323 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 317 through 322 removed outlier: 3.600A pdb=" N GLU A 329 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 141 through 146 removed outlier: 5.826A pdb=" N GLY A 146 " --> pdb=" O PRO A 150 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 163 through 165 removed outlier: 6.816A pdb=" N MET A 164 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA A 287 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP A 201 " --> pdb=" O ILE A 291 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLY A 252 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N VAL A 267 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N TYR A 250 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 271 through 273 Processing sheet with id=AB1, first strand: chain 'B' and resid 8 through 10 removed outlier: 6.207A pdb=" N GLN B 14 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLN C 46 " --> pdb=" O GLN B 14 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LYS B 16 " --> pdb=" O GLN C 46 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 8 through 10 removed outlier: 6.465A pdb=" N TYR C 69 " --> pdb=" O SER g 24 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER g 24 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N THR C 71 " --> pdb=" O LEU g 22 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 30 through 33 removed outlier: 6.600A pdb=" N ARG B 30 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N PHE B 301 " --> pdb=" O ARG B 30 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ILE B 32 " --> pdb=" O PHE B 301 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 317 through 322 Processing sheet with id=AB5, first strand: chain 'B' and resid 141 through 146 removed outlier: 5.915A pdb=" N GLY B 146 " --> pdb=" O PRO B 150 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 163 through 165 removed outlier: 6.741A pdb=" N MET B 164 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA B 287 " --> pdb=" O GLY B 205 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP B 201 " --> pdb=" O ILE B 291 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY B 252 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL B 267 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N TYR B 250 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 271 through 273 Processing sheet with id=AB8, first strand: chain 'C' and resid 8 through 10 removed outlier: 6.220A pdb=" N GLN C 9 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ASP D 42 " --> pdb=" O GLN C 9 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N GLN C 14 " --> pdb=" O VAL D 44 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLN D 46 " --> pdb=" O GLN C 14 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LYS C 16 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N VAL D 48 " --> pdb=" O LYS C 16 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS C 18 " --> pdb=" O VAL D 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'C' and resid 8 through 10 removed outlier: 6.220A pdb=" N GLN C 9 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ASP D 42 " --> pdb=" O GLN C 9 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.555A pdb=" N ARG C 30 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N PHE C 301 " --> pdb=" O ARG C 30 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N ILE C 32 " --> pdb=" O PHE C 301 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 317 through 322 removed outlier: 3.641A pdb=" N GLU C 329 " --> pdb=" O ILE C 85 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 141 through 146 removed outlier: 5.501A pdb=" N GLY C 146 " --> pdb=" O PRO C 150 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 163 through 165 removed outlier: 6.837A pdb=" N MET C 164 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N ALA C 287 " --> pdb=" O GLY C 205 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP C 201 " --> pdb=" O ILE C 291 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N TYR C 202 " --> pdb=" O TRP C 266 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ASN C 268 " --> pdb=" O TYR C 202 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE C 204 " --> pdb=" O ASN C 268 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N MET C 263 " --> pdb=" O GLU C 253 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N GLU C 253 " --> pdb=" O MET C 263 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N ILE C 265 " --> pdb=" O MET C 251 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 271 through 273 Processing sheet with id=AC6, first strand: chain 'D' and resid 8 through 10 removed outlier: 5.958A pdb=" N GLN D 9 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASP E 42 " --> pdb=" O GLN D 9 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'D' and resid 8 through 10 removed outlier: 5.958A pdb=" N GLN D 9 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 7.729A pdb=" N ASP E 42 " --> pdb=" O GLN D 9 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'D' and resid 30 through 33 removed outlier: 6.493A pdb=" N ARG D 30 " --> pdb=" O ARG D 299 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N PHE D 301 " --> pdb=" O ARG D 30 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 32 " --> pdb=" O PHE D 301 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 317 through 322 removed outlier: 3.506A pdb=" N GLU D 329 " --> pdb=" O ILE D 85 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 141 through 146 removed outlier: 3.510A pdb=" N VAL D 142 " --> pdb=" O VAL D 154 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N GLY D 146 " --> pdb=" O PRO D 150 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 163 through 165 removed outlier: 6.782A pdb=" N MET D 164 " --> pdb=" O THR D 351 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N ALA D 287 " --> pdb=" O GLY D 205 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ASP D 201 " --> pdb=" O ILE D 291 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY D 252 " --> pdb=" O ILE D 265 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL D 267 " --> pdb=" O TYR D 250 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N TYR D 250 " --> pdb=" O VAL D 267 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 271 through 273 Processing sheet with id=AD4, first strand: chain 'E' and resid 8 through 10 removed outlier: 6.155A pdb=" N GLN E 9 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ASP F 42 " --> pdb=" O GLN E 9 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N GLN E 14 " --> pdb=" O VAL F 44 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N GLN F 46 " --> pdb=" O GLN E 14 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LYS E 16 " --> pdb=" O GLN F 46 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'E' and resid 8 through 10 removed outlier: 6.155A pdb=" N GLN E 9 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ASP F 42 " --> pdb=" O GLN E 9 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 30 through 33 removed outlier: 6.952A pdb=" N ARG E 30 " --> pdb=" O ARG E 299 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N PHE E 301 " --> pdb=" O ARG E 30 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ILE E 32 " --> pdb=" O PHE E 301 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'E' and resid 317 through 323 removed outlier: 3.643A pdb=" N VAL E 328 " --> pdb=" O GLN E 323 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 141 through 146 removed outlier: 3.528A pdb=" N VAL E 142 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N GLY E 146 " --> pdb=" O PRO E 150 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 163 through 165 removed outlier: 6.649A pdb=" N MET E 164 " --> pdb=" O THR E 351 " (cutoff:3.500A) removed outlier: 5.631A pdb=" N ALA E 287 " --> pdb=" O GLY E 205 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ASP E 201 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N MET E 263 " --> pdb=" O GLU E 253 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N GLU E 253 " --> pdb=" O MET E 263 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ILE E 265 " --> pdb=" O MET E 251 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 271 through 273 Processing sheet with id=AE2, first strand: chain 'F' and resid 30 through 33 removed outlier: 6.519A pdb=" N ARG F 30 " --> pdb=" O ARG F 299 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N PHE F 301 " --> pdb=" O ARG F 30 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ILE F 32 " --> pdb=" O PHE F 301 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'F' and resid 141 through 144 removed outlier: 3.861A pdb=" N VAL F 152 " --> pdb=" O VAL F 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'F' and resid 163 through 165 removed outlier: 5.699A pdb=" N ALA F 287 " --> pdb=" O GLY F 205 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP F 201 " --> pdb=" O ILE F 291 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLY F 252 " --> pdb=" O ILE F 265 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL F 267 " --> pdb=" O TYR F 250 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N TYR F 250 " --> pdb=" O VAL F 267 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'F' and resid 271 through 273 Processing sheet with id=AE6, first strand: chain 'G' and resid 30 through 33 removed outlier: 6.580A pdb=" N ARG G 30 " --> pdb=" O ARG G 299 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N PHE G 301 " --> pdb=" O ARG G 30 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE G 32 " --> pdb=" O PHE G 301 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'G' and resid 39 through 43 removed outlier: 4.211A pdb=" N ASN G 70 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N TYR G 69 " --> pdb=" O SER a 24 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N SER a 24 " --> pdb=" O TYR G 69 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR G 71 " --> pdb=" O LEU a 22 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'G' and resid 82 through 85 removed outlier: 3.508A pdb=" N GLU G 329 " --> pdb=" O ILE G 85 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'G' and resid 141 through 144 Processing sheet with id=AF1, first strand: chain 'G' and resid 163 through 165 removed outlier: 3.654A pdb=" N ASP G 201 " --> pdb=" O ILE G 291 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N MET G 263 " --> pdb=" O GLU G 253 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLU G 253 " --> pdb=" O MET G 263 " (cutoff:3.500A) removed outlier: 5.414A pdb=" N ILE G 265 " --> pdb=" O MET G 251 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'G' and resid 271 through 273 Processing sheet with id=AF3, first strand: chain 'a' and resid 38 through 43 removed outlier: 5.968A pdb=" N VAL a 38 " --> pdb=" O ILE a 103 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 38 through 43 removed outlier: 5.968A pdb=" N VAL a 38 " --> pdb=" O ILE a 103 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'b' and resid 38 through 43 removed outlier: 6.290A pdb=" N VAL b 38 " --> pdb=" O ILE b 103 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'b' and resid 38 through 43 removed outlier: 6.290A pdb=" N VAL b 38 " --> pdb=" O ILE b 103 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'c' and resid 38 through 43 removed outlier: 6.118A pdb=" N VAL c 38 " --> pdb=" O ILE c 103 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'c' and resid 38 through 43 removed outlier: 6.118A pdb=" N VAL c 38 " --> pdb=" O ILE c 103 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'd' and resid 39 through 43 Processing sheet with id=AG1, first strand: chain 'd' and resid 105 through 108 Processing sheet with id=AG2, first strand: chain 'e' and resid 38 through 43 removed outlier: 6.011A pdb=" N VAL e 38 " --> pdb=" O ILE e 103 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'e' and resid 38 through 43 removed outlier: 6.011A pdb=" N VAL e 38 " --> pdb=" O ILE e 103 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'f' and resid 38 through 43 removed outlier: 6.065A pdb=" N VAL f 38 " --> pdb=" O ILE f 103 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'f' and resid 38 through 43 removed outlier: 6.065A pdb=" N VAL f 38 " --> pdb=" O ILE f 103 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'g' and resid 38 through 43 removed outlier: 6.044A pdb=" N VAL g 38 " --> pdb=" O ILE g 103 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N GLY g 104 " --> pdb=" O ILE g 86 " (cutoff:3.500A) removed outlier: 11.686A pdb=" N ILE g 86 " --> pdb=" O GLY g 104 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE g 54 " --> pdb=" O ILE g 86 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'g' and resid 38 through 43 removed outlier: 6.044A pdb=" N VAL g 38 " --> pdb=" O ILE g 103 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N HIS g 134 " --> pdb=" O ILE g 103 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N GLY g 105 " --> pdb=" O HIS g 134 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N GLY g 136 " --> pdb=" O GLY g 105 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N PHE g 107 " --> pdb=" O GLY g 136 " (cutoff:3.500A) 907 hydrogen bonds defined for protein. 2469 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: 5.60 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8499 1.34 - 1.46: 5496 1.46 - 1.58: 12053 1.58 - 1.70: 0 1.70 - 1.82: 271 Bond restraints: 26319 Sorted by residual: bond pdb=" CA GLN G 275 " pdb=" C GLN G 275 " ideal model delta sigma weight residual 1.523 1.480 0.043 1.80e-02 3.09e+03 5.78e+00 bond pdb=" CA ILE C 90 " pdb=" CB ILE C 90 " ideal model delta sigma weight residual 1.545 1.523 0.022 1.05e-02 9.07e+03 4.46e+00 bond pdb=" CG1 ILE A 39 " pdb=" CD1 ILE A 39 " ideal model delta sigma weight residual 1.513 1.431 0.082 3.90e-02 6.57e+02 4.44e+00 bond pdb=" CA VAL G 48 " pdb=" C VAL G 48 " ideal model delta sigma weight residual 1.523 1.497 0.026 1.27e-02 6.20e+03 4.05e+00 bond pdb=" CA PRO C 92 " pdb=" CB PRO C 92 " ideal model delta sigma weight residual 1.533 1.505 0.028 1.42e-02 4.96e+03 4.00e+00 ... (remaining 26314 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 33517 1.61 - 3.21: 1957 3.21 - 4.82: 258 4.82 - 6.42: 15 6.42 - 8.03: 8 Bond angle restraints: 35755 Sorted by residual: angle pdb=" N ARG D 110 " pdb=" CA ARG D 110 " pdb=" C ARG D 110 " ideal model delta sigma weight residual 111.07 106.42 4.65 1.07e+00 8.73e-01 1.89e+01 angle pdb=" N ARG C 93 " pdb=" CA ARG C 93 " pdb=" C ARG C 93 " ideal model delta sigma weight residual 110.53 116.26 -5.73 1.32e+00 5.74e-01 1.88e+01 angle pdb=" N ASP D 224 " pdb=" CA ASP D 224 " pdb=" C ASP D 224 " ideal model delta sigma weight residual 113.72 108.14 5.58 1.52e+00 4.33e-01 1.35e+01 angle pdb=" N GLY D 68 " pdb=" CA GLY D 68 " pdb=" C GLY D 68 " ideal model delta sigma weight residual 111.12 118.02 -6.90 1.89e+00 2.80e-01 1.33e+01 angle pdb=" O VAL D 44 " pdb=" C VAL D 44 " pdb=" N ILE D 45 " ideal model delta sigma weight residual 123.18 119.41 3.77 1.04e+00 9.25e-01 1.31e+01 ... (remaining 35750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 13910 17.95 - 35.89: 1265 35.89 - 53.84: 258 53.84 - 71.78: 68 71.78 - 89.72: 41 Dihedral angle restraints: 15542 sinusoidal: 6085 harmonic: 9457 Sorted by residual: dihedral pdb=" CA ASN d 137 " pdb=" C ASN d 137 " pdb=" N LEU d 138 " pdb=" CA LEU d 138 " ideal model delta harmonic sigma weight residual 180.00 152.07 27.93 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ASN a 137 " pdb=" C ASN a 137 " pdb=" N LEU a 138 " pdb=" CA LEU a 138 " ideal model delta harmonic sigma weight residual 180.00 152.25 27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CA TYR F 8 " pdb=" C TYR F 8 " pdb=" N GLN F 9 " pdb=" CA GLN F 9 " ideal model delta harmonic sigma weight residual 180.00 152.42 27.58 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 15539 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 2419 0.040 - 0.080: 996 0.080 - 0.120: 333 0.120 - 0.159: 122 0.159 - 0.199: 6 Chirality restraints: 3876 Sorted by residual: chirality pdb=" CA ILE c 88 " pdb=" N ILE c 88 " pdb=" C ILE c 88 " pdb=" CB ILE c 88 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CA ILE b 88 " pdb=" N ILE b 88 " pdb=" C ILE b 88 " pdb=" CB ILE b 88 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CA PRO G 95 " pdb=" N PRO G 95 " pdb=" C PRO G 95 " pdb=" CB PRO G 95 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 8.05e-01 ... (remaining 3873 not shown) Planarity restraints: 4683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 80 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO E 81 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO E 81 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO E 81 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG G 153 " 0.185 9.50e-02 1.11e+02 8.29e-02 4.36e+00 pdb=" NE ARG G 153 " -0.009 2.00e-02 2.50e+03 pdb=" CZ ARG G 153 " -0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG G 153 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG G 153 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 240 " 0.181 9.50e-02 1.11e+02 8.12e-02 4.05e+00 pdb=" NE ARG A 240 " -0.011 2.00e-02 2.50e+03 pdb=" CZ ARG A 240 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 240 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 240 " 0.006 2.00e-02 2.50e+03 ... (remaining 4680 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 274 2.59 - 3.17: 23184 3.17 - 3.75: 38089 3.75 - 4.32: 56949 4.32 - 4.90: 94861 Nonbonded interactions: 213357 Sorted by model distance: nonbonded pdb=" N GLU f 49 " pdb=" OE1 GLU f 49 " model vdw 2.018 3.120 nonbonded pdb=" N GLU b 49 " pdb=" OE1 GLU b 49 " model vdw 2.018 3.120 nonbonded pdb=" N GLU d 49 " pdb=" OE1 GLU d 49 " model vdw 2.021 3.120 nonbonded pdb=" N GLU a 49 " pdb=" OE1 GLU a 49 " model vdw 2.067 3.120 nonbonded pdb=" O PRO a 67 " pdb=" OG1 THR a 68 " model vdw 2.124 3.040 ... (remaining 213352 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 through 217 or resid 237 through 354)) selection = (chain 'B' and (resid 4 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 through 217 or resid 237 through 354)) selection = (chain 'C' and (resid 4 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 through 217 or resid 237 through 354)) selection = (chain 'D' and (resid 4 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 through 217 or resid 237 through 354)) selection = (chain 'E' and (resid 4 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 through 217 or resid 237 through 354)) selection = (chain 'F' and (resid 4 through 15 or (resid 16 and (name N or name CA or name C \ or name O or name CB )) or resid 17 or (resid 18 and (name N or name CA or name \ C or name O or name CB )) or resid 19 through 217 or resid 237 through 354)) selection = chain 'G' } ncs_group { reference = (chain 'a' and (resid 10 through 69 or (resid 70 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 139)) selection = (chain 'b' and (resid 10 through 69 or (resid 70 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 139)) selection = (chain 'c' and (resid 10 through 69 or (resid 70 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 139)) selection = (chain 'd' and (resid 10 through 69 or (resid 70 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 139)) selection = (chain 'e' and (resid 10 through 69 or (resid 70 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 139)) selection = (chain 'f' and (resid 10 through 69 or (resid 70 through 77 and (name N or name \ CA or name C or name O or name CB )) or resid 78 through 139)) selection = chain 'g' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 43.480 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: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 24.480 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 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 : 0.009 0.099 26319 Z= 0.392 Angle : 0.824 8.030 35755 Z= 0.462 Chirality : 0.051 0.199 3876 Planarity : 0.007 0.083 4683 Dihedral : 15.451 89.725 9514 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.23 % Rotamer: Outliers : 1.59 % Allowed : 12.91 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: -1.52 (0.13), residues: 3274 helix: -0.52 (0.19), residues: 627 sheet: -0.24 (0.18), residues: 752 loop : -1.53 (0.13), residues: 1895 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 15 TYR 0.025 0.003 TYR F 69 PHE 0.027 0.003 PHE E 212 TRP 0.023 0.002 TRP G 242 HIS 0.013 0.003 HIS b 115 Details of bonding type rmsd covalent geometry : bond 0.00891 (26319) covalent geometry : angle 0.82414 (35755) hydrogen bonds : bond 0.16635 ( 875) hydrogen bonds : angle 8.17624 ( 2469) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 768 time to evaluate : 1.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8773 (p90) cc_final: 0.8495 (p90) REVERT: A 89 MET cc_start: 0.7628 (mtt) cc_final: 0.7125 (mtp) REVERT: A 246 GLU cc_start: 0.8236 (tt0) cc_final: 0.8031 (tt0) REVERT: A 277 ASP cc_start: 0.8090 (t0) cc_final: 0.7564 (t70) REVERT: A 307 LYS cc_start: 0.8826 (tptt) cc_final: 0.8550 (mptt) REVERT: A 324 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7424 (tt0) REVERT: B 18 LYS cc_start: 0.8377 (mtpp) cc_final: 0.8162 (mtpt) REVERT: B 70 ASN cc_start: 0.9189 (m-40) cc_final: 0.8815 (m-40) REVERT: B 126 GLU cc_start: 0.8569 (tt0) cc_final: 0.8333 (mt-10) REVERT: B 159 ASP cc_start: 0.8353 (t0) cc_final: 0.8070 (t0) REVERT: B 268 ASN cc_start: 0.9027 (t0) cc_final: 0.8659 (t0) REVERT: B 275 GLN cc_start: 0.8183 (mt0) cc_final: 0.7957 (mt0) REVERT: B 277 ASP cc_start: 0.8439 (t0) cc_final: 0.7677 (t0) REVERT: B 307 LYS cc_start: 0.9303 (ttpp) cc_final: 0.9074 (tptt) REVERT: B 323 GLN cc_start: 0.8400 (tt0) cc_final: 0.8117 (tt0) REVERT: C 119 MET cc_start: 0.8844 (tmm) cc_final: 0.8639 (tmm) REVERT: C 324 GLU cc_start: 0.8736 (mm-30) cc_final: 0.7150 (pt0) REVERT: D 307 LYS cc_start: 0.9214 (tttm) cc_final: 0.8753 (mptt) REVERT: D 324 GLU cc_start: 0.8546 (mm-30) cc_final: 0.6981 (tt0) REVERT: E 111 ASP cc_start: 0.8903 (t0) cc_final: 0.8667 (t0) REVERT: E 339 MET cc_start: 0.8796 (mmp) cc_final: 0.8534 (mmp) REVERT: F 178 MET cc_start: 0.8462 (mmt) cc_final: 0.7721 (mtt) REVERT: F 307 LYS cc_start: 0.8996 (tptp) cc_final: 0.8477 (mptt) REVERT: F 353 MET cc_start: 0.8843 (mtp) cc_final: 0.8523 (mtt) REVERT: G 37 ASP cc_start: 0.3853 (OUTLIER) cc_final: 0.2347 (p0) REVERT: G 262 ARG cc_start: 0.8346 (ptt-90) cc_final: 0.6878 (mmt180) REVERT: G 283 MET cc_start: 0.9083 (tpp) cc_final: 0.8485 (tpp) REVERT: G 324 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7442 (tt0) REVERT: G 333 SER cc_start: 0.8883 (m) cc_final: 0.8678 (p) REVERT: G 353 MET cc_start: 0.8135 (mmm) cc_final: 0.7712 (mmm) REVERT: a 62 MET cc_start: 0.8784 (mmp) cc_final: 0.8376 (mmt) REVERT: a 133 ILE cc_start: 0.9135 (mt) cc_final: 0.8896 (mm) REVERT: b 36 ASP cc_start: 0.6944 (p0) cc_final: 0.6655 (p0) REVERT: b 91 GLN cc_start: 0.8580 (OUTLIER) cc_final: 0.8291 (mm-40) REVERT: c 36 ASP cc_start: 0.7146 (p0) cc_final: 0.6441 (p0) REVERT: c 123 LYS cc_start: 0.9104 (mttm) cc_final: 0.8889 (mtpt) REVERT: c 132 ASN cc_start: 0.7700 (m-40) cc_final: 0.7154 (t0) REVERT: d 37 ILE cc_start: 0.8705 (mt) cc_final: 0.8422 (mt) REVERT: d 62 MET cc_start: 0.8510 (mmm) cc_final: 0.8221 (mmt) REVERT: d 91 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8518 (mm-40) REVERT: e 62 MET cc_start: 0.8871 (mmm) cc_final: 0.8468 (mmt) REVERT: e 97 GLN cc_start: 0.8825 (mt0) cc_final: 0.8531 (mt0) REVERT: f 34 GLU cc_start: 0.6048 (mm-30) cc_final: 0.5792 (tp30) REVERT: f 82 GLN cc_start: 0.8942 (mp10) cc_final: 0.8637 (mp10) REVERT: g 15 TYR cc_start: 0.8312 (m-80) cc_final: 0.7832 (m-80) REVERT: g 84 VAL cc_start: 0.9602 (p) cc_final: 0.9353 (m) REVERT: g 119 ASP cc_start: 0.8978 (p0) cc_final: 0.8764 (p0) REVERT: g 121 LEU cc_start: 0.9218 (tp) cc_final: 0.8853 (tt) outliers start: 42 outliers final: 21 residues processed: 791 average time/residue: 0.1606 time to fit residues: 205.4585 Evaluate side-chains 658 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 634 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain C residue 92 PRO Chi-restraints excluded: chain C residue 315 ASP Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain E residue 89 MET Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 316 TYR Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain G residue 37 ASP Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 91 GLN Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain d residue 21 ASP Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain d residue 106 VAL Chi-restraints excluded: chain e residue 14 ASN Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 137 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 ASN B 88 ASN C 138 GLN D 70 ASN E 88 ASN ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 GLN ** d 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 HIS e 115 HIS ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 115 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.086531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 22)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.076741 restraints weight = 50180.112| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.68 r_work: 0.2881 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 26319 Z= 0.236 Angle : 0.692 8.404 35755 Z= 0.369 Chirality : 0.048 0.216 3876 Planarity : 0.005 0.054 4683 Dihedral : 7.001 58.527 3646 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 4.24 % Allowed : 14.69 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: -1.00 (0.14), residues: 3274 helix: 0.32 (0.21), residues: 594 sheet: -0.51 (0.18), residues: 825 loop : -1.05 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 264 TYR 0.020 0.002 TYR D 69 PHE 0.022 0.002 PHE b 128 TRP 0.020 0.001 TRP A 221 HIS 0.007 0.001 HIS C 121 Details of bonding type rmsd covalent geometry : bond 0.00562 (26319) covalent geometry : angle 0.69237 (35755) hydrogen bonds : bond 0.04893 ( 875) hydrogen bonds : angle 6.25425 ( 2469) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 807 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 695 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8587 (ptpt) cc_final: 0.6667 (mmtm) REVERT: A 89 MET cc_start: 0.7838 (mtt) cc_final: 0.7276 (mtp) REVERT: A 307 LYS cc_start: 0.8967 (tptt) cc_final: 0.8454 (mppt) REVERT: A 324 GLU cc_start: 0.8744 (mm-30) cc_final: 0.7573 (tt0) REVERT: A 329 GLU cc_start: 0.8271 (mt-10) cc_final: 0.7996 (tt0) REVERT: B 126 GLU cc_start: 0.8820 (tt0) cc_final: 0.8593 (mt-10) REVERT: B 147 GLN cc_start: 0.8761 (mt0) cc_final: 0.8509 (tt0) REVERT: B 159 ASP cc_start: 0.8434 (t0) cc_final: 0.8171 (t0) REVERT: B 268 ASN cc_start: 0.9114 (t0) cc_final: 0.8675 (t0) REVERT: B 275 GLN cc_start: 0.8278 (mt0) cc_final: 0.7973 (mm-40) REVERT: B 277 ASP cc_start: 0.8652 (t0) cc_final: 0.7801 (t0) REVERT: B 296 GLU cc_start: 0.8301 (tp30) cc_final: 0.7571 (tp30) REVERT: B 307 LYS cc_start: 0.9339 (ttpp) cc_final: 0.8955 (tptt) REVERT: B 323 GLN cc_start: 0.8579 (tt0) cc_final: 0.8191 (tt0) REVERT: C 15 ARG cc_start: 0.8679 (mtp85) cc_final: 0.8446 (tpp80) REVERT: C 32 ILE cc_start: 0.9154 (tp) cc_final: 0.8859 (pt) REVERT: C 130 GLU cc_start: 0.8873 (tp30) cc_final: 0.8485 (mm-30) REVERT: C 324 GLU cc_start: 0.8851 (mm-30) cc_final: 0.7224 (pt0) REVERT: C 339 MET cc_start: 0.9239 (mmp) cc_final: 0.9001 (mmp) REVERT: D 37 ASP cc_start: 0.8565 (m-30) cc_final: 0.8363 (t0) REVERT: D 58 ASN cc_start: 0.8573 (OUTLIER) cc_final: 0.8292 (m110) REVERT: D 219 GLU cc_start: 0.8778 (mp0) cc_final: 0.8552 (mp0) REVERT: D 307 LYS cc_start: 0.9067 (tttm) cc_final: 0.8371 (mptt) REVERT: D 332 MET cc_start: 0.8824 (OUTLIER) cc_final: 0.8440 (ttm) REVERT: D 353 MET cc_start: 0.8934 (mtp) cc_final: 0.8689 (mtt) REVERT: E 60 GLN cc_start: 0.8736 (mt0) cc_final: 0.8070 (mm-40) REVERT: E 111 ASP cc_start: 0.9118 (t0) cc_final: 0.8779 (m-30) REVERT: E 119 MET cc_start: 0.8799 (tmm) cc_final: 0.8542 (tmm) REVERT: E 130 GLU cc_start: 0.8614 (tp30) cc_final: 0.8338 (tp30) REVERT: E 307 LYS cc_start: 0.6583 (mptt) cc_final: 0.5971 (mptt) REVERT: E 329 GLU cc_start: 0.8860 (mp0) cc_final: 0.8585 (mt-10) REVERT: F 130 GLU cc_start: 0.8489 (tp30) cc_final: 0.8140 (tp30) REVERT: F 178 MET cc_start: 0.8430 (mmt) cc_final: 0.8023 (mtt) REVERT: F 307 LYS cc_start: 0.9023 (tptp) cc_final: 0.8307 (mptt) REVERT: F 353 MET cc_start: 0.8984 (mtp) cc_final: 0.8618 (mtt) REVERT: G 213 VAL cc_start: 0.9413 (t) cc_final: 0.9143 (m) REVERT: G 241 LEU cc_start: 0.9106 (tt) cc_final: 0.8784 (tt) REVERT: G 262 ARG cc_start: 0.8331 (ptt-90) cc_final: 0.6897 (mmt180) REVERT: G 324 GLU cc_start: 0.8601 (mm-30) cc_final: 0.7424 (tt0) REVERT: G 333 SER cc_start: 0.8956 (m) cc_final: 0.8682 (p) REVERT: G 353 MET cc_start: 0.8144 (mmm) cc_final: 0.7824 (mmm) REVERT: a 40 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5955 (tt0) REVERT: a 49 GLU cc_start: 0.8031 (mp0) cc_final: 0.7706 (mp0) REVERT: a 62 MET cc_start: 0.8926 (mmp) cc_final: 0.8629 (mmt) REVERT: a 130 ARG cc_start: 0.7994 (tpp-160) cc_final: 0.4980 (tmt-80) REVERT: a 133 ILE cc_start: 0.9139 (mt) cc_final: 0.8895 (mm) REVERT: b 82 GLN cc_start: 0.8911 (mp10) cc_final: 0.8661 (pm20) REVERT: b 91 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8226 (mm-40) REVERT: c 26 GLU cc_start: 0.8653 (pm20) cc_final: 0.8291 (mm-30) REVERT: c 36 ASP cc_start: 0.7261 (p0) cc_final: 0.6648 (p0) REVERT: c 49 GLU cc_start: 0.8295 (mp0) cc_final: 0.7972 (mp0) REVERT: c 123 LYS cc_start: 0.9155 (mttm) cc_final: 0.8938 (mtpt) REVERT: c 132 ASN cc_start: 0.7664 (OUTLIER) cc_final: 0.7225 (t0) REVERT: d 29 GLN cc_start: 0.7471 (mt0) cc_final: 0.7170 (mm-40) REVERT: d 36 ASP cc_start: 0.7334 (m-30) cc_final: 0.7124 (m-30) REVERT: d 37 ILE cc_start: 0.8758 (mt) cc_final: 0.8481 (mt) REVERT: d 49 GLU cc_start: 0.8423 (mp0) cc_final: 0.8116 (mp0) REVERT: d 91 GLN cc_start: 0.8884 (OUTLIER) cc_final: 0.7880 (mp10) REVERT: d 118 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8545 (tp) REVERT: e 21 ASP cc_start: 0.9106 (p0) cc_final: 0.8795 (p0) REVERT: e 97 GLN cc_start: 0.8886 (mt0) cc_final: 0.8556 (mt0) REVERT: e 99 VAL cc_start: 0.8657 (t) cc_final: 0.8447 (p) REVERT: e 108 ASN cc_start: 0.8880 (t0) cc_final: 0.8562 (t0) REVERT: f 34 GLU cc_start: 0.6634 (mm-30) cc_final: 0.6110 (tp30) REVERT: f 118 LEU cc_start: 0.9092 (tp) cc_final: 0.8735 (tt) REVERT: g 15 TYR cc_start: 0.8429 (m-80) cc_final: 0.7806 (m-80) REVERT: g 84 VAL cc_start: 0.9351 (p) cc_final: 0.9105 (m) REVERT: g 119 ASP cc_start: 0.9208 (OUTLIER) cc_final: 0.8959 (p0) outliers start: 112 outliers final: 72 residues processed: 749 average time/residue: 0.1566 time to fit residues: 191.6249 Evaluate side-chains 700 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 620 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain D residue 322 ASP Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 316 TYR Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 67 SER Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain a residue 40 GLU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 119 ASP Chi-restraints excluded: chain b residue 40 GLU Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 91 GLN Chi-restraints excluded: chain b residue 95 SER Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain c residue 39 THR Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain c residue 119 ASP Chi-restraints excluded: chain c residue 129 ASP Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain c residue 137 ASN Chi-restraints excluded: chain d residue 38 VAL Chi-restraints excluded: chain d residue 54 ILE Chi-restraints excluded: chain d residue 63 VAL Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain d residue 106 VAL Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 119 ASP Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain f residue 137 ASN Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 119 ASP Chi-restraints excluded: chain g residue 120 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 30 optimal weight: 5.9990 chunk 130 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 chunk 250 optimal weight: 6.9990 chunk 286 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 35 optimal weight: 10.0000 chunk 320 optimal weight: 9.9990 chunk 229 optimal weight: 0.9980 chunk 134 optimal weight: 0.8980 overall best weight: 4.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN E 9 GLN E 88 ASN E 285 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 109 HIS c 125 GLN ** d 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 98 ASN ** g 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.086355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.076565 restraints weight = 50175.751| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.68 r_work: 0.2891 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2766 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 26319 Z= 0.222 Angle : 0.637 8.608 35755 Z= 0.336 Chirality : 0.047 0.231 3876 Planarity : 0.004 0.050 4683 Dihedral : 6.573 58.892 3628 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.34 % Allowed : 16.55 % Favored : 78.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: -1.01 (0.14), residues: 3274 helix: 0.42 (0.21), residues: 606 sheet: -0.61 (0.18), residues: 854 loop : -1.06 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 15 TYR 0.018 0.002 TYR D 69 PHE 0.019 0.002 PHE b 128 TRP 0.015 0.001 TRP D 221 HIS 0.007 0.001 HIS e 109 Details of bonding type rmsd covalent geometry : bond 0.00529 (26319) covalent geometry : angle 0.63690 (35755) hydrogen bonds : bond 0.04406 ( 875) hydrogen bonds : angle 5.85761 ( 2469) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 798 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 657 time to evaluate : 0.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8599 (ptpt) cc_final: 0.7083 (mmtt) REVERT: A 69 TYR cc_start: 0.8513 (p90) cc_final: 0.7883 (p90) REVERT: A 307 LYS cc_start: 0.8955 (tptt) cc_final: 0.8412 (mppt) REVERT: B 126 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8539 (mt-10) REVERT: B 159 ASP cc_start: 0.8400 (t0) cc_final: 0.8062 (t0) REVERT: B 251 MET cc_start: 0.8811 (mmm) cc_final: 0.8594 (mmm) REVERT: B 268 ASN cc_start: 0.9118 (t0) cc_final: 0.8560 (t0) REVERT: B 274 ASP cc_start: 0.8169 (t70) cc_final: 0.7944 (t0) REVERT: B 275 GLN cc_start: 0.8322 (mt0) cc_final: 0.8021 (mm-40) REVERT: B 277 ASP cc_start: 0.8663 (t0) cc_final: 0.7859 (t0) REVERT: B 296 GLU cc_start: 0.8381 (tp30) cc_final: 0.7840 (tp30) REVERT: B 307 LYS cc_start: 0.9286 (ttpp) cc_final: 0.8892 (tptt) REVERT: B 315 ASP cc_start: 0.8850 (OUTLIER) cc_final: 0.8335 (m-30) REVERT: B 323 GLN cc_start: 0.8572 (tt0) cc_final: 0.8188 (tt0) REVERT: C 15 ARG cc_start: 0.8727 (mtp85) cc_final: 0.8524 (tpp80) REVERT: C 36 GLU cc_start: 0.9278 (mp0) cc_final: 0.9049 (mp0) REVERT: C 71 THR cc_start: 0.9161 (m) cc_final: 0.8761 (p) REVERT: C 130 GLU cc_start: 0.8896 (tp30) cc_final: 0.8496 (tp30) REVERT: C 227 MET cc_start: 0.8416 (mtp) cc_final: 0.8077 (mmm) REVERT: C 324 GLU cc_start: 0.8808 (mm-30) cc_final: 0.7169 (pt0) REVERT: D 37 ASP cc_start: 0.8607 (m-30) cc_final: 0.8394 (t70) REVERT: D 307 LYS cc_start: 0.9089 (tttm) cc_final: 0.8373 (mptt) REVERT: D 324 GLU cc_start: 0.8711 (mm-30) cc_final: 0.7120 (tt0) REVERT: D 332 MET cc_start: 0.8844 (OUTLIER) cc_final: 0.8583 (ttm) REVERT: E 15 ARG cc_start: 0.7994 (mtt-85) cc_final: 0.7717 (mtp180) REVERT: E 60 GLN cc_start: 0.8840 (mt0) cc_final: 0.8004 (mm-40) REVERT: E 111 ASP cc_start: 0.9074 (t0) cc_final: 0.8745 (m-30) REVERT: E 307 LYS cc_start: 0.6563 (mptt) cc_final: 0.6063 (mptt) REVERT: E 329 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8581 (mt-10) REVERT: F 130 GLU cc_start: 0.8491 (tp30) cc_final: 0.8126 (tp30) REVERT: F 178 MET cc_start: 0.8451 (mmt) cc_final: 0.8041 (mtt) REVERT: F 304 ILE cc_start: 0.8731 (mm) cc_final: 0.8518 (mt) REVERT: F 307 LYS cc_start: 0.9034 (tptp) cc_final: 0.8506 (mptt) REVERT: G 213 VAL cc_start: 0.9406 (t) cc_final: 0.9147 (m) REVERT: G 324 GLU cc_start: 0.8579 (mm-30) cc_final: 0.7276 (tt0) REVERT: G 333 SER cc_start: 0.8908 (m) cc_final: 0.8555 (p) REVERT: G 343 ASP cc_start: 0.8815 (t0) cc_final: 0.8614 (t0) REVERT: G 353 MET cc_start: 0.8106 (mmm) cc_final: 0.7764 (mmm) REVERT: a 40 GLU cc_start: 0.6433 (OUTLIER) cc_final: 0.5903 (tt0) REVERT: a 49 GLU cc_start: 0.8168 (mp0) cc_final: 0.7840 (mp0) REVERT: a 95 SER cc_start: 0.9497 (p) cc_final: 0.9265 (t) REVERT: a 130 ARG cc_start: 0.8208 (tpp-160) cc_final: 0.5180 (tpt170) REVERT: a 133 ILE cc_start: 0.9197 (mt) cc_final: 0.8985 (mm) REVERT: b 91 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8282 (mm-40) REVERT: b 123 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8482 (mtmm) REVERT: c 26 GLU cc_start: 0.8662 (pm20) cc_final: 0.8264 (mm-30) REVERT: c 34 GLU cc_start: 0.6735 (mm-30) cc_final: 0.6002 (mm-30) REVERT: c 36 ASP cc_start: 0.7292 (p0) cc_final: 0.6712 (p0) REVERT: c 49 GLU cc_start: 0.8338 (mp0) cc_final: 0.8069 (mp0) REVERT: c 62 MET cc_start: 0.8522 (mmm) cc_final: 0.8223 (mmt) REVERT: c 132 ASN cc_start: 0.7658 (OUTLIER) cc_final: 0.7237 (t0) REVERT: d 29 GLN cc_start: 0.7254 (mt0) cc_final: 0.6993 (mm-40) REVERT: d 34 GLU cc_start: 0.5998 (mm-30) cc_final: 0.5712 (mm-30) REVERT: d 36 ASP cc_start: 0.7493 (m-30) cc_final: 0.7279 (m-30) REVERT: d 37 ILE cc_start: 0.8753 (mt) cc_final: 0.8491 (mt) REVERT: d 49 GLU cc_start: 0.8474 (mp0) cc_final: 0.8084 (mp0) REVERT: d 91 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: d 118 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8466 (tp) REVERT: e 21 ASP cc_start: 0.9112 (p0) cc_final: 0.8816 (p0) REVERT: e 34 GLU cc_start: 0.5314 (mm-30) cc_final: 0.4985 (mm-30) REVERT: e 91 GLN cc_start: 0.9243 (mm-40) cc_final: 0.8786 (mm-40) REVERT: e 103 ILE cc_start: 0.8763 (tp) cc_final: 0.8502 (tp) REVERT: e 133 ILE cc_start: 0.8761 (mm) cc_final: 0.8557 (mm) REVERT: f 34 GLU cc_start: 0.6597 (mm-30) cc_final: 0.6367 (tp30) REVERT: f 95 SER cc_start: 0.9164 (p) cc_final: 0.8938 (t) REVERT: f 108 ASN cc_start: 0.8763 (t0) cc_final: 0.8531 (t0) REVERT: f 118 LEU cc_start: 0.9068 (tp) cc_final: 0.8722 (tt) REVERT: g 84 VAL cc_start: 0.9353 (p) cc_final: 0.9085 (m) REVERT: g 119 ASP cc_start: 0.9283 (OUTLIER) cc_final: 0.9037 (p0) outliers start: 141 outliers final: 95 residues processed: 727 average time/residue: 0.1309 time to fit residues: 156.9287 Evaluate side-chains 722 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 616 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 ASP Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain D residue 69 TYR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 218 LYS Chi-restraints excluded: chain D residue 226 LEU Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 316 TYR Chi-restraints excluded: chain E residue 329 GLU Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 67 SER Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 193 SER Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 40 GLU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 109 HIS Chi-restraints excluded: chain b residue 40 GLU Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 91 GLN Chi-restraints excluded: chain b residue 95 SER Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 123 LYS Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 82 GLN Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 119 ASP Chi-restraints excluded: chain c residue 129 ASP Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain c residue 137 ASN Chi-restraints excluded: chain d residue 63 VAL Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 106 VAL Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 119 ASP Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain e residue 14 ASN Chi-restraints excluded: chain e residue 70 THR Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 109 HIS Chi-restraints excluded: chain e residue 119 ASP Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 103 ILE Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain f residue 137 ASN Chi-restraints excluded: chain f residue 138 LEU Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 119 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 2 optimal weight: 5.9990 chunk 254 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 81 optimal weight: 8.9990 chunk 310 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 296 optimal weight: 3.9990 chunk 151 optimal weight: 8.9990 chunk 97 optimal weight: 9.9990 chunk 270 optimal weight: 20.0000 chunk 64 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 60 GLN D 58 ASN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 109 HIS c 125 GLN ** d 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 109 HIS ** g 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.087298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.077563 restraints weight = 49562.353| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 2.66 r_work: 0.2849 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 26319 Z= 0.179 Angle : 0.595 7.997 35755 Z= 0.314 Chirality : 0.045 0.247 3876 Planarity : 0.004 0.045 4683 Dihedral : 6.232 59.090 3626 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 4.85 % Allowed : 18.29 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: -0.93 (0.14), residues: 3274 helix: 0.62 (0.21), residues: 601 sheet: -0.65 (0.18), residues: 859 loop : -0.99 (0.14), residues: 1814 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 30 TYR 0.016 0.001 TYR D 69 PHE 0.017 0.001 PHE b 128 TRP 0.015 0.001 TRP A 221 HIS 0.006 0.001 HIS e 109 Details of bonding type rmsd covalent geometry : bond 0.00424 (26319) covalent geometry : angle 0.59530 (35755) hydrogen bonds : bond 0.04093 ( 875) hydrogen bonds : angle 5.63173 ( 2469) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 792 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 664 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8565 (ptpt) cc_final: 0.7082 (mmtt) REVERT: A 69 TYR cc_start: 0.8520 (p90) cc_final: 0.7888 (p90) REVERT: A 89 MET cc_start: 0.7736 (mtt) cc_final: 0.7267 (mtp) REVERT: A 307 LYS cc_start: 0.8904 (tptt) cc_final: 0.8340 (mppt) REVERT: B 126 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8574 (mt-10) REVERT: B 130 GLU cc_start: 0.8770 (tp30) cc_final: 0.8467 (tp30) REVERT: B 159 ASP cc_start: 0.8321 (t0) cc_final: 0.7995 (t0) REVERT: B 268 ASN cc_start: 0.9143 (t0) cc_final: 0.8455 (t0) REVERT: B 275 GLN cc_start: 0.8387 (mt0) cc_final: 0.8064 (mm-40) REVERT: B 277 ASP cc_start: 0.8594 (t0) cc_final: 0.7747 (t0) REVERT: B 296 GLU cc_start: 0.8465 (tp30) cc_final: 0.7587 (tp30) REVERT: B 307 LYS cc_start: 0.9315 (ttpp) cc_final: 0.8904 (tptt) REVERT: B 315 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8351 (m-30) REVERT: B 323 GLN cc_start: 0.8453 (tt0) cc_final: 0.8068 (tt0) REVERT: C 71 THR cc_start: 0.9147 (m) cc_final: 0.8780 (p) REVERT: C 130 GLU cc_start: 0.8911 (tp30) cc_final: 0.8319 (tp30) REVERT: C 324 GLU cc_start: 0.8789 (mm-30) cc_final: 0.7226 (pt0) REVERT: D 219 GLU cc_start: 0.8828 (mp0) cc_final: 0.8616 (mp0) REVERT: D 307 LYS cc_start: 0.9013 (tttm) cc_final: 0.8255 (mptt) REVERT: D 324 GLU cc_start: 0.8729 (mm-30) cc_final: 0.7098 (tt0) REVERT: E 60 GLN cc_start: 0.8815 (mt0) cc_final: 0.7848 (mm-40) REVERT: E 111 ASP cc_start: 0.9094 (t0) cc_final: 0.8790 (m-30) REVERT: E 251 MET cc_start: 0.8430 (mmm) cc_final: 0.7963 (mmm) REVERT: E 307 LYS cc_start: 0.6606 (mptt) cc_final: 0.5989 (mptt) REVERT: E 339 MET cc_start: 0.8416 (mmm) cc_final: 0.8157 (mmp) REVERT: F 130 GLU cc_start: 0.8441 (tp30) cc_final: 0.8070 (tp30) REVERT: F 178 MET cc_start: 0.8448 (mmt) cc_final: 0.8077 (mtt) REVERT: F 283 MET cc_start: 0.9066 (tpt) cc_final: 0.8767 (tpt) REVERT: F 307 LYS cc_start: 0.9054 (tptp) cc_final: 0.8422 (mptt) REVERT: F 333 SER cc_start: 0.8204 (m) cc_final: 0.7699 (p) REVERT: G 75 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8246 (mtpp) REVERT: G 203 ILE cc_start: 0.9155 (OUTLIER) cc_final: 0.8921 (mt) REVERT: G 213 VAL cc_start: 0.9390 (t) cc_final: 0.9133 (m) REVERT: G 324 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7210 (tt0) REVERT: G 333 SER cc_start: 0.8874 (m) cc_final: 0.8561 (p) REVERT: G 343 ASP cc_start: 0.8828 (t0) cc_final: 0.8568 (t0) REVERT: G 353 MET cc_start: 0.8176 (mmm) cc_final: 0.7890 (mmm) REVERT: a 40 GLU cc_start: 0.6513 (OUTLIER) cc_final: 0.5936 (tt0) REVERT: a 49 GLU cc_start: 0.8248 (mp0) cc_final: 0.7929 (mp0) REVERT: a 95 SER cc_start: 0.9503 (p) cc_final: 0.9274 (t) REVERT: a 115 HIS cc_start: 0.7347 (OUTLIER) cc_final: 0.6555 (p90) REVERT: a 130 ARG cc_start: 0.8240 (tpp-160) cc_final: 0.5150 (tpt170) REVERT: a 133 ILE cc_start: 0.9218 (mt) cc_final: 0.9013 (mm) REVERT: a 135 ILE cc_start: 0.8438 (mt) cc_final: 0.8214 (mt) REVERT: b 108 ASN cc_start: 0.8779 (t0) cc_final: 0.8366 (t0) REVERT: b 123 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8473 (mtmm) REVERT: c 26 GLU cc_start: 0.8625 (pm20) cc_final: 0.8254 (mm-30) REVERT: c 36 ASP cc_start: 0.7330 (p0) cc_final: 0.7023 (p0) REVERT: c 49 GLU cc_start: 0.8337 (mp0) cc_final: 0.8067 (mp0) REVERT: c 62 MET cc_start: 0.8596 (mmm) cc_final: 0.8322 (mmt) REVERT: c 132 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7656 (t0) REVERT: d 34 GLU cc_start: 0.5828 (mm-30) cc_final: 0.5475 (mm-30) REVERT: d 37 ILE cc_start: 0.8736 (mt) cc_final: 0.8465 (mt) REVERT: d 49 GLU cc_start: 0.8489 (mp0) cc_final: 0.8102 (mp0) REVERT: d 91 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.7944 (mp10) REVERT: d 118 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8480 (tp) REVERT: e 21 ASP cc_start: 0.9106 (p0) cc_final: 0.8803 (p0) REVERT: e 34 GLU cc_start: 0.5362 (mm-30) cc_final: 0.4942 (mm-30) REVERT: e 91 GLN cc_start: 0.9200 (mm-40) cc_final: 0.8806 (mm-40) REVERT: e 103 ILE cc_start: 0.8769 (tp) cc_final: 0.8419 (tp) REVERT: e 108 ASN cc_start: 0.8783 (t0) cc_final: 0.8474 (t0) REVERT: e 123 LYS cc_start: 0.9389 (mtpp) cc_final: 0.9155 (mtmm) REVERT: e 133 ILE cc_start: 0.8712 (mm) cc_final: 0.8504 (mm) REVERT: f 95 SER cc_start: 0.9163 (p) cc_final: 0.8947 (t) REVERT: f 108 ASN cc_start: 0.8668 (t0) cc_final: 0.8413 (t0) REVERT: f 118 LEU cc_start: 0.9100 (tp) cc_final: 0.8814 (tp) REVERT: g 84 VAL cc_start: 0.9369 (p) cc_final: 0.9083 (m) REVERT: g 119 ASP cc_start: 0.9347 (OUTLIER) cc_final: 0.9120 (p0) outliers start: 128 outliers final: 85 residues processed: 732 average time/residue: 0.1306 time to fit residues: 157.0237 Evaluate side-chains 722 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 626 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 316 TYR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 300 CYS Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain a residue 40 GLU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 109 HIS Chi-restraints excluded: chain a residue 115 HIS Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 40 GLU Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 123 LYS Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 82 GLN Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain c residue 119 ASP Chi-restraints excluded: chain c residue 120 THR Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain c residue 137 ASN Chi-restraints excluded: chain d residue 63 VAL Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 119 ASP Chi-restraints excluded: chain e residue 109 HIS Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 119 ASP Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 103 ILE Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain f residue 137 ASN Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 119 ASP Chi-restraints excluded: chain g residue 120 THR Chi-restraints excluded: chain g residue 137 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 153 optimal weight: 5.9990 chunk 319 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 226 optimal weight: 20.0000 chunk 273 optimal weight: 0.0870 chunk 15 optimal weight: 9.9990 chunk 164 optimal weight: 0.6980 chunk 307 optimal weight: 6.9990 chunk 166 optimal weight: 1.9990 overall best weight: 2.9564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 91 GLN ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 91 GLN c 125 GLN ** d 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 109 HIS ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 125 GLN ** g 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.087828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.078137 restraints weight = 49524.290| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 2.66 r_work: 0.2908 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 26319 Z= 0.173 Angle : 0.592 9.864 35755 Z= 0.309 Chirality : 0.044 0.239 3876 Planarity : 0.004 0.042 4683 Dihedral : 5.987 59.721 3622 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 5.23 % Allowed : 18.82 % Favored : 75.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: -0.89 (0.14), residues: 3274 helix: 0.67 (0.21), residues: 601 sheet: -0.65 (0.18), residues: 858 loop : -0.96 (0.14), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 262 TYR 0.015 0.001 TYR D 69 PHE 0.014 0.001 PHE b 128 TRP 0.014 0.001 TRP A 221 HIS 0.006 0.001 HIS e 109 Details of bonding type rmsd covalent geometry : bond 0.00412 (26319) covalent geometry : angle 0.59211 (35755) hydrogen bonds : bond 0.03975 ( 875) hydrogen bonds : angle 5.53403 ( 2469) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 655 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8538 (p90) cc_final: 0.7960 (p90) REVERT: A 89 MET cc_start: 0.7815 (mtt) cc_final: 0.7317 (mtp) REVERT: A 227 MET cc_start: 0.7986 (OUTLIER) cc_final: 0.7419 (mtp) REVERT: A 307 LYS cc_start: 0.8894 (tptt) cc_final: 0.8316 (mppt) REVERT: B 126 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8534 (mt-10) REVERT: B 130 GLU cc_start: 0.8774 (tp30) cc_final: 0.8514 (tp30) REVERT: B 159 ASP cc_start: 0.8316 (t0) cc_final: 0.7967 (t0) REVERT: B 251 MET cc_start: 0.8787 (mmm) cc_final: 0.8359 (mmm) REVERT: B 274 ASP cc_start: 0.8365 (t0) cc_final: 0.8162 (t70) REVERT: B 277 ASP cc_start: 0.8636 (t0) cc_final: 0.7819 (t0) REVERT: B 296 GLU cc_start: 0.8485 (tp30) cc_final: 0.7744 (tp30) REVERT: B 307 LYS cc_start: 0.9264 (ttpp) cc_final: 0.8844 (tptt) REVERT: B 315 ASP cc_start: 0.8712 (OUTLIER) cc_final: 0.8278 (m-30) REVERT: C 130 GLU cc_start: 0.8984 (tp30) cc_final: 0.8341 (tp30) REVERT: C 324 GLU cc_start: 0.8811 (mm-30) cc_final: 0.7243 (pt0) REVERT: D 41 PHE cc_start: 0.7742 (m-80) cc_final: 0.7516 (m-80) REVERT: D 219 GLU cc_start: 0.8821 (mp0) cc_final: 0.8605 (mp0) REVERT: D 307 LYS cc_start: 0.8985 (tttm) cc_final: 0.8252 (mptt) REVERT: D 316 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7736 (t80) REVERT: D 324 GLU cc_start: 0.8732 (mm-30) cc_final: 0.7096 (tt0) REVERT: E 60 GLN cc_start: 0.8801 (mt0) cc_final: 0.7911 (mm-40) REVERT: E 111 ASP cc_start: 0.9089 (t0) cc_final: 0.8769 (m-30) REVERT: E 283 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.7959 (tpp) REVERT: E 307 LYS cc_start: 0.6516 (mptt) cc_final: 0.5844 (mptt) REVERT: F 130 GLU cc_start: 0.8471 (tp30) cc_final: 0.8090 (tp30) REVERT: F 178 MET cc_start: 0.8429 (mmt) cc_final: 0.8011 (mtt) REVERT: F 307 LYS cc_start: 0.9028 (tptp) cc_final: 0.8416 (mppt) REVERT: F 324 GLU cc_start: 0.8518 (mm-30) cc_final: 0.7348 (pt0) REVERT: F 333 SER cc_start: 0.8231 (m) cc_final: 0.7853 (p) REVERT: G 75 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8224 (mtpp) REVERT: G 203 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8920 (mt) REVERT: G 213 VAL cc_start: 0.9361 (t) cc_final: 0.9109 (m) REVERT: G 324 GLU cc_start: 0.8484 (mm-30) cc_final: 0.7153 (tt0) REVERT: G 333 SER cc_start: 0.8904 (m) cc_final: 0.8610 (p) REVERT: G 339 MET cc_start: 0.8889 (mmm) cc_final: 0.8664 (mmp) REVERT: G 343 ASP cc_start: 0.8848 (t0) cc_final: 0.8513 (t0) REVERT: a 40 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.5893 (tt0) REVERT: a 49 GLU cc_start: 0.8246 (mp0) cc_final: 0.7914 (mp0) REVERT: a 95 SER cc_start: 0.9491 (p) cc_final: 0.9257 (t) REVERT: a 115 HIS cc_start: 0.7434 (OUTLIER) cc_final: 0.6645 (p90) REVERT: a 130 ARG cc_start: 0.8251 (tpp-160) cc_final: 0.5110 (tpt170) REVERT: a 133 ILE cc_start: 0.9260 (mt) cc_final: 0.9060 (mm) REVERT: c 26 GLU cc_start: 0.8649 (pm20) cc_final: 0.8288 (mm-30) REVERT: c 34 GLU cc_start: 0.6270 (mm-30) cc_final: 0.5611 (mm-30) REVERT: c 36 ASP cc_start: 0.7179 (p0) cc_final: 0.6462 (m-30) REVERT: c 49 GLU cc_start: 0.8353 (mp0) cc_final: 0.8049 (mp0) REVERT: c 130 ARG cc_start: 0.7735 (tpp-160) cc_final: 0.5369 (mmm160) REVERT: c 132 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7684 (t0) REVERT: d 34 GLU cc_start: 0.5628 (mm-30) cc_final: 0.5233 (mm-30) REVERT: d 37 ILE cc_start: 0.8691 (mt) cc_final: 0.8452 (mt) REVERT: d 49 GLU cc_start: 0.8474 (mp0) cc_final: 0.8048 (mp0) REVERT: d 91 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.7950 (mp10) REVERT: d 118 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8454 (tp) REVERT: e 21 ASP cc_start: 0.9114 (p0) cc_final: 0.8811 (p0) REVERT: e 91 GLN cc_start: 0.9204 (mm-40) cc_final: 0.8825 (mm-40) REVERT: e 103 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8184 (tp) REVERT: e 108 ASN cc_start: 0.8780 (t0) cc_final: 0.8440 (t0) REVERT: e 123 LYS cc_start: 0.9401 (mtpp) cc_final: 0.9170 (mtmm) REVERT: e 133 ILE cc_start: 0.8716 (mm) cc_final: 0.8488 (mm) REVERT: f 95 SER cc_start: 0.9166 (p) cc_final: 0.8953 (t) REVERT: f 108 ASN cc_start: 0.8606 (t0) cc_final: 0.8376 (t0) REVERT: f 118 LEU cc_start: 0.9095 (tp) cc_final: 0.8800 (tp) REVERT: g 84 VAL cc_start: 0.9457 (p) cc_final: 0.9182 (m) REVERT: g 119 ASP cc_start: 0.9370 (OUTLIER) cc_final: 0.9164 (p0) outliers start: 138 outliers final: 103 residues processed: 723 average time/residue: 0.1282 time to fit residues: 152.1962 Evaluate side-chains 747 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 630 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 248 VAL Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 316 TYR Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 190 SER Chi-restraints excluded: chain G residue 203 ILE Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 300 CYS Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 40 GLU Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 109 HIS Chi-restraints excluded: chain a residue 115 HIS Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 21 ASP Chi-restraints excluded: chain b residue 40 GLU Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 123 LYS Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 82 GLN Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 119 ASP Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 106 VAL Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 119 ASP Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain e residue 103 ILE Chi-restraints excluded: chain e residue 109 HIS Chi-restraints excluded: chain e residue 119 ASP Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 103 ILE Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain f residue 137 ASN Chi-restraints excluded: chain f residue 138 LEU Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 119 ASP Chi-restraints excluded: chain g residue 123 LYS Chi-restraints excluded: chain g residue 133 ILE Chi-restraints excluded: chain g residue 137 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 280 optimal weight: 6.9990 chunk 24 optimal weight: 8.9990 chunk 87 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 chunk 260 optimal weight: 8.9990 chunk 249 optimal weight: 0.0270 chunk 123 optimal weight: 4.9990 chunk 177 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 overall best weight: 1.3444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 GLN ** d 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 109 HIS f 91 GLN ** f 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 125 GLN ** g 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.089662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.080028 restraints weight = 49290.668| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 2.67 r_work: 0.2907 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26319 Z= 0.120 Angle : 0.564 10.216 35755 Z= 0.293 Chirality : 0.043 0.216 3876 Planarity : 0.004 0.041 4683 Dihedral : 5.722 58.900 3622 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 3.94 % Allowed : 20.37 % Favored : 75.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: -0.76 (0.15), residues: 3274 helix: 0.90 (0.22), residues: 594 sheet: -0.67 (0.18), residues: 849 loop : -0.86 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 264 TYR 0.010 0.001 TYR D 8 PHE 0.013 0.001 PHE b 128 TRP 0.013 0.001 TRP A 221 HIS 0.017 0.001 HIS e 109 Details of bonding type rmsd covalent geometry : bond 0.00280 (26319) covalent geometry : angle 0.56379 (35755) hydrogen bonds : bond 0.03726 ( 875) hydrogen bonds : angle 5.34712 ( 2469) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 672 time to evaluate : 0.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8324 (p90) cc_final: 0.7765 (p90) REVERT: A 89 MET cc_start: 0.7704 (mtt) cc_final: 0.7221 (mtp) REVERT: A 227 MET cc_start: 0.7614 (OUTLIER) cc_final: 0.7128 (mtp) REVERT: A 289 MET cc_start: 0.8900 (ttp) cc_final: 0.8632 (tmm) REVERT: A 307 LYS cc_start: 0.8756 (tptt) cc_final: 0.8130 (mptt) REVERT: A 324 GLU cc_start: 0.8495 (mm-30) cc_final: 0.7464 (tt0) REVERT: A 329 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7764 (tt0) REVERT: B 126 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8403 (mt-10) REVERT: B 130 GLU cc_start: 0.8571 (tp30) cc_final: 0.8298 (tp30) REVERT: B 159 ASP cc_start: 0.8134 (t0) cc_final: 0.7793 (t0) REVERT: B 176 MET cc_start: 0.9140 (mmm) cc_final: 0.8925 (mmm) REVERT: B 251 MET cc_start: 0.8497 (mmm) cc_final: 0.8079 (mmm) REVERT: B 277 ASP cc_start: 0.8373 (t0) cc_final: 0.7577 (t0) REVERT: B 296 GLU cc_start: 0.8287 (tp30) cc_final: 0.7588 (tp30) REVERT: B 307 LYS cc_start: 0.9257 (ttpp) cc_final: 0.8850 (tptt) REVERT: C 71 THR cc_start: 0.9010 (m) cc_final: 0.8641 (p) REVERT: C 130 GLU cc_start: 0.8831 (tp30) cc_final: 0.8126 (tp30) REVERT: C 324 GLU cc_start: 0.8606 (mm-30) cc_final: 0.7131 (pt0) REVERT: C 339 MET cc_start: 0.8760 (mmm) cc_final: 0.8517 (mmp) REVERT: D 37 ASP cc_start: 0.8438 (t70) cc_final: 0.8137 (t0) REVERT: D 41 PHE cc_start: 0.7565 (m-80) cc_final: 0.7271 (m-80) REVERT: D 99 LEU cc_start: 0.8555 (mt) cc_final: 0.8355 (mt) REVERT: D 219 GLU cc_start: 0.8613 (mp0) cc_final: 0.8388 (mp0) REVERT: D 307 LYS cc_start: 0.8981 (tttm) cc_final: 0.8146 (mptt) REVERT: D 316 TYR cc_start: 0.8354 (OUTLIER) cc_final: 0.7693 (t80) REVERT: D 324 GLU cc_start: 0.8635 (mm-30) cc_final: 0.7095 (tt0) REVERT: E 60 GLN cc_start: 0.8628 (mt0) cc_final: 0.7871 (mm110) REVERT: E 111 ASP cc_start: 0.8882 (t0) cc_final: 0.8659 (m-30) REVERT: E 307 LYS cc_start: 0.6076 (mptt) cc_final: 0.5401 (mptt) REVERT: F 69 TYR cc_start: 0.8373 (p90) cc_final: 0.7747 (p90) REVERT: F 130 GLU cc_start: 0.8163 (tp30) cc_final: 0.7780 (tp30) REVERT: F 178 MET cc_start: 0.8325 (mmt) cc_final: 0.7991 (mtt) REVERT: F 283 MET cc_start: 0.8898 (tpt) cc_final: 0.8588 (tpt) REVERT: F 307 LYS cc_start: 0.8959 (tptp) cc_final: 0.8388 (mptt) REVERT: F 333 SER cc_start: 0.7992 (m) cc_final: 0.7656 (p) REVERT: G 75 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8191 (mtpp) REVERT: G 130 GLU cc_start: 0.8265 (tp30) cc_final: 0.7661 (tp30) REVERT: G 213 VAL cc_start: 0.9327 (t) cc_final: 0.9101 (m) REVERT: G 324 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7091 (tt0) REVERT: G 333 SER cc_start: 0.8811 (m) cc_final: 0.8554 (p) REVERT: G 343 ASP cc_start: 0.8749 (t0) cc_final: 0.8345 (t0) REVERT: a 49 GLU cc_start: 0.8127 (mp0) cc_final: 0.7840 (mp0) REVERT: a 95 SER cc_start: 0.9493 (p) cc_final: 0.9246 (t) REVERT: a 115 HIS cc_start: 0.7367 (OUTLIER) cc_final: 0.6554 (p90) REVERT: a 130 ARG cc_start: 0.8186 (tpp-160) cc_final: 0.5121 (tpt170) REVERT: b 108 ASN cc_start: 0.8705 (t0) cc_final: 0.8383 (t0) REVERT: c 34 GLU cc_start: 0.6016 (mm-30) cc_final: 0.5558 (mm-30) REVERT: c 36 ASP cc_start: 0.7113 (p0) cc_final: 0.6729 (m-30) REVERT: c 49 GLU cc_start: 0.8136 (mp0) cc_final: 0.7747 (mp0) REVERT: c 130 ARG cc_start: 0.7566 (tpp-160) cc_final: 0.5313 (mmm160) REVERT: c 132 ASN cc_start: 0.7753 (OUTLIER) cc_final: 0.7467 (t0) REVERT: d 34 GLU cc_start: 0.5713 (mm-30) cc_final: 0.5491 (mm-30) REVERT: d 37 ILE cc_start: 0.8513 (mt) cc_final: 0.8286 (mt) REVERT: d 49 GLU cc_start: 0.8310 (mp0) cc_final: 0.7855 (mp0) REVERT: d 91 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: d 102 TYR cc_start: 0.8974 (m-80) cc_final: 0.8555 (m-80) REVERT: d 118 LEU cc_start: 0.8718 (tp) cc_final: 0.8503 (tt) REVERT: e 21 ASP cc_start: 0.9047 (p0) cc_final: 0.8757 (p0) REVERT: e 91 GLN cc_start: 0.9100 (mm-40) cc_final: 0.8847 (mm-40) REVERT: e 103 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8164 (tp) REVERT: e 123 LYS cc_start: 0.9349 (mtpp) cc_final: 0.9143 (mtmm) REVERT: e 133 ILE cc_start: 0.8683 (mm) cc_final: 0.8454 (mm) REVERT: f 30 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.8052 (mp) REVERT: f 118 LEU cc_start: 0.9070 (tp) cc_final: 0.8777 (tp) REVERT: g 84 VAL cc_start: 0.9401 (p) cc_final: 0.9119 (m) REVERT: g 119 ASP cc_start: 0.9286 (OUTLIER) cc_final: 0.9072 (p0) outliers start: 104 outliers final: 78 residues processed: 727 average time/residue: 0.1344 time to fit residues: 160.1694 Evaluate side-chains 720 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 632 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 316 TYR Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 109 HIS Chi-restraints excluded: chain a residue 115 HIS Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 40 GLU Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 123 LYS Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 82 GLN Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 119 ASP Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 119 ASP Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain e residue 103 ILE Chi-restraints excluded: chain e residue 119 ASP Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 103 ILE Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain f residue 138 LEU Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 119 ASP Chi-restraints excluded: chain g residue 123 LYS Chi-restraints excluded: chain g residue 133 ILE Chi-restraints excluded: chain g residue 137 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 252 optimal weight: 8.9990 chunk 247 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 286 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 11 optimal weight: 0.8980 chunk 276 optimal weight: 3.9990 chunk 298 optimal weight: 0.7980 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 GLN B 14 GLN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 GLN G 70 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 GLN ** a 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.090136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.080503 restraints weight = 49373.308| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.67 r_work: 0.2984 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 26319 Z= 0.128 Angle : 0.565 11.033 35755 Z= 0.292 Chirality : 0.043 0.170 3876 Planarity : 0.004 0.040 4683 Dihedral : 5.579 57.752 3618 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.20 % Allowed : 21.01 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: -0.76 (0.15), residues: 3274 helix: 0.91 (0.22), residues: 594 sheet: -0.64 (0.17), residues: 878 loop : -0.88 (0.15), residues: 1802 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 15 TYR 0.013 0.001 TYR F 250 PHE 0.014 0.001 PHE b 128 TRP 0.017 0.001 TRP D 27 HIS 0.006 0.001 HIS F 83 Details of bonding type rmsd covalent geometry : bond 0.00305 (26319) covalent geometry : angle 0.56492 (35755) hydrogen bonds : bond 0.03649 ( 875) hydrogen bonds : angle 5.23812 ( 2469) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 666 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8502 (p90) cc_final: 0.7951 (p90) REVERT: A 89 MET cc_start: 0.8006 (mtt) cc_final: 0.7511 (mtp) REVERT: A 207 ASP cc_start: 0.9070 (m-30) cc_final: 0.8815 (m-30) REVERT: A 227 MET cc_start: 0.7873 (OUTLIER) cc_final: 0.7408 (mtp) REVERT: A 268 ASN cc_start: 0.8929 (t0) cc_final: 0.8644 (t0) REVERT: A 307 LYS cc_start: 0.8699 (tptt) cc_final: 0.8145 (mptt) REVERT: A 324 GLU cc_start: 0.8572 (mm-30) cc_final: 0.7479 (tt0) REVERT: A 329 GLU cc_start: 0.8340 (mt-10) cc_final: 0.7972 (tt0) REVERT: B 126 GLU cc_start: 0.8745 (OUTLIER) cc_final: 0.8515 (mt-10) REVERT: B 130 GLU cc_start: 0.8781 (tp30) cc_final: 0.8541 (tp30) REVERT: B 159 ASP cc_start: 0.8273 (t0) cc_final: 0.7998 (t0) REVERT: B 277 ASP cc_start: 0.8463 (t0) cc_final: 0.7777 (t0) REVERT: B 296 GLU cc_start: 0.8504 (tp30) cc_final: 0.7722 (tp30) REVERT: B 307 LYS cc_start: 0.9277 (ttpp) cc_final: 0.8826 (tptt) REVERT: C 41 PHE cc_start: 0.8212 (m-10) cc_final: 0.7861 (m-80) REVERT: C 71 THR cc_start: 0.9060 (m) cc_final: 0.8685 (p) REVERT: C 130 GLU cc_start: 0.9006 (tp30) cc_final: 0.8382 (tp30) REVERT: C 324 GLU cc_start: 0.8620 (mm-30) cc_final: 0.7104 (pt0) REVERT: D 37 ASP cc_start: 0.8605 (t70) cc_final: 0.8222 (t0) REVERT: D 41 PHE cc_start: 0.7745 (m-80) cc_final: 0.7356 (m-80) REVERT: D 99 LEU cc_start: 0.8622 (mt) cc_final: 0.8389 (mt) REVERT: D 125 HIS cc_start: 0.8289 (m-70) cc_final: 0.7961 (m170) REVERT: D 219 GLU cc_start: 0.8786 (mp0) cc_final: 0.8577 (mp0) REVERT: D 307 LYS cc_start: 0.8955 (tttm) cc_final: 0.8083 (mptt) REVERT: D 316 TYR cc_start: 0.8400 (OUTLIER) cc_final: 0.7697 (t80) REVERT: D 324 GLU cc_start: 0.8690 (mm-30) cc_final: 0.7131 (tt0) REVERT: E 60 GLN cc_start: 0.8744 (mt0) cc_final: 0.7745 (mm110) REVERT: E 111 ASP cc_start: 0.9031 (t0) cc_final: 0.8766 (m-30) REVERT: E 251 MET cc_start: 0.8160 (mmm) cc_final: 0.7101 (mmm) REVERT: E 283 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.7857 (tpp) REVERT: E 307 LYS cc_start: 0.6445 (mptt) cc_final: 0.5418 (mptt) REVERT: F 69 TYR cc_start: 0.8427 (p90) cc_final: 0.7835 (p90) REVERT: F 130 GLU cc_start: 0.8515 (tp30) cc_final: 0.8140 (tp30) REVERT: F 178 MET cc_start: 0.8418 (mmt) cc_final: 0.8086 (mtt) REVERT: F 307 LYS cc_start: 0.9005 (tptp) cc_final: 0.8373 (mptt) REVERT: F 324 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7381 (pt0) REVERT: F 333 SER cc_start: 0.8034 (m) cc_final: 0.7719 (p) REVERT: G 75 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8182 (mtpp) REVERT: G 130 GLU cc_start: 0.8608 (tp30) cc_final: 0.8020 (tp30) REVERT: G 213 VAL cc_start: 0.9288 (t) cc_final: 0.9031 (m) REVERT: G 324 GLU cc_start: 0.8279 (mm-30) cc_final: 0.7100 (tt0) REVERT: G 333 SER cc_start: 0.8844 (m) cc_final: 0.8573 (p) REVERT: G 343 ASP cc_start: 0.8862 (t0) cc_final: 0.8450 (t0) REVERT: G 353 MET cc_start: 0.7987 (mpp) cc_final: 0.7555 (mpp) REVERT: a 49 GLU cc_start: 0.8291 (mp0) cc_final: 0.7963 (mp0) REVERT: a 78 VAL cc_start: 0.9517 (t) cc_final: 0.9299 (p) REVERT: a 95 SER cc_start: 0.9481 (p) cc_final: 0.9247 (t) REVERT: a 115 HIS cc_start: 0.7408 (OUTLIER) cc_final: 0.6629 (p90) REVERT: a 118 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8934 (tt) REVERT: a 130 ARG cc_start: 0.8256 (tpp-160) cc_final: 0.5211 (tpt170) REVERT: c 36 ASP cc_start: 0.7334 (p0) cc_final: 0.6896 (m-30) REVERT: c 49 GLU cc_start: 0.8273 (mp0) cc_final: 0.7832 (mp0) REVERT: c 132 ASN cc_start: 0.7896 (OUTLIER) cc_final: 0.7607 (t0) REVERT: d 34 GLU cc_start: 0.6113 (mm-30) cc_final: 0.5758 (mm-30) REVERT: d 37 ILE cc_start: 0.8570 (mt) cc_final: 0.8347 (mt) REVERT: d 49 GLU cc_start: 0.8407 (mp0) cc_final: 0.7936 (mp0) REVERT: d 91 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8091 (mp10) REVERT: d 102 TYR cc_start: 0.9026 (m-80) cc_final: 0.8586 (m-80) REVERT: d 103 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8259 (mp) REVERT: d 118 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8430 (tt) REVERT: e 21 ASP cc_start: 0.9132 (p0) cc_final: 0.8837 (p0) REVERT: e 91 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8926 (mm-40) REVERT: e 103 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8181 (tp) REVERT: e 108 ASN cc_start: 0.8697 (t0) cc_final: 0.8286 (t0) REVERT: e 123 LYS cc_start: 0.9390 (mtpp) cc_final: 0.9173 (mtmm) REVERT: e 133 ILE cc_start: 0.8630 (mm) cc_final: 0.8391 (mm) REVERT: f 30 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8026 (mp) REVERT: f 118 LEU cc_start: 0.9093 (tp) cc_final: 0.8787 (tp) REVERT: g 84 VAL cc_start: 0.9421 (p) cc_final: 0.9133 (m) REVERT: g 119 ASP cc_start: 0.9317 (OUTLIER) cc_final: 0.9111 (p0) outliers start: 111 outliers final: 86 residues processed: 723 average time/residue: 0.1296 time to fit residues: 153.0162 Evaluate side-chains 733 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 633 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 316 TYR Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 207 ASP Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 109 HIS Chi-restraints excluded: chain a residue 115 HIS Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 21 ASP Chi-restraints excluded: chain b residue 40 GLU Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 123 LYS Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 82 GLN Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 119 ASP Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain e residue 14 ASN Chi-restraints excluded: chain e residue 103 ILE Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 119 ASP Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 103 ILE Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 119 ASP Chi-restraints excluded: chain g residue 123 LYS Chi-restraints excluded: chain g residue 133 ILE Chi-restraints excluded: chain g residue 137 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 145 optimal weight: 0.9980 chunk 78 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 159 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 161 optimal weight: 10.0000 chunk 62 optimal weight: 4.9990 chunk 247 optimal weight: 7.9990 chunk 142 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN D 33 ASN E 285 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN G 138 GLN ** a 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 HIS ** e 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.092567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.082970 restraints weight = 49013.526| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.67 r_work: 0.3026 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 26319 Z= 0.112 Angle : 0.559 11.845 35755 Z= 0.288 Chirality : 0.043 0.162 3876 Planarity : 0.004 0.043 4683 Dihedral : 5.416 58.233 3618 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.52 % Allowed : 21.62 % Favored : 74.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: -0.67 (0.15), residues: 3274 helix: 0.92 (0.22), residues: 600 sheet: -0.56 (0.18), residues: 828 loop : -0.82 (0.14), residues: 1846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 264 TYR 0.011 0.001 TYR g 102 PHE 0.017 0.001 PHE g 31 TRP 0.035 0.001 TRP F 209 HIS 0.006 0.001 HIS a 109 Details of bonding type rmsd covalent geometry : bond 0.00260 (26319) covalent geometry : angle 0.55924 (35755) hydrogen bonds : bond 0.03518 ( 875) hydrogen bonds : angle 5.13771 ( 2469) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 671 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8976 (mp0) cc_final: 0.8594 (mp0) REVERT: A 69 TYR cc_start: 0.8333 (p90) cc_final: 0.7787 (p90) REVERT: A 89 MET cc_start: 0.7989 (mtt) cc_final: 0.7516 (mtp) REVERT: A 207 ASP cc_start: 0.8943 (m-30) cc_final: 0.8656 (m-30) REVERT: A 251 MET cc_start: 0.8567 (mmt) cc_final: 0.8221 (mmt) REVERT: A 253 GLU cc_start: 0.7155 (tt0) cc_final: 0.6918 (tt0) REVERT: A 268 ASN cc_start: 0.8906 (t0) cc_final: 0.8618 (t0) REVERT: A 289 MET cc_start: 0.8863 (tmm) cc_final: 0.8547 (ppp) REVERT: A 307 LYS cc_start: 0.8683 (tptt) cc_final: 0.8234 (mptt) REVERT: A 324 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7192 (tt0) REVERT: B 69 TYR cc_start: 0.9203 (p90) cc_final: 0.8821 (p90) REVERT: B 130 GLU cc_start: 0.8572 (tp30) cc_final: 0.8312 (tp30) REVERT: B 159 ASP cc_start: 0.8075 (t0) cc_final: 0.7841 (t0) REVERT: B 277 ASP cc_start: 0.8241 (t0) cc_final: 0.7568 (t0) REVERT: B 296 GLU cc_start: 0.8299 (tp30) cc_final: 0.7510 (tp30) REVERT: B 307 LYS cc_start: 0.9235 (ttpp) cc_final: 0.8789 (tptt) REVERT: C 41 PHE cc_start: 0.8069 (m-10) cc_final: 0.7781 (m-80) REVERT: C 71 THR cc_start: 0.8960 (m) cc_final: 0.8577 (p) REVERT: C 130 GLU cc_start: 0.8842 (tp30) cc_final: 0.8161 (tp30) REVERT: C 324 GLU cc_start: 0.8327 (mm-30) cc_final: 0.7045 (pt0) REVERT: D 41 PHE cc_start: 0.7542 (m-80) cc_final: 0.7113 (m-80) REVERT: D 99 LEU cc_start: 0.8430 (mt) cc_final: 0.8213 (mt) REVERT: D 164 MET cc_start: 0.9029 (ptp) cc_final: 0.8756 (pmm) REVERT: D 307 LYS cc_start: 0.8881 (tttm) cc_final: 0.8116 (mptt) REVERT: D 316 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7545 (t80) REVERT: D 324 GLU cc_start: 0.8579 (mm-30) cc_final: 0.6936 (tt0) REVERT: E 60 GLN cc_start: 0.8445 (mt0) cc_final: 0.7687 (mm-40) REVERT: E 251 MET cc_start: 0.7825 (mmm) cc_final: 0.6765 (mmm) REVERT: E 283 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.7654 (tpp) REVERT: E 307 LYS cc_start: 0.6259 (mptt) cc_final: 0.5507 (mptt) REVERT: F 69 TYR cc_start: 0.8265 (p90) cc_final: 0.7694 (p90) REVERT: F 130 GLU cc_start: 0.8220 (tp30) cc_final: 0.7845 (tp30) REVERT: F 178 MET cc_start: 0.8271 (mmt) cc_final: 0.7998 (mtt) REVERT: F 264 ARG cc_start: 0.7714 (mtt90) cc_final: 0.7488 (mtt-85) REVERT: F 307 LYS cc_start: 0.8933 (tptp) cc_final: 0.8398 (mptt) REVERT: F 333 SER cc_start: 0.7960 (m) cc_final: 0.7738 (p) REVERT: G 15 ARG cc_start: 0.7497 (mtm180) cc_final: 0.6658 (tpt170) REVERT: G 64 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7212 (pp) REVERT: G 130 GLU cc_start: 0.8378 (tp30) cc_final: 0.7766 (tp30) REVERT: G 213 VAL cc_start: 0.9247 (t) cc_final: 0.9020 (m) REVERT: G 324 GLU cc_start: 0.8097 (mm-30) cc_final: 0.6833 (tt0) REVERT: G 333 SER cc_start: 0.8724 (m) cc_final: 0.8503 (p) REVERT: G 343 ASP cc_start: 0.8792 (t0) cc_final: 0.8381 (t0) REVERT: a 49 GLU cc_start: 0.8082 (mp0) cc_final: 0.7805 (mp0) REVERT: a 95 SER cc_start: 0.9463 (p) cc_final: 0.9210 (t) REVERT: a 115 HIS cc_start: 0.7218 (OUTLIER) cc_final: 0.6407 (p90) REVERT: a 118 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8909 (tt) REVERT: a 123 LYS cc_start: 0.8731 (mtmm) cc_final: 0.8499 (mtmm) REVERT: a 130 ARG cc_start: 0.8192 (tpp-160) cc_final: 0.5151 (tpt170) REVERT: b 91 GLN cc_start: 0.9223 (mm110) cc_final: 0.8961 (mm-40) REVERT: c 36 ASP cc_start: 0.7088 (p0) cc_final: 0.6788 (m-30) REVERT: c 49 GLU cc_start: 0.8027 (mp0) cc_final: 0.7586 (mp0) REVERT: c 132 ASN cc_start: 0.7668 (OUTLIER) cc_final: 0.7443 (t0) REVERT: d 37 ILE cc_start: 0.8404 (mt) cc_final: 0.8147 (mt) REVERT: d 49 GLU cc_start: 0.8245 (mp0) cc_final: 0.7723 (mp0) REVERT: d 91 GLN cc_start: 0.8919 (OUTLIER) cc_final: 0.7990 (mp10) REVERT: d 94 LYS cc_start: 0.8919 (mmmt) cc_final: 0.8564 (mmmt) REVERT: d 102 TYR cc_start: 0.8908 (m-80) cc_final: 0.8522 (m-80) REVERT: d 103 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8082 (mp) REVERT: d 118 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8424 (tt) REVERT: e 21 ASP cc_start: 0.9053 (p0) cc_final: 0.8771 (p0) REVERT: e 91 GLN cc_start: 0.9102 (mm-40) cc_final: 0.8844 (mm-40) REVERT: e 103 ILE cc_start: 0.8512 (OUTLIER) cc_final: 0.8008 (tp) REVERT: e 108 ASN cc_start: 0.8633 (t0) cc_final: 0.8234 (t0) REVERT: e 133 ILE cc_start: 0.8557 (mm) cc_final: 0.8355 (mm) REVERT: f 30 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.7911 (mt) REVERT: f 118 LEU cc_start: 0.9112 (tp) cc_final: 0.8776 (tp) REVERT: f 138 LEU cc_start: 0.7954 (mt) cc_final: 0.7472 (tp) REVERT: g 84 VAL cc_start: 0.9377 (p) cc_final: 0.9096 (m) REVERT: g 119 ASP cc_start: 0.9295 (OUTLIER) cc_final: 0.9090 (p0) outliers start: 93 outliers final: 67 residues processed: 726 average time/residue: 0.1405 time to fit residues: 167.0302 Evaluate side-chains 728 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 649 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 316 TYR Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain a residue 115 HIS Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 40 GLU Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain b residue 123 LYS Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain c residue 119 ASP Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain e residue 14 ASN Chi-restraints excluded: chain e residue 103 ILE Chi-restraints excluded: chain e residue 109 HIS Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 119 ASP Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 82 GLN Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 119 ASP Chi-restraints excluded: chain g residue 133 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 162 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 169 optimal weight: 9.9990 chunk 315 optimal weight: 0.3980 chunk 61 optimal weight: 8.9990 chunk 163 optimal weight: 7.9990 chunk 224 optimal weight: 6.9990 overall best weight: 5.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 GLN D 33 ASN ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN G 125 HIS ** a 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 125 GLN ** d 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 137 ASN ** e 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 98 ASN ** g 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.084685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.074961 restraints weight = 51134.740| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.68 r_work: 0.2839 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 26319 Z= 0.300 Angle : 0.706 13.653 35755 Z= 0.360 Chirality : 0.047 0.199 3876 Planarity : 0.005 0.045 4683 Dihedral : 5.893 56.267 3616 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 4.81 % Allowed : 20.79 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: -0.94 (0.14), residues: 3274 helix: 0.61 (0.22), residues: 600 sheet: -0.62 (0.19), residues: 766 loop : -1.03 (0.14), residues: 1908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 264 TYR 0.019 0.002 TYR D 69 PHE 0.018 0.002 PHE b 128 TRP 0.028 0.002 TRP B 209 HIS 0.012 0.002 HIS C 121 Details of bonding type rmsd covalent geometry : bond 0.00714 (26319) covalent geometry : angle 0.70611 (35755) hydrogen bonds : bond 0.04119 ( 875) hydrogen bonds : angle 5.55250 ( 2469) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 637 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7948 (mtt) cc_final: 0.7443 (mtp) REVERT: A 268 ASN cc_start: 0.8921 (t0) cc_final: 0.8683 (t0) REVERT: A 296 GLU cc_start: 0.9008 (tp30) cc_final: 0.8698 (tp30) REVERT: A 307 LYS cc_start: 0.8805 (tptt) cc_final: 0.8310 (mppt) REVERT: A 324 GLU cc_start: 0.8651 (mm-30) cc_final: 0.7425 (tt0) REVERT: B 130 GLU cc_start: 0.8787 (tp30) cc_final: 0.8546 (tp30) REVERT: B 159 ASP cc_start: 0.8365 (t0) cc_final: 0.7999 (t0) REVERT: B 277 ASP cc_start: 0.8592 (t0) cc_final: 0.7833 (t0) REVERT: B 296 GLU cc_start: 0.8536 (tp30) cc_final: 0.7814 (tp30) REVERT: B 307 LYS cc_start: 0.9307 (ttpp) cc_final: 0.8839 (tptt) REVERT: C 130 GLU cc_start: 0.9041 (tp30) cc_final: 0.8392 (tp30) REVERT: C 219 GLU cc_start: 0.8730 (mp0) cc_final: 0.8525 (mp0) REVERT: C 324 GLU cc_start: 0.8802 (mm-30) cc_final: 0.7243 (pt0) REVERT: D 296 GLU cc_start: 0.8753 (mt-10) cc_final: 0.8404 (mm-30) REVERT: D 307 LYS cc_start: 0.9043 (tttm) cc_final: 0.8205 (mptt) REVERT: D 316 TYR cc_start: 0.8718 (OUTLIER) cc_final: 0.7585 (t80) REVERT: E 60 GLN cc_start: 0.8752 (mt0) cc_final: 0.7608 (mm-40) REVERT: E 283 MET cc_start: 0.8984 (OUTLIER) cc_final: 0.7999 (tpp) REVERT: E 307 LYS cc_start: 0.6720 (mptt) cc_final: 0.6233 (mptt) REVERT: F 69 TYR cc_start: 0.8650 (p90) cc_final: 0.8441 (p90) REVERT: F 88 ASN cc_start: 0.9130 (m-40) cc_final: 0.8812 (m-40) REVERT: F 130 GLU cc_start: 0.8487 (tp30) cc_final: 0.8141 (tp30) REVERT: F 178 MET cc_start: 0.8426 (mmt) cc_final: 0.8059 (mtt) REVERT: F 307 LYS cc_start: 0.9045 (tptp) cc_final: 0.8414 (mptt) REVERT: F 324 GLU cc_start: 0.8532 (mm-30) cc_final: 0.7372 (pt0) REVERT: F 333 SER cc_start: 0.8259 (m) cc_final: 0.7884 (p) REVERT: G 75 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8508 (mtpp) REVERT: G 213 VAL cc_start: 0.9350 (t) cc_final: 0.9090 (m) REVERT: G 324 GLU cc_start: 0.8429 (mm-30) cc_final: 0.7063 (tt0) REVERT: G 333 SER cc_start: 0.8863 (m) cc_final: 0.8586 (p) REVERT: G 343 ASP cc_start: 0.8974 (t0) cc_final: 0.8760 (t0) REVERT: a 40 GLU cc_start: 0.6344 (OUTLIER) cc_final: 0.5703 (tt0) REVERT: a 49 GLU cc_start: 0.8282 (mp0) cc_final: 0.7996 (mp0) REVERT: a 82 GLN cc_start: 0.8742 (pm20) cc_final: 0.8101 (pm20) REVERT: a 115 HIS cc_start: 0.7585 (OUTLIER) cc_final: 0.6763 (p90) REVERT: a 123 LYS cc_start: 0.8897 (mtmm) cc_final: 0.8639 (mtmm) REVERT: a 130 ARG cc_start: 0.8300 (tpp-160) cc_final: 0.5171 (tpt170) REVERT: c 34 GLU cc_start: 0.6228 (mm-30) cc_final: 0.5865 (mm-30) REVERT: c 36 ASP cc_start: 0.7239 (p0) cc_final: 0.6684 (m-30) REVERT: c 49 GLU cc_start: 0.8387 (mp0) cc_final: 0.8053 (mp0) REVERT: c 132 ASN cc_start: 0.8276 (OUTLIER) cc_final: 0.7833 (t0) REVERT: d 37 ILE cc_start: 0.8653 (mt) cc_final: 0.8439 (mt) REVERT: d 49 GLU cc_start: 0.8472 (mp0) cc_final: 0.7981 (mp0) REVERT: d 91 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.7859 (mp10) REVERT: d 103 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8354 (mp) REVERT: d 118 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8492 (tp) REVERT: e 21 ASP cc_start: 0.9116 (p0) cc_final: 0.8827 (p0) REVERT: e 91 GLN cc_start: 0.9162 (mm-40) cc_final: 0.8761 (mm-40) REVERT: e 103 ILE cc_start: 0.8816 (OUTLIER) cc_final: 0.8424 (tp) REVERT: e 133 ILE cc_start: 0.8701 (mm) cc_final: 0.8454 (mm) REVERT: f 30 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8205 (mp) REVERT: f 118 LEU cc_start: 0.9188 (tp) cc_final: 0.8854 (tp) REVERT: g 84 VAL cc_start: 0.9492 (p) cc_final: 0.9232 (m) REVERT: g 119 ASP cc_start: 0.9354 (OUTLIER) cc_final: 0.9110 (p0) REVERT: g 120 THR cc_start: 0.7976 (OUTLIER) cc_final: 0.7772 (p) outliers start: 127 outliers final: 94 residues processed: 705 average time/residue: 0.1320 time to fit residues: 153.7676 Evaluate side-chains 724 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 617 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 42 ASP Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 316 TYR Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 179 ILE Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 51 VAL Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain a residue 39 THR Chi-restraints excluded: chain a residue 40 GLU Chi-restraints excluded: chain a residue 109 HIS Chi-restraints excluded: chain a residue 115 HIS Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 21 ASP Chi-restraints excluded: chain b residue 40 GLU Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain d residue 22 LEU Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 106 VAL Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 119 ASP Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain e residue 14 ASN Chi-restraints excluded: chain e residue 103 ILE Chi-restraints excluded: chain e residue 109 HIS Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 119 ASP Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 82 GLN Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain g residue 38 VAL Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 119 ASP Chi-restraints excluded: chain g residue 120 THR Chi-restraints excluded: chain g residue 123 LYS Chi-restraints excluded: chain g residue 133 ILE Chi-restraints excluded: chain g residue 137 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 322 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 28 optimal weight: 10.0000 chunk 207 optimal weight: 2.9990 chunk 269 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 178 optimal weight: 4.9990 chunk 113 optimal weight: 0.5980 chunk 174 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN G 125 HIS G 138 GLN ** a 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 98 ASN ** g 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.090005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.080349 restraints weight = 49091.599| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.67 r_work: 0.2931 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 26319 Z= 0.136 Angle : 0.617 13.086 35755 Z= 0.315 Chirality : 0.044 0.225 3876 Planarity : 0.004 0.044 4683 Dihedral : 5.628 58.218 3616 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.56 % Allowed : 22.07 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: -0.88 (0.15), residues: 3274 helix: 0.72 (0.22), residues: 600 sheet: -0.65 (0.18), residues: 830 loop : -0.97 (0.14), residues: 1844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 264 TYR 0.018 0.001 TYR F 250 PHE 0.015 0.001 PHE a 128 TRP 0.032 0.001 TRP F 209 HIS 0.010 0.001 HIS a 109 Details of bonding type rmsd covalent geometry : bond 0.00323 (26319) covalent geometry : angle 0.61678 (35755) hydrogen bonds : bond 0.03713 ( 875) hydrogen bonds : angle 5.33525 ( 2469) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6548 Ramachandran restraints generated. 3274 Oldfield, 0 Emsley, 3274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 725 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 631 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8522 (p90) cc_final: 0.8066 (p90) REVERT: A 89 MET cc_start: 0.7984 (mtt) cc_final: 0.7481 (mtp) REVERT: A 227 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7407 (mtp) REVERT: A 251 MET cc_start: 0.8696 (mmt) cc_final: 0.8389 (mmt) REVERT: A 268 ASN cc_start: 0.8903 (t0) cc_final: 0.8669 (t0) REVERT: A 289 MET cc_start: 0.9007 (tmm) cc_final: 0.8712 (ppp) REVERT: A 296 GLU cc_start: 0.8952 (tp30) cc_final: 0.8669 (tp30) REVERT: A 307 LYS cc_start: 0.8785 (tptt) cc_final: 0.8269 (mppt) REVERT: A 324 GLU cc_start: 0.8625 (mm-30) cc_final: 0.7421 (tt0) REVERT: B 64 ILE cc_start: 0.8726 (mt) cc_final: 0.8327 (mm) REVERT: B 130 GLU cc_start: 0.8748 (tp30) cc_final: 0.8537 (tp30) REVERT: B 159 ASP cc_start: 0.8327 (t0) cc_final: 0.8045 (t0) REVERT: B 277 ASP cc_start: 0.8512 (t0) cc_final: 0.7753 (t0) REVERT: B 296 GLU cc_start: 0.8556 (tp30) cc_final: 0.7843 (tp30) REVERT: B 307 LYS cc_start: 0.9235 (ttpp) cc_final: 0.8784 (tptt) REVERT: C 71 THR cc_start: 0.9066 (m) cc_final: 0.8702 (p) REVERT: C 130 GLU cc_start: 0.8955 (tp30) cc_final: 0.8298 (tp30) REVERT: C 219 GLU cc_start: 0.8708 (mp0) cc_final: 0.8506 (mp0) REVERT: C 324 GLU cc_start: 0.8733 (mm-30) cc_final: 0.7358 (pt0) REVERT: D 41 PHE cc_start: 0.7691 (m-80) cc_final: 0.7207 (m-80) REVERT: D 296 GLU cc_start: 0.8739 (mt-10) cc_final: 0.8374 (mm-30) REVERT: D 307 LYS cc_start: 0.8968 (tttm) cc_final: 0.8070 (mptt) REVERT: D 316 TYR cc_start: 0.8548 (OUTLIER) cc_final: 0.7968 (t80) REVERT: D 324 GLU cc_start: 0.8741 (mm-30) cc_final: 0.7141 (tt0) REVERT: E 60 GLN cc_start: 0.8531 (mt0) cc_final: 0.7573 (mm110) REVERT: E 283 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.7848 (tpp) REVERT: E 307 LYS cc_start: 0.6365 (mptt) cc_final: 0.5495 (mptt) REVERT: F 88 ASN cc_start: 0.9098 (m-40) cc_final: 0.8809 (m-40) REVERT: F 112 ARG cc_start: 0.8480 (mmt-90) cc_final: 0.8270 (mmt90) REVERT: F 130 GLU cc_start: 0.8483 (tp30) cc_final: 0.8125 (tp30) REVERT: F 178 MET cc_start: 0.8489 (mmt) cc_final: 0.8063 (mtt) REVERT: F 246 GLU cc_start: 0.8274 (tt0) cc_final: 0.8049 (tp30) REVERT: F 307 LYS cc_start: 0.8965 (tptp) cc_final: 0.8357 (mptt) REVERT: F 333 SER cc_start: 0.8026 (m) cc_final: 0.7749 (p) REVERT: G 75 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8387 (mtpp) REVERT: G 130 GLU cc_start: 0.8613 (tp30) cc_final: 0.7994 (tp30) REVERT: G 213 VAL cc_start: 0.9307 (t) cc_final: 0.9055 (m) REVERT: G 324 GLU cc_start: 0.8324 (mm-30) cc_final: 0.6950 (tt0) REVERT: G 333 SER cc_start: 0.8788 (m) cc_final: 0.8580 (p) REVERT: G 343 ASP cc_start: 0.8895 (t0) cc_final: 0.8663 (t0) REVERT: a 49 GLU cc_start: 0.8248 (mp0) cc_final: 0.7964 (mp0) REVERT: a 82 GLN cc_start: 0.8727 (pm20) cc_final: 0.8116 (pm20) REVERT: a 95 SER cc_start: 0.9495 (p) cc_final: 0.9244 (t) REVERT: a 115 HIS cc_start: 0.7490 (OUTLIER) cc_final: 0.6666 (p90) REVERT: a 118 LEU cc_start: 0.9133 (tp) cc_final: 0.8857 (tt) REVERT: a 123 LYS cc_start: 0.8814 (mtmm) cc_final: 0.8572 (mtmm) REVERT: a 130 ARG cc_start: 0.8315 (tpp-160) cc_final: 0.5341 (tpt170) REVERT: b 63 VAL cc_start: 0.8118 (OUTLIER) cc_final: 0.7771 (m) REVERT: b 91 GLN cc_start: 0.9262 (mm110) cc_final: 0.8976 (mm-40) REVERT: c 36 ASP cc_start: 0.7299 (p0) cc_final: 0.6877 (m-30) REVERT: c 49 GLU cc_start: 0.8330 (mp0) cc_final: 0.8001 (mp0) REVERT: c 132 ASN cc_start: 0.8190 (OUTLIER) cc_final: 0.7817 (t0) REVERT: d 49 GLU cc_start: 0.8426 (mp0) cc_final: 0.7951 (mp0) REVERT: d 91 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.7973 (mp10) REVERT: d 103 ILE cc_start: 0.8537 (OUTLIER) cc_final: 0.8273 (mp) REVERT: d 118 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8497 (tp) REVERT: e 21 ASP cc_start: 0.9131 (p0) cc_final: 0.8777 (p0) REVERT: e 34 GLU cc_start: 0.5367 (mm-30) cc_final: 0.4994 (mm-30) REVERT: e 91 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8838 (mm-40) REVERT: e 103 ILE cc_start: 0.8712 (OUTLIER) cc_final: 0.8108 (tp) REVERT: e 108 ASN cc_start: 0.8751 (t0) cc_final: 0.8411 (t0) REVERT: e 133 ILE cc_start: 0.8609 (mm) cc_final: 0.8391 (mm) REVERT: f 30 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8120 (mp) REVERT: f 118 LEU cc_start: 0.9183 (tp) cc_final: 0.8856 (tp) REVERT: g 84 VAL cc_start: 0.9451 (p) cc_final: 0.9179 (m) outliers start: 94 outliers final: 73 residues processed: 682 average time/residue: 0.1383 time to fit residues: 155.4973 Evaluate side-chains 705 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 620 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 254 LEU Chi-restraints excluded: chain A residue 263 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 20 LEU Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 142 VAL Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 316 TYR Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain G residue 11 LEU Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain a residue 115 HIS Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 40 GLU Chi-restraints excluded: chain b residue 63 VAL Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 82 GLN Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 118 LEU Chi-restraints excluded: chain d residue 119 ASP Chi-restraints excluded: chain e residue 14 ASN Chi-restraints excluded: chain e residue 103 ILE Chi-restraints excluded: chain e residue 109 HIS Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 119 ASP Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 82 GLN Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 123 LYS Chi-restraints excluded: chain g residue 133 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 99 optimal weight: 0.0980 chunk 134 optimal weight: 3.9990 chunk 247 optimal weight: 7.9990 chunk 163 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 251 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 190 optimal weight: 7.9990 chunk 196 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 119 optimal weight: 5.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 GLN F 285 GLN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 137 ASN ** e 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 125 GLN ** g 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.087819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.078205 restraints weight = 49912.953| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.63 r_work: 0.2872 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2747 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 26319 Z= 0.200 Angle : 0.636 13.218 35755 Z= 0.325 Chirality : 0.045 0.216 3876 Planarity : 0.004 0.046 4683 Dihedral : 5.679 57.790 3616 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.71 % Allowed : 22.23 % Favored : 74.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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 aren not related in a simple way. whole: -0.87 (0.15), residues: 3274 helix: 0.70 (0.22), residues: 600 sheet: -0.59 (0.19), residues: 729 loop : -0.98 (0.14), residues: 1945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 264 TYR 0.017 0.001 TYR F 250 PHE 0.019 0.002 PHE g 31 TRP 0.044 0.001 TRP F 209 HIS 0.009 0.001 HIS a 109 Details of bonding type rmsd covalent geometry : bond 0.00481 (26319) covalent geometry : angle 0.63568 (35755) hydrogen bonds : bond 0.03824 ( 875) hydrogen bonds : angle 5.38260 ( 2469) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11760.60 seconds wall clock time: 200 minutes 20.00 seconds (12020.00 seconds total)