Starting phenix.real_space_refine on Sat May 24 15:11:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vji_43282/05_2025/8vji_43282.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vji_43282/05_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_43282/05_2025/8vji_43282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vji_43282/05_2025/8vji_43282.map" model { file = "/net/cci-nas-00/data/ceres_data/8vji_43282/05_2025/8vji_43282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vji_43282/05_2025/8vji_43282.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 22.15, per 1000 atoms: 0.86 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: 6.11 Conformation dependent library (CDL) restraints added in 3.1 seconds 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: 3.38 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: 9.52 Time building geometry restraints manager: 7.20 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: 44.080 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: 0.060 Extract box with map and model: 1.090 Check model and map are aligned: 0.200 Set scattering table: 0.230 Process input model: 63.870 Find NCS groups from input model: 1.160 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 113.710 ------------------------------------------------------------------------------- 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 : 9.96 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.002 TRP G 242 HIS 0.013 0.003 HIS b 115 PHE 0.027 0.003 PHE E 212 TYR 0.025 0.003 TYR F 69 ARG 0.015 0.001 ARG B 15 Details of bonding type rmsd hydrogen bonds : bond 0.16635 ( 875) hydrogen bonds : angle 8.17624 ( 2469) covalent geometry : bond 0.00891 (26319) covalent geometry : angle 0.82414 (35755) *********************** 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 : 2.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.7628 (mtt) cc_final: 0.7128 (mtp) REVERT: A 246 GLU cc_start: 0.8236 (tt0) cc_final: 0.8030 (tt0) REVERT: A 274 ASP cc_start: 0.7822 (t0) cc_final: 0.7570 (t70) REVERT: A 277 ASP cc_start: 0.8090 (t0) cc_final: 0.7561 (t70) REVERT: A 307 LYS cc_start: 0.8826 (tptt) cc_final: 0.8551 (mptt) REVERT: A 324 GLU cc_start: 0.8513 (mm-30) cc_final: 0.7425 (tt0) REVERT: B 18 LYS cc_start: 0.8377 (mtpp) cc_final: 0.8163 (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: 0.8121 (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: 0.8664 (t0) 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: 0.8476 (mptt) REVERT: F 353 MET cc_start: 0.8843 (mtp) cc_final: 0.8522 (mtt) REVERT: G 37 ASP cc_start: 0.3853 (OUTLIER) cc_final: 0.2349 (p0) REVERT: G 262 ARG cc_start: 0.8346 (ptt-90) cc_final: 0.6879 (mmt180) REVERT: G 283 MET cc_start: 0.9083 (tpp) cc_final: 0.8484 (tpp) REVERT: G 324 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7443 (tt0) REVERT: G 333 SER cc_start: 0.8883 (m) cc_final: 0.8680 (p) REVERT: G 353 MET cc_start: 0.8135 (mmm) cc_final: 0.7714 (mmm) REVERT: a 62 MET cc_start: 0.8784 (mmp) cc_final: 0.8377 (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: 0.6657 (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: 0.6440 (p0) REVERT: c 123 LYS cc_start: 0.9104 (mttm) cc_final: 0.8888 (mtpt) REVERT: c 132 ASN cc_start: 0.7700 (m-40) cc_final: 0.7155 (t0) REVERT: d 37 ILE cc_start: 0.8705 (mt) cc_final: 0.8418 (mt) REVERT: d 62 MET cc_start: 0.8510 (mmm) cc_final: 0.8216 (mmt) REVERT: d 91 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8517 (mm-40) REVERT: e 62 MET cc_start: 0.8871 (mmm) cc_final: 0.8469 (mmt) REVERT: e 97 GLN cc_start: 0.8825 (mt0) cc_final: 0.8532 (mt0) REVERT: f 34 GLU cc_start: 0.6048 (mm-30) cc_final: 0.5791 (tp30) REVERT: f 82 GLN cc_start: 0.8942 (mp10) cc_final: 0.8636 (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: 0.8852 (tt) outliers start: 42 outliers final: 22 residues processed: 791 average time/residue: 0.3518 time to fit residues: 446.7350 Evaluate side-chains 662 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 637 time to evaluate : 2.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 90 ILE 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 276 optimal weight: 7.9990 chunk 247 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 84 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 256 optimal weight: 0.2980 chunk 99 optimal weight: 0.9980 chunk 155 optimal weight: 2.9990 chunk 190 optimal weight: 6.9990 chunk 296 optimal weight: 9.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- 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 D 70 ASN E 88 ASN G 70 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 = 0.3219 r_free = 0.3219 target = 0.090126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.080337 restraints weight = 48822.205| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.63 r_work: 0.2938 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 26319 Z= 0.150 Angle : 0.641 8.103 35755 Z= 0.343 Chirality : 0.046 0.215 3876 Planarity : 0.004 0.053 4683 Dihedral : 6.782 56.827 3648 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.63 % Allowed : 14.27 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.14), residues: 3274 helix: 0.79 (0.21), residues: 564 sheet: -0.30 (0.19), residues: 742 loop : -0.83 (0.14), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 221 HIS 0.005 0.001 HIS D 83 PHE 0.019 0.001 PHE b 128 TYR 0.016 0.001 TYR D 69 ARG 0.008 0.001 ARG G 240 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 875) hydrogen bonds : angle 6.14613 ( 2469) covalent geometry : bond 0.00345 (26319) covalent geometry : angle 0.64143 (35755) *********************** 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 843 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 747 time to evaluate : 2.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8516 (ptpt) cc_final: 0.8241 (ptpp) REVERT: A 69 TYR cc_start: 0.8593 (p90) cc_final: 0.8241 (p90) REVERT: A 89 MET cc_start: 0.7711 (mtt) cc_final: 0.7108 (mtp) REVERT: A 227 MET cc_start: 0.7966 (mtp) cc_final: 0.7763 (mtp) REVERT: A 263 MET cc_start: 0.8544 (mtm) cc_final: 0.8279 (mtp) REVERT: A 307 LYS cc_start: 0.8995 (tptt) cc_final: 0.8516 (mppt) REVERT: A 324 GLU cc_start: 0.8708 (mm-30) cc_final: 0.7637 (tt0) REVERT: A 329 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7902 (tt0) REVERT: B 130 GLU cc_start: 0.8738 (tp30) cc_final: 0.8463 (tp30) REVERT: B 147 GLN cc_start: 0.8670 (mt0) cc_final: 0.8427 (tt0) REVERT: B 159 ASP cc_start: 0.8380 (t0) cc_final: 0.8161 (t0) REVERT: B 186 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: B 268 ASN cc_start: 0.9039 (t0) cc_final: 0.8543 (t0) REVERT: B 275 GLN cc_start: 0.8221 (mt0) cc_final: 0.7951 (mm-40) REVERT: B 277 ASP cc_start: 0.8583 (t0) cc_final: 0.7712 (t0) REVERT: B 296 GLU cc_start: 0.8251 (tp30) cc_final: 0.7528 (tp30) REVERT: B 307 LYS cc_start: 0.9310 (ttpp) cc_final: 0.8889 (tptt) REVERT: B 323 GLN cc_start: 0.8471 (tt0) cc_final: 0.8099 (tt0) REVERT: C 15 ARG cc_start: 0.8624 (mtp85) cc_final: 0.8376 (tpp80) REVERT: C 324 GLU cc_start: 0.8688 (mm-30) cc_final: 0.6969 (pt0) REVERT: D 58 ASN cc_start: 0.8490 (OUTLIER) cc_final: 0.8170 (m110) REVERT: D 219 GLU cc_start: 0.8729 (mp0) cc_final: 0.8505 (mp0) REVERT: D 307 LYS cc_start: 0.9055 (tttm) cc_final: 0.8382 (mptt) REVERT: D 332 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8447 (ttm) REVERT: D 353 MET cc_start: 0.8934 (mtp) cc_final: 0.8657 (mtt) REVERT: E 60 GLN cc_start: 0.8712 (mt0) cc_final: 0.8109 (mm-40) REVERT: E 111 ASP cc_start: 0.9100 (t0) cc_final: 0.8782 (m-30) REVERT: E 130 GLU cc_start: 0.8634 (tp30) cc_final: 0.8412 (tp30) REVERT: E 329 GLU cc_start: 0.8763 (mp0) cc_final: 0.8508 (mt-10) REVERT: E 339 MET cc_start: 0.8333 (mmm) cc_final: 0.8043 (mmp) REVERT: F 130 GLU cc_start: 0.8435 (tp30) cc_final: 0.8063 (tp30) REVERT: F 178 MET cc_start: 0.8469 (mmt) cc_final: 0.8076 (mtt) REVERT: F 307 LYS cc_start: 0.8954 (tptp) cc_final: 0.8238 (mptt) REVERT: F 324 GLU cc_start: 0.8680 (mm-30) cc_final: 0.7284 (pt0) REVERT: G 15 ARG cc_start: 0.7567 (mtm180) cc_final: 0.6687 (tpt170) REVERT: G 75 LYS cc_start: 0.8616 (mtpt) cc_final: 0.8317 (mtpp) REVERT: G 147 GLN cc_start: 0.8006 (mt0) cc_final: 0.7294 (pt0) REVERT: G 213 VAL cc_start: 0.9402 (t) cc_final: 0.9144 (m) REVERT: G 241 LEU cc_start: 0.9052 (tt) cc_final: 0.8722 (tt) REVERT: G 262 ARG cc_start: 0.8318 (ptt-90) cc_final: 0.6904 (mmt180) REVERT: G 283 MET cc_start: 0.9204 (tpp) cc_final: 0.8566 (tpp) REVERT: G 324 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7393 (tt0) REVERT: G 333 SER cc_start: 0.8914 (m) cc_final: 0.8671 (p) REVERT: G 353 MET cc_start: 0.8187 (mmm) cc_final: 0.7847 (mmm) REVERT: a 49 GLU cc_start: 0.8054 (mp0) cc_final: 0.7755 (mp0) REVERT: a 62 MET cc_start: 0.8853 (mmp) cc_final: 0.8610 (mmt) REVERT: a 95 SER cc_start: 0.9520 (p) cc_final: 0.9270 (t) REVERT: a 133 ILE cc_start: 0.9101 (mt) cc_final: 0.8894 (mm) REVERT: b 36 ASP cc_start: 0.7301 (p0) cc_final: 0.7020 (p0) REVERT: b 91 GLN cc_start: 0.8634 (OUTLIER) cc_final: 0.8290 (mm-40) REVERT: c 26 GLU cc_start: 0.8623 (pm20) cc_final: 0.8286 (mm-30) REVERT: c 34 GLU cc_start: 0.6218 (mm-30) cc_final: 0.5442 (mm-30) REVERT: c 36 ASP cc_start: 0.7237 (p0) cc_final: 0.6654 (p0) REVERT: c 49 GLU cc_start: 0.8236 (mp0) cc_final: 0.7920 (mp0) REVERT: c 123 LYS cc_start: 0.9161 (mttm) cc_final: 0.8954 (mtpt) REVERT: c 132 ASN cc_start: 0.7690 (OUTLIER) cc_final: 0.7289 (t0) REVERT: d 29 GLN cc_start: 0.7462 (mt0) cc_final: 0.7096 (mm-40) REVERT: d 37 ILE cc_start: 0.8686 (mt) cc_final: 0.8412 (mt) REVERT: d 49 GLU cc_start: 0.8399 (mp0) cc_final: 0.8087 (mp0) REVERT: d 62 MET cc_start: 0.8582 (mmm) cc_final: 0.8231 (mmt) REVERT: d 91 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8363 (mm-40) REVERT: e 21 ASP cc_start: 0.9132 (p0) cc_final: 0.8844 (p0) REVERT: e 103 ILE cc_start: 0.8675 (tp) cc_final: 0.8327 (tp) REVERT: f 34 GLU cc_start: 0.6402 (mm-30) cc_final: 0.5844 (tp30) REVERT: f 36 ASP cc_start: 0.7684 (p0) cc_final: 0.7482 (p0) REVERT: f 95 SER cc_start: 0.9147 (p) cc_final: 0.8931 (t) REVERT: f 118 LEU cc_start: 0.9026 (tp) cc_final: 0.8681 (tt) REVERT: g 15 TYR cc_start: 0.8383 (m-80) cc_final: 0.7709 (m-80) REVERT: g 84 VAL cc_start: 0.9317 (p) cc_final: 0.9051 (m) REVERT: g 119 ASP cc_start: 0.9206 (OUTLIER) cc_final: 0.8976 (p0) REVERT: g 138 LEU cc_start: 0.9325 (mt) cc_final: 0.9064 (mt) outliers start: 96 outliers final: 60 residues processed: 796 average time/residue: 0.3231 time to fit residues: 416.6077 Evaluate side-chains 708 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 641 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU 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 B residue 63 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 186 GLN 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 164 MET Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 218 LYS 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 193 SER Chi-restraints excluded: chain E residue 224 ASP 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 71 THR 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 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 316 TYR 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 b residue 123 LYS 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 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 133 ILE Chi-restraints excluded: chain f residue 137 ASN Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 119 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 123 optimal weight: 9.9990 chunk 141 optimal weight: 10.0000 chunk 310 optimal weight: 0.6980 chunk 317 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 198 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 318 optimal weight: 9.9990 chunk 265 optimal weight: 9.9990 chunk 321 optimal weight: 0.7980 chunk 142 optimal weight: 7.9990 overall best weight: 4.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN C 138 GLN E 9 GLN E 88 ASN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN ** a 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 97 GLN ** 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 f 125 GLN ** 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 = 0.3163 r_free = 0.3163 target = 0.086714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.076875 restraints weight = 49766.368| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 2.67 r_work: 0.2897 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 26319 Z= 0.220 Angle : 0.638 10.470 35755 Z= 0.336 Chirality : 0.046 0.237 3876 Planarity : 0.004 0.052 4683 Dihedral : 6.456 58.662 3625 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.04 % Allowed : 15.64 % Favored : 79.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.14), residues: 3274 helix: 0.53 (0.21), residues: 606 sheet: -0.53 (0.17), residues: 879 loop : -1.02 (0.14), residues: 1789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 221 HIS 0.006 0.001 HIS C 121 PHE 0.018 0.002 PHE b 128 TYR 0.018 0.002 TYR D 69 ARG 0.006 0.001 ARG E 15 Details of bonding type rmsd hydrogen bonds : bond 0.04422 ( 875) hydrogen bonds : angle 5.81362 ( 2469) covalent geometry : bond 0.00520 (26319) covalent geometry : angle 0.63793 (35755) *********************** 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 795 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 662 time to evaluate : 3.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8587 (ptpt) cc_final: 0.7063 (mmtt) REVERT: A 69 TYR cc_start: 0.8678 (p90) cc_final: 0.8303 (p90) REVERT: A 89 MET cc_start: 0.7678 (mtt) cc_final: 0.7074 (mtp) REVERT: A 207 ASP cc_start: 0.9081 (m-30) cc_final: 0.8829 (m-30) REVERT: A 235 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8449 (mt-10) REVERT: A 263 MET cc_start: 0.8617 (mtm) cc_final: 0.8340 (mtp) REVERT: A 307 LYS cc_start: 0.8956 (tptt) cc_final: 0.8444 (mppt) REVERT: B 159 ASP cc_start: 0.8414 (t0) cc_final: 0.8096 (t0) REVERT: B 268 ASN cc_start: 0.9111 (t0) cc_final: 0.8546 (t0) REVERT: B 274 ASP cc_start: 0.8183 (t70) cc_final: 0.7953 (t0) REVERT: B 275 GLN cc_start: 0.8279 (mt0) cc_final: 0.7969 (mm-40) REVERT: B 277 ASP cc_start: 0.8651 (t0) cc_final: 0.7854 (t0) REVERT: B 296 GLU cc_start: 0.8346 (tp30) cc_final: 0.7539 (tp30) REVERT: B 307 LYS cc_start: 0.9306 (ttpp) cc_final: 0.8908 (tptt) REVERT: B 315 ASP cc_start: 0.8985 (OUTLIER) cc_final: 0.8490 (m-30) REVERT: C 15 ARG cc_start: 0.8715 (mtp85) cc_final: 0.8496 (tpp80) REVERT: C 36 GLU cc_start: 0.9272 (mp0) cc_final: 0.9069 (mp0) REVERT: C 130 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8565 (tp30) REVERT: C 324 GLU cc_start: 0.8670 (mm-30) cc_final: 0.6971 (pt0) REVERT: D 37 ASP cc_start: 0.8759 (t70) cc_final: 0.8411 (t0) REVERT: D 58 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8240 (m110) REVERT: D 219 GLU cc_start: 0.8830 (mp0) cc_final: 0.8584 (mp0) REVERT: D 307 LYS cc_start: 0.9099 (tttm) cc_final: 0.8377 (mptt) REVERT: D 324 GLU cc_start: 0.8713 (mm-30) cc_final: 0.7163 (tt0) REVERT: D 332 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8539 (ttm) REVERT: E 60 GLN cc_start: 0.8862 (mt0) cc_final: 0.8051 (mm-40) REVERT: E 65 LYS cc_start: 0.5436 (mmtm) cc_final: 0.5048 (mmtm) REVERT: E 111 ASP cc_start: 0.9082 (t0) cc_final: 0.8779 (m-30) REVERT: E 329 GLU cc_start: 0.8815 (mp0) cc_final: 0.8600 (mt-10) REVERT: E 339 MET cc_start: 0.8377 (mmm) cc_final: 0.8145 (mmp) REVERT: F 130 GLU cc_start: 0.8466 (tp30) cc_final: 0.8104 (tp30) REVERT: F 178 MET cc_start: 0.8443 (mmt) cc_final: 0.8053 (mtt) REVERT: F 283 MET cc_start: 0.9081 (tpt) cc_final: 0.8688 (tpt) REVERT: F 304 ILE cc_start: 0.8572 (mm) cc_final: 0.8306 (mt) REVERT: F 307 LYS cc_start: 0.8996 (tptp) cc_final: 0.8500 (mptt) REVERT: F 324 GLU cc_start: 0.8595 (mm-30) cc_final: 0.7257 (pt0) REVERT: F 333 SER cc_start: 0.8086 (m) cc_final: 0.7776 (p) REVERT: G 130 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8310 (tm-30) REVERT: G 213 VAL cc_start: 0.9390 (t) cc_final: 0.9132 (m) REVERT: G 324 GLU cc_start: 0.8564 (mm-30) cc_final: 0.7213 (tt0) REVERT: G 333 SER cc_start: 0.8884 (m) cc_final: 0.8551 (p) REVERT: G 353 MET cc_start: 0.8130 (mmm) cc_final: 0.7779 (mmm) REVERT: a 40 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.5972 (tt0) REVERT: a 49 GLU cc_start: 0.8111 (mp0) cc_final: 0.7770 (mp0) REVERT: a 62 MET cc_start: 0.8933 (mmt) cc_final: 0.8601 (mmt) REVERT: a 130 ARG cc_start: 0.8730 (mmm-85) cc_final: 0.4870 (tpt170) REVERT: a 133 ILE cc_start: 0.9176 (mt) cc_final: 0.8970 (mm) REVERT: b 91 GLN cc_start: 0.8657 (OUTLIER) cc_final: 0.8289 (mm-40) REVERT: c 26 GLU cc_start: 0.8642 (pm20) cc_final: 0.8265 (mm-30) REVERT: c 34 GLU cc_start: 0.6645 (mm-30) cc_final: 0.5915 (mm-30) REVERT: c 36 ASP cc_start: 0.7273 (p0) cc_final: 0.6686 (p0) REVERT: c 49 GLU cc_start: 0.8432 (mp0) cc_final: 0.8181 (mp0) REVERT: c 132 ASN cc_start: 0.7682 (OUTLIER) cc_final: 0.7254 (t0) REVERT: d 29 GLN cc_start: 0.7279 (mt0) cc_final: 0.6957 (mm-40) REVERT: d 36 ASP cc_start: 0.7532 (m-30) cc_final: 0.7302 (m-30) REVERT: d 37 ILE cc_start: 0.8708 (mt) cc_final: 0.8443 (mt) REVERT: d 49 GLU cc_start: 0.8495 (mp0) cc_final: 0.8110 (mp0) REVERT: d 91 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8280 (mm-40) REVERT: e 21 ASP cc_start: 0.9098 (p0) cc_final: 0.8805 (p0) REVERT: e 34 GLU cc_start: 0.6025 (mm-30) cc_final: 0.5671 (mm-30) REVERT: e 40 GLU cc_start: 0.6114 (OUTLIER) cc_final: 0.5847 (tt0) REVERT: e 91 GLN cc_start: 0.9236 (mm-40) cc_final: 0.9026 (mm-40) REVERT: e 103 ILE cc_start: 0.8749 (tp) cc_final: 0.8471 (tp) REVERT: e 108 ASN cc_start: 0.8626 (t0) cc_final: 0.8374 (t0) REVERT: f 34 GLU cc_start: 0.6556 (mm-30) cc_final: 0.6263 (tp30) REVERT: f 36 ASP cc_start: 0.7784 (p0) cc_final: 0.7555 (p0) REVERT: f 95 SER cc_start: 0.9167 (p) cc_final: 0.8951 (t) REVERT: f 118 LEU cc_start: 0.9067 (tp) cc_final: 0.8718 (tt) REVERT: g 14 ASN cc_start: 0.9235 (t0) cc_final: 0.9025 (t0) REVERT: g 15 TYR cc_start: 0.8332 (m-80) cc_final: 0.7468 (m-80) REVERT: g 66 ASP cc_start: 0.8972 (t0) cc_final: 0.8675 (t70) REVERT: g 84 VAL cc_start: 0.9323 (p) cc_final: 0.9059 (m) REVERT: g 119 ASP cc_start: 0.9276 (OUTLIER) cc_final: 0.9033 (p0) outliers start: 133 outliers final: 89 residues processed: 724 average time/residue: 0.3444 time to fit residues: 409.4999 Evaluate side-chains 719 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 621 time to evaluate : 3.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU 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 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 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 85 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 152 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 10 LEU Chi-restraints excluded: chain D residue 58 ASN 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 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 103 THR 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 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 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 244 ASP Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain a residue 40 GLU Chi-restraints excluded: chain a residue 106 VAL 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 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 119 ASP 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 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 103 ILE Chi-restraints excluded: chain d residue 106 VAL Chi-restraints excluded: chain d residue 119 ASP Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain e residue 40 GLU 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 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 0 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 164 optimal weight: 0.6980 chunk 319 optimal weight: 9.9990 chunk 320 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 233 optimal weight: 9.9990 chunk 286 optimal weight: 10.0000 chunk 152 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 overall best weight: 3.4386 ------------------------------------------------------------------------------- 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** B 323 GLN C 58 ASN C 345 ASN E 88 ASN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 249 GLN 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 109 HIS ** 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 Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.086059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.076323 restraints weight = 50459.878| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 2.69 r_work: 0.2904 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 26319 Z= 0.190 Angle : 0.600 8.088 35755 Z= 0.316 Chirality : 0.045 0.234 3876 Planarity : 0.004 0.046 4683 Dihedral : 6.221 57.789 3625 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 4.96 % Allowed : 18.06 % Favored : 76.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.14), residues: 3274 helix: 0.70 (0.21), residues: 600 sheet: -0.57 (0.18), residues: 869 loop : -0.98 (0.14), residues: 1805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 221 HIS 0.006 0.001 HIS C 121 PHE 0.017 0.002 PHE b 128 TYR 0.019 0.001 TYR F 69 ARG 0.006 0.000 ARG G 262 Details of bonding type rmsd hydrogen bonds : bond 0.04109 ( 875) hydrogen bonds : angle 5.60474 ( 2469) covalent geometry : bond 0.00449 (26319) covalent geometry : angle 0.60012 (35755) *********************** 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 783 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 652 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8560 (ptpt) cc_final: 0.7075 (mmtt) REVERT: A 69 TYR cc_start: 0.8670 (p90) cc_final: 0.8319 (p90) REVERT: A 296 GLU cc_start: 0.9092 (tp30) cc_final: 0.8811 (tp30) REVERT: A 304 ILE cc_start: 0.8655 (mm) cc_final: 0.8454 (mt) REVERT: A 307 LYS cc_start: 0.8927 (tptt) cc_final: 0.8379 (mppt) REVERT: B 159 ASP cc_start: 0.8361 (t0) cc_final: 0.8015 (t0) REVERT: B 251 MET cc_start: 0.8824 (mmm) cc_final: 0.8396 (mmm) REVERT: B 268 ASN cc_start: 0.9111 (t0) cc_final: 0.8447 (t0) REVERT: B 274 ASP cc_start: 0.8165 (t70) cc_final: 0.7956 (t70) REVERT: B 275 GLN cc_start: 0.8316 (mt0) cc_final: 0.8102 (mm-40) REVERT: B 277 ASP cc_start: 0.8613 (t0) cc_final: 0.7804 (t0) REVERT: B 296 GLU cc_start: 0.8399 (tp30) cc_final: 0.7591 (tp30) REVERT: B 307 LYS cc_start: 0.9288 (ttpp) cc_final: 0.8843 (tptt) REVERT: B 315 ASP cc_start: 0.8867 (OUTLIER) cc_final: 0.8382 (m-30) REVERT: C 15 ARG cc_start: 0.8742 (mtp85) cc_final: 0.8538 (tpp80) REVERT: C 130 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8575 (tp30) REVERT: C 324 GLU cc_start: 0.8680 (mm-30) cc_final: 0.7013 (pt0) REVERT: D 58 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8270 (m110) REVERT: D 274 ASP cc_start: 0.8381 (t70) cc_final: 0.8019 (t70) REVERT: D 307 LYS cc_start: 0.9042 (tttm) cc_final: 0.8270 (mptt) REVERT: D 324 GLU cc_start: 0.8715 (mm-30) cc_final: 0.7094 (tt0) REVERT: E 15 ARG cc_start: 0.8480 (mtt-85) cc_final: 0.8275 (mtt-85) REVERT: E 60 GLN cc_start: 0.8800 (mt0) cc_final: 0.7828 (mm-40) REVERT: E 111 ASP cc_start: 0.9077 (t0) cc_final: 0.8768 (m-30) REVERT: E 251 MET cc_start: 0.8539 (mmm) cc_final: 0.8058 (mmm) REVERT: F 130 GLU cc_start: 0.8443 (tp30) cc_final: 0.8063 (tp30) REVERT: F 178 MET cc_start: 0.8399 (mmt) cc_final: 0.8018 (mtt) REVERT: F 283 MET cc_start: 0.9071 (tpt) cc_final: 0.8783 (tpt) REVERT: F 304 ILE cc_start: 0.8658 (mm) cc_final: 0.8438 (mt) REVERT: F 307 LYS cc_start: 0.8993 (tptp) cc_final: 0.8375 (mptt) REVERT: F 333 SER cc_start: 0.8208 (m) cc_final: 0.7911 (p) REVERT: G 213 VAL cc_start: 0.9377 (t) cc_final: 0.9124 (m) REVERT: G 324 GLU cc_start: 0.8530 (mm-30) cc_final: 0.7229 (tt0) REVERT: G 333 SER cc_start: 0.8907 (m) cc_final: 0.8588 (p) REVERT: G 353 MET cc_start: 0.8153 (mmm) cc_final: 0.7841 (mmm) REVERT: a 40 GLU cc_start: 0.6505 (OUTLIER) cc_final: 0.5926 (tt0) REVERT: a 49 GLU cc_start: 0.8251 (mp0) cc_final: 0.7931 (mp0) REVERT: a 95 SER cc_start: 0.9494 (p) cc_final: 0.9262 (t) REVERT: a 115 HIS cc_start: 0.7478 (OUTLIER) cc_final: 0.6685 (p90) REVERT: a 130 ARG cc_start: 0.8844 (mmm-85) cc_final: 0.4940 (tpt170) REVERT: a 133 ILE cc_start: 0.9211 (mt) cc_final: 0.8993 (mm) REVERT: b 91 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8310 (mm-40) REVERT: c 26 GLU cc_start: 0.8616 (pm20) cc_final: 0.8255 (mm-30) REVERT: c 36 ASP cc_start: 0.7310 (p0) cc_final: 0.7006 (p0) REVERT: c 49 GLU cc_start: 0.8382 (mp0) cc_final: 0.8104 (mp0) REVERT: c 132 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7662 (t0) REVERT: d 29 GLN cc_start: 0.7252 (mt0) cc_final: 0.7050 (mm-40) REVERT: d 34 GLU cc_start: 0.5793 (mm-30) cc_final: 0.5429 (mm-30) REVERT: d 37 ILE cc_start: 0.8661 (mt) cc_final: 0.8388 (mt) REVERT: d 49 GLU cc_start: 0.8520 (mp0) cc_final: 0.8104 (mp0) REVERT: d 91 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7932 (mp10) REVERT: e 21 ASP cc_start: 0.9072 (p0) cc_final: 0.8782 (p0) REVERT: e 40 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.6141 (tt0) REVERT: e 91 GLN cc_start: 0.9184 (mm-40) cc_final: 0.8735 (mm110) REVERT: e 103 ILE cc_start: 0.8828 (tp) cc_final: 0.8620 (tp) REVERT: e 108 ASN cc_start: 0.8661 (t0) cc_final: 0.8309 (t0) REVERT: f 36 ASP cc_start: 0.7638 (p0) cc_final: 0.7372 (p0) REVERT: f 95 SER cc_start: 0.9133 (p) cc_final: 0.8919 (t) REVERT: f 118 LEU cc_start: 0.9076 (tp) cc_final: 0.8658 (tt) REVERT: g 66 ASP cc_start: 0.9008 (t0) cc_final: 0.8700 (t70) REVERT: g 84 VAL cc_start: 0.9347 (p) cc_final: 0.9074 (m) REVERT: g 119 ASP cc_start: 0.9357 (OUTLIER) cc_final: 0.9139 (p0) outliers start: 131 outliers final: 94 residues processed: 719 average time/residue: 0.3295 time to fit residues: 387.9981 Evaluate side-chains 725 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 622 time to evaluate : 2.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU 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 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 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 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 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 58 ASN Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 218 LYS 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 288 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 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 F residue 300 CYS Chi-restraints excluded: chain F residue 328 VAL 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 300 CYS Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain G residue 320 MET 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 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 91 GLN 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 119 ASP 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 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 103 ILE Chi-restraints excluded: chain d residue 106 VAL Chi-restraints excluded: chain d residue 119 ASP Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 88 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 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 121 optimal weight: 0.9980 chunk 267 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 167 optimal weight: 0.8980 chunk 165 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 274 optimal weight: 0.0570 chunk 281 optimal weight: 8.9990 chunk 44 optimal weight: 9.9990 chunk 158 optimal weight: 6.9990 chunk 286 optimal weight: 9.9990 overall best weight: 2.7902 ------------------------------------------------------------------------------- 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 ** 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 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 109 HIS ** 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 125 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.088438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.078730 restraints weight = 49591.112| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.66 r_work: 0.2925 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 26319 Z= 0.164 Angle : 0.583 9.227 35755 Z= 0.304 Chirality : 0.044 0.208 3876 Planarity : 0.004 0.044 4683 Dihedral : 6.016 58.007 3625 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.96 % Allowed : 18.59 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.80 (0.14), residues: 3274 helix: 0.79 (0.21), residues: 594 sheet: -0.63 (0.18), residues: 841 loop : -0.90 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 221 HIS 0.006 0.001 HIS a 109 PHE 0.016 0.001 PHE b 128 TYR 0.017 0.001 TYR F 69 ARG 0.006 0.000 ARG G 262 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 875) hydrogen bonds : angle 5.46228 ( 2469) covalent geometry : bond 0.00389 (26319) covalent geometry : angle 0.58295 (35755) *********************** 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: 131 poor density : 662 time to evaluate : 2.742 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8650 (p90) cc_final: 0.8311 (p90) REVERT: A 89 MET cc_start: 0.7787 (mtt) cc_final: 0.7325 (mtp) REVERT: A 207 ASP cc_start: 0.9093 (m-30) cc_final: 0.8842 (m-30) REVERT: A 235 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8415 (mt-10) REVERT: A 307 LYS cc_start: 0.8755 (tptt) cc_final: 0.8136 (mptt) REVERT: B 159 ASP cc_start: 0.8349 (t0) cc_final: 0.8009 (t0) REVERT: B 251 MET cc_start: 0.8755 (mmm) cc_final: 0.8395 (mmm) REVERT: B 274 ASP cc_start: 0.8229 (t70) cc_final: 0.7997 (t70) REVERT: B 275 GLN cc_start: 0.8354 (mt0) cc_final: 0.8119 (mm-40) REVERT: B 277 ASP cc_start: 0.8615 (t0) cc_final: 0.7803 (t0) REVERT: B 296 GLU cc_start: 0.8467 (tp30) cc_final: 0.7711 (tp30) REVERT: B 307 LYS cc_start: 0.9249 (ttpp) cc_final: 0.8828 (tptt) REVERT: B 315 ASP cc_start: 0.8752 (OUTLIER) cc_final: 0.8272 (m-30) REVERT: C 41 PHE cc_start: 0.8080 (m-10) cc_final: 0.7744 (m-80) REVERT: C 130 GLU cc_start: 0.9005 (mm-30) cc_final: 0.8505 (tp30) REVERT: C 254 LEU cc_start: 0.8107 (mp) cc_final: 0.7872 (mt) REVERT: C 324 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7013 (pt0) REVERT: D 37 ASP cc_start: 0.8673 (t0) cc_final: 0.8329 (t70) REVERT: D 41 PHE cc_start: 0.7712 (m-80) cc_final: 0.7478 (m-80) REVERT: D 58 ASN cc_start: 0.8570 (OUTLIER) cc_final: 0.8315 (m110) REVERT: D 274 ASP cc_start: 0.8344 (t70) cc_final: 0.7918 (t70) REVERT: D 307 LYS cc_start: 0.8982 (tttm) cc_final: 0.8258 (mptt) REVERT: D 316 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7682 (t80) REVERT: D 324 GLU cc_start: 0.8703 (mm-30) cc_final: 0.7098 (tt0) REVERT: E 15 ARG cc_start: 0.8470 (mtt-85) cc_final: 0.8176 (mtt-85) REVERT: E 60 GLN cc_start: 0.8820 (mt0) cc_final: 0.7931 (mm-40) REVERT: E 111 ASP cc_start: 0.9082 (t0) cc_final: 0.8767 (m-30) REVERT: E 119 MET cc_start: 0.8725 (tmm) cc_final: 0.8517 (tmm) REVERT: F 69 TYR cc_start: 0.8388 (p90) cc_final: 0.8086 (p90) REVERT: F 130 GLU cc_start: 0.8436 (tp30) cc_final: 0.8057 (tp30) REVERT: F 178 MET cc_start: 0.8371 (mmt) cc_final: 0.8075 (mtt) REVERT: F 246 GLU cc_start: 0.8165 (tp30) cc_final: 0.7832 (tp30) REVERT: F 307 LYS cc_start: 0.9018 (tptp) cc_final: 0.8400 (mptt) REVERT: F 324 GLU cc_start: 0.8506 (mm-30) cc_final: 0.7336 (pt0) REVERT: F 333 SER cc_start: 0.8227 (m) cc_final: 0.7850 (p) REVERT: G 75 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8173 (mtpp) REVERT: G 213 VAL cc_start: 0.9355 (t) cc_final: 0.9105 (m) REVERT: G 242 TRP cc_start: 0.8734 (m100) cc_final: 0.8498 (m100) REVERT: G 324 GLU cc_start: 0.8462 (mm-30) cc_final: 0.7114 (tt0) REVERT: G 333 SER cc_start: 0.8881 (m) cc_final: 0.8605 (p) REVERT: G 339 MET cc_start: 0.8791 (mmm) cc_final: 0.8548 (mmp) REVERT: G 343 ASP cc_start: 0.8821 (t0) cc_final: 0.8611 (t0) REVERT: a 40 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.5888 (tt0) REVERT: a 49 GLU cc_start: 0.8216 (mp0) cc_final: 0.7897 (mp0) REVERT: a 95 SER cc_start: 0.9488 (p) cc_final: 0.9251 (t) REVERT: a 115 HIS cc_start: 0.7522 (OUTLIER) cc_final: 0.6737 (p90) REVERT: b 91 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8010 (mp10) REVERT: b 123 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8414 (mtmm) REVERT: c 26 GLU cc_start: 0.8603 (pm20) cc_final: 0.8247 (mm-30) REVERT: c 36 ASP cc_start: 0.7168 (p0) cc_final: 0.6436 (m-30) REVERT: c 49 GLU cc_start: 0.8400 (mp0) cc_final: 0.8106 (mp0) REVERT: c 130 ARG cc_start: 0.7726 (tpp-160) cc_final: 0.5383 (mmm160) REVERT: c 132 ASN cc_start: 0.7935 (OUTLIER) cc_final: 0.7614 (t0) REVERT: d 37 ILE cc_start: 0.8623 (mt) cc_final: 0.8378 (mt) REVERT: d 49 GLU cc_start: 0.8516 (mp0) cc_final: 0.8091 (mp0) REVERT: d 91 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.7997 (mp10) REVERT: d 103 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8203 (mp) REVERT: e 21 ASP cc_start: 0.9095 (p0) cc_final: 0.8801 (p0) REVERT: e 40 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.5906 (tt0) REVERT: e 91 GLN cc_start: 0.9189 (mm-40) cc_final: 0.8770 (mm110) REVERT: e 108 ASN cc_start: 0.8717 (t0) cc_final: 0.8405 (t0) REVERT: e 123 LYS cc_start: 0.9407 (mtpp) cc_final: 0.9193 (mtmm) REVERT: f 36 ASP cc_start: 0.7576 (p0) cc_final: 0.7346 (p0) REVERT: f 95 SER cc_start: 0.9137 (p) cc_final: 0.8931 (t) REVERT: f 118 LEU cc_start: 0.9079 (tp) cc_final: 0.8620 (tt) REVERT: g 119 ASP cc_start: 0.9381 (OUTLIER) cc_final: 0.9168 (p0) outliers start: 131 outliers final: 100 residues processed: 728 average time/residue: 0.3203 time to fit residues: 381.8373 Evaluate side-chains 740 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 627 time to evaluate : 2.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU 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 255 VAL 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 99 LEU 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 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 58 ASN Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 193 SER 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 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 315 ASP Chi-restraints excluded: chain E residue 316 TYR Chi-restraints excluded: chain E residue 320 MET 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 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 152 VAL Chi-restraints excluded: chain G residue 190 SER 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 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 91 GLN 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 119 ASP 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 39 THR 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 103 ILE Chi-restraints excluded: chain d residue 106 VAL 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 40 GLU Chi-restraints excluded: chain e residue 88 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 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 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 137 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 249 optimal weight: 0.7980 chunk 286 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 222 optimal weight: 0.9990 chunk 85 optimal weight: 9.9990 chunk 205 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 192 optimal weight: 5.9990 chunk 184 optimal weight: 5.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 GLN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN D 33 ASN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.088130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.078486 restraints weight = 49582.115| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.62 r_work: 0.2874 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 26319 Z= 0.187 Angle : 0.591 10.036 35755 Z= 0.308 Chirality : 0.044 0.195 3876 Planarity : 0.004 0.042 4683 Dihedral : 5.968 59.853 3625 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 5.23 % Allowed : 19.05 % Favored : 75.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.14), residues: 3274 helix: 0.83 (0.22), residues: 594 sheet: -0.75 (0.18), residues: 842 loop : -0.91 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 221 HIS 0.006 0.001 HIS a 109 PHE 0.015 0.001 PHE b 128 TYR 0.016 0.001 TYR F 69 ARG 0.006 0.000 ARG E 264 Details of bonding type rmsd hydrogen bonds : bond 0.03904 ( 875) hydrogen bonds : angle 5.41852 ( 2469) covalent geometry : bond 0.00446 (26319) covalent geometry : angle 0.59138 (35755) *********************** 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 784 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 646 time to evaluate : 2.971 Fit side-chains REVERT: A 69 TYR cc_start: 0.8689 (p90) cc_final: 0.8373 (p90) REVERT: A 89 MET cc_start: 0.7814 (mtt) cc_final: 0.7330 (mtp) REVERT: A 227 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7762 (mtp) REVERT: A 235 GLU cc_start: 0.8659 (mt-10) cc_final: 0.8438 (mt-10) REVERT: A 307 LYS cc_start: 0.8781 (tptt) cc_final: 0.8160 (mptt) REVERT: B 159 ASP cc_start: 0.8369 (t0) cc_final: 0.8027 (t0) REVERT: B 276 ASN cc_start: 0.9053 (m-40) cc_final: 0.8842 (m-40) REVERT: B 277 ASP cc_start: 0.8585 (t0) cc_final: 0.7732 (t0) REVERT: B 296 GLU cc_start: 0.8518 (tp30) cc_final: 0.7775 (tp30) REVERT: B 307 LYS cc_start: 0.9304 (ttpp) cc_final: 0.8831 (tptt) REVERT: B 315 ASP cc_start: 0.8756 (OUTLIER) cc_final: 0.8377 (m-30) REVERT: C 41 PHE cc_start: 0.8080 (m-10) cc_final: 0.7779 (m-80) REVERT: C 130 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8501 (tp30) REVERT: C 324 GLU cc_start: 0.8756 (mm-30) cc_final: 0.7064 (pt0) REVERT: D 41 PHE cc_start: 0.7690 (m-80) cc_final: 0.7433 (m-80) REVERT: D 58 ASN cc_start: 0.8582 (OUTLIER) cc_final: 0.8286 (m110) REVERT: D 274 ASP cc_start: 0.8421 (t70) cc_final: 0.8071 (t70) REVERT: D 307 LYS cc_start: 0.9007 (tttm) cc_final: 0.8141 (mptt) REVERT: D 316 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7813 (t80) REVERT: D 324 GLU cc_start: 0.8751 (mm-30) cc_final: 0.7135 (tt0) REVERT: E 15 ARG cc_start: 0.8445 (mtt-85) cc_final: 0.8211 (mtt-85) REVERT: E 60 GLN cc_start: 0.8827 (mt0) cc_final: 0.7826 (mm-40) REVERT: E 111 ASP cc_start: 0.9093 (t0) cc_final: 0.8787 (m-30) REVERT: E 251 MET cc_start: 0.8412 (mmm) cc_final: 0.7896 (mmm) REVERT: E 283 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.7966 (tpp) REVERT: F 69 TYR cc_start: 0.8437 (p90) cc_final: 0.7782 (p90) REVERT: F 130 GLU cc_start: 0.8430 (tp30) cc_final: 0.8067 (tp30) REVERT: F 178 MET cc_start: 0.8412 (mmt) cc_final: 0.8084 (mtt) REVERT: F 283 MET cc_start: 0.9075 (tpt) cc_final: 0.8839 (tpt) REVERT: F 307 LYS cc_start: 0.9022 (tptp) cc_final: 0.8419 (mppt) REVERT: F 333 SER cc_start: 0.8212 (m) cc_final: 0.7880 (p) REVERT: G 75 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8198 (mtpp) REVERT: G 213 VAL cc_start: 0.9361 (t) cc_final: 0.9102 (m) REVERT: G 324 GLU cc_start: 0.8412 (mm-30) cc_final: 0.7224 (tt0) REVERT: G 333 SER cc_start: 0.8869 (m) cc_final: 0.8601 (p) REVERT: G 343 ASP cc_start: 0.8846 (t0) cc_final: 0.8600 (t0) REVERT: a 40 GLU cc_start: 0.6508 (OUTLIER) cc_final: 0.5917 (tt0) REVERT: a 49 GLU cc_start: 0.8213 (mp0) cc_final: 0.7913 (mp0) REVERT: a 95 SER cc_start: 0.9500 (p) cc_final: 0.9269 (t) REVERT: a 115 HIS cc_start: 0.7475 (OUTLIER) cc_final: 0.6699 (p90) REVERT: b 91 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8030 (mp10) REVERT: b 108 ASN cc_start: 0.8785 (t0) cc_final: 0.8469 (t0) REVERT: b 123 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8429 (mtmm) REVERT: b 137 ASN cc_start: 0.8814 (m-40) cc_final: 0.8598 (m-40) REVERT: c 26 GLU cc_start: 0.8636 (pm20) cc_final: 0.8332 (mm-30) REVERT: c 36 ASP cc_start: 0.7113 (p0) cc_final: 0.6622 (m-30) REVERT: c 49 GLU cc_start: 0.8375 (mp0) cc_final: 0.8094 (mp0) REVERT: c 95 SER cc_start: 0.9278 (p) cc_final: 0.9043 (t) REVERT: c 132 ASN cc_start: 0.8018 (OUTLIER) cc_final: 0.7717 (t0) REVERT: d 37 ILE cc_start: 0.8722 (mt) cc_final: 0.8498 (mt) REVERT: d 49 GLU cc_start: 0.8530 (mp0) cc_final: 0.8119 (mp0) REVERT: d 56 LYS cc_start: 0.9116 (mtmt) cc_final: 0.8864 (mttt) REVERT: d 91 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: d 103 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8254 (mp) REVERT: e 21 ASP cc_start: 0.9110 (p0) cc_final: 0.8811 (p0) REVERT: e 34 GLU cc_start: 0.5257 (mm-30) cc_final: 0.4931 (mm-30) REVERT: e 40 GLU cc_start: 0.6297 (OUTLIER) cc_final: 0.5805 (tt0) REVERT: e 91 GLN cc_start: 0.9195 (mm-40) cc_final: 0.8747 (mm110) REVERT: e 108 ASN cc_start: 0.8747 (t0) cc_final: 0.8370 (t0) REVERT: e 123 LYS cc_start: 0.9428 (mtpp) cc_final: 0.9222 (mtmm) REVERT: f 30 ILE cc_start: 0.8574 (OUTLIER) cc_final: 0.8046 (mp) REVERT: f 36 ASP cc_start: 0.7617 (p0) cc_final: 0.7277 (p0) REVERT: f 95 SER cc_start: 0.9139 (p) cc_final: 0.8933 (t) REVERT: f 118 LEU cc_start: 0.9115 (tp) cc_final: 0.8795 (tp) REVERT: g 84 VAL cc_start: 0.9351 (p) cc_final: 0.9063 (m) REVERT: g 98 ASN cc_start: 0.8888 (m110) cc_final: 0.8607 (m-40) REVERT: g 119 ASP cc_start: 0.9366 (OUTLIER) cc_final: 0.9154 (p0) outliers start: 138 outliers final: 102 residues processed: 719 average time/residue: 0.3281 time to fit residues: 385.4680 Evaluate side-chains 749 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 631 time to evaluate : 2.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU 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 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 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 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 142 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 255 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 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 58 ASN 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 193 SER 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 E residue 320 MET 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 300 CYS Chi-restraints excluded: chain F residue 328 VAL Chi-restraints excluded: chain G residue 38 MET 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 190 SER 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 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 91 GLN 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 132 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 119 ASP Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain e residue 14 ASN Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 88 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 103 ILE Chi-restraints excluded: chain f residue 108 ASN 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 137 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 313 optimal weight: 0.6980 chunk 98 optimal weight: 7.9990 chunk 254 optimal weight: 4.9990 chunk 227 optimal weight: 20.0000 chunk 255 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 chunk 307 optimal weight: 1.9990 chunk 152 optimal weight: 10.0000 chunk 218 optimal weight: 2.9990 chunk 260 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- 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 270 GLN D 33 ASN ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN G 70 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 125 GLN g 115 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.087316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.077636 restraints weight = 49914.863| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.66 r_work: 0.2924 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 26319 Z= 0.178 Angle : 0.597 11.170 35755 Z= 0.309 Chirality : 0.044 0.202 3876 Planarity : 0.004 0.044 4683 Dihedral : 5.870 59.258 3623 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.96 % Allowed : 19.84 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.14), residues: 3274 helix: 0.82 (0.22), residues: 594 sheet: -0.62 (0.19), residues: 775 loop : -0.94 (0.14), residues: 1905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 27 HIS 0.006 0.001 HIS a 109 PHE 0.016 0.001 PHE b 128 TYR 0.016 0.001 TYR F 69 ARG 0.005 0.000 ARG E 264 Details of bonding type rmsd hydrogen bonds : bond 0.03822 ( 875) hydrogen bonds : angle 5.36366 ( 2469) covalent geometry : bond 0.00426 (26319) covalent geometry : angle 0.59727 (35755) *********************** 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 771 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 640 time to evaluate : 2.851 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8749 (p90) cc_final: 0.8398 (p90) REVERT: A 89 MET cc_start: 0.7851 (mtt) cc_final: 0.7353 (mtp) REVERT: A 227 MET cc_start: 0.8068 (OUTLIER) cc_final: 0.7773 (mtp) REVERT: A 235 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8469 (mt-10) REVERT: A 307 LYS cc_start: 0.8761 (tptt) cc_final: 0.8112 (mptt) REVERT: B 130 GLU cc_start: 0.8757 (tp30) cc_final: 0.8443 (tp30) REVERT: B 159 ASP cc_start: 0.8379 (t0) cc_final: 0.8017 (t0) REVERT: B 251 MET cc_start: 0.8605 (mmm) cc_final: 0.8303 (mtp) REVERT: B 277 ASP cc_start: 0.8575 (t0) cc_final: 0.7738 (t0) REVERT: B 296 GLU cc_start: 0.8532 (tp30) cc_final: 0.7781 (tp30) REVERT: B 307 LYS cc_start: 0.9261 (ttpp) cc_final: 0.8849 (tptt) REVERT: C 41 PHE cc_start: 0.8079 (m-10) cc_final: 0.7826 (m-80) REVERT: C 130 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8497 (tp30) REVERT: C 324 GLU cc_start: 0.8708 (mm-30) cc_final: 0.7085 (pt0) REVERT: D 58 ASN cc_start: 0.8514 (OUTLIER) cc_final: 0.8246 (m110) REVERT: D 307 LYS cc_start: 0.8993 (tttm) cc_final: 0.8107 (mptt) REVERT: D 316 TYR cc_start: 0.8470 (OUTLIER) cc_final: 0.7751 (t80) REVERT: E 15 ARG cc_start: 0.8418 (mtt-85) cc_final: 0.8208 (mtt-85) REVERT: E 60 GLN cc_start: 0.8774 (mt0) cc_final: 0.7785 (mm-40) REVERT: E 111 ASP cc_start: 0.9073 (t0) cc_final: 0.8764 (m-30) REVERT: E 119 MET cc_start: 0.8814 (tmm) cc_final: 0.8595 (tmm) REVERT: E 251 MET cc_start: 0.8384 (mmm) cc_final: 0.7906 (mmm) REVERT: E 283 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.7953 (tpp) REVERT: F 69 TYR cc_start: 0.8467 (p90) cc_final: 0.7771 (p90) REVERT: F 130 GLU cc_start: 0.8452 (tp30) cc_final: 0.8070 (tp30) REVERT: F 178 MET cc_start: 0.8444 (mmt) cc_final: 0.8107 (mtt) REVERT: F 246 GLU cc_start: 0.8171 (tp30) cc_final: 0.7916 (tp30) REVERT: F 307 LYS cc_start: 0.8995 (tptp) cc_final: 0.8400 (mppt) REVERT: F 324 GLU cc_start: 0.8531 (mm-30) cc_final: 0.7386 (pt0) REVERT: F 333 SER cc_start: 0.8237 (m) cc_final: 0.7854 (p) REVERT: G 75 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8416 (mtpp) REVERT: G 213 VAL cc_start: 0.9342 (t) cc_final: 0.9077 (m) REVERT: G 324 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7192 (tt0) REVERT: G 333 SER cc_start: 0.8887 (m) cc_final: 0.8608 (p) REVERT: G 343 ASP cc_start: 0.8897 (t0) cc_final: 0.8617 (t0) REVERT: G 353 MET cc_start: 0.7905 (mpp) cc_final: 0.7407 (mpp) REVERT: a 40 GLU cc_start: 0.6696 (OUTLIER) cc_final: 0.6133 (tt0) REVERT: a 49 GLU cc_start: 0.8315 (mp0) cc_final: 0.8000 (mp0) REVERT: a 78 VAL cc_start: 0.9507 (t) cc_final: 0.9286 (p) REVERT: a 95 SER cc_start: 0.9492 (p) cc_final: 0.9253 (t) REVERT: a 115 HIS cc_start: 0.7517 (OUTLIER) cc_final: 0.6729 (p90) REVERT: b 91 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7985 (mp10) REVERT: b 108 ASN cc_start: 0.8773 (t0) cc_final: 0.8517 (t0) REVERT: b 123 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8451 (mtmm) REVERT: b 137 ASN cc_start: 0.8801 (m-40) cc_final: 0.8592 (m-40) REVERT: c 26 GLU cc_start: 0.8607 (pm20) cc_final: 0.8337 (mm-30) REVERT: c 36 ASP cc_start: 0.7144 (p0) cc_final: 0.6735 (m-30) REVERT: c 49 GLU cc_start: 0.8359 (mp0) cc_final: 0.8059 (mp0) REVERT: c 95 SER cc_start: 0.9267 (p) cc_final: 0.9035 (t) REVERT: c 132 ASN cc_start: 0.8172 (OUTLIER) cc_final: 0.7813 (t0) REVERT: d 37 ILE cc_start: 0.8664 (mt) cc_final: 0.8450 (mt) REVERT: d 49 GLU cc_start: 0.8520 (mp0) cc_final: 0.8070 (mp0) REVERT: d 91 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.7960 (mp10) REVERT: d 103 ILE cc_start: 0.8520 (OUTLIER) cc_final: 0.8148 (mp) REVERT: e 21 ASP cc_start: 0.9115 (p0) cc_final: 0.8826 (p0) REVERT: e 34 GLU cc_start: 0.5385 (mm-30) cc_final: 0.5012 (mm-30) REVERT: e 40 GLU cc_start: 0.6258 (OUTLIER) cc_final: 0.5676 (tt0) REVERT: e 91 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8696 (mm110) REVERT: e 108 ASN cc_start: 0.8752 (t0) cc_final: 0.8425 (t0) REVERT: e 123 LYS cc_start: 0.9427 (mtpp) cc_final: 0.9214 (mtmm) REVERT: f 30 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8135 (mp) REVERT: f 36 ASP cc_start: 0.7606 (p0) cc_final: 0.7382 (p0) REVERT: f 95 SER cc_start: 0.9142 (p) cc_final: 0.8934 (t) REVERT: f 118 LEU cc_start: 0.9118 (tp) cc_final: 0.8803 (tp) REVERT: g 84 VAL cc_start: 0.9363 (p) cc_final: 0.9079 (m) REVERT: g 119 ASP cc_start: 0.9337 (OUTLIER) cc_final: 0.9132 (p0) outliers start: 131 outliers final: 99 residues processed: 706 average time/residue: 0.3247 time to fit residues: 376.8016 Evaluate side-chains 735 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 621 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU 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 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 248 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 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 99 LEU 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 198 VAL Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain B residue 353 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 58 ASN 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 293 SER 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 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 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 236 THR Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 300 CYS 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 190 SER 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 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 91 GLN 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 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 106 VAL Chi-restraints excluded: chain d residue 119 ASP Chi-restraints excluded: chain e residue 14 ASN Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 63 VAL Chi-restraints excluded: chain e residue 86 ILE Chi-restraints excluded: chain e residue 88 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 103 ILE Chi-restraints excluded: chain f residue 108 ASN 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 137 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 185 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 284 optimal weight: 0.3980 chunk 180 optimal weight: 5.9990 chunk 261 optimal weight: 0.0980 chunk 98 optimal weight: 4.9990 chunk 320 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 290 optimal weight: 1.9990 chunk 280 optimal weight: 3.9990 chunk 219 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN F 275 GLN G 70 ASN G 138 GLN ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 109 HIS ** f 91 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 = 0.3247 r_free = 0.3247 target = 0.091577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.081944 restraints weight = 49066.713| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.67 r_work: 0.3031 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 26319 Z= 0.109 Angle : 0.571 13.452 35755 Z= 0.293 Chirality : 0.043 0.164 3876 Planarity : 0.004 0.046 4683 Dihedral : 5.576 58.732 3621 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 3.48 % Allowed : 21.73 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.15), residues: 3274 helix: 0.93 (0.22), residues: 596 sheet: -0.62 (0.18), residues: 825 loop : -0.83 (0.14), residues: 1853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 27 HIS 0.006 0.001 HIS a 109 PHE 0.012 0.001 PHE b 128 TYR 0.014 0.001 TYR F 69 ARG 0.005 0.000 ARG B 30 Details of bonding type rmsd hydrogen bonds : bond 0.03551 ( 875) hydrogen bonds : angle 5.15269 ( 2469) covalent geometry : bond 0.00252 (26319) covalent geometry : angle 0.57052 (35755) *********************** 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 767 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 675 time to evaluate : 2.777 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8583 (p90) cc_final: 0.8165 (p90) REVERT: A 89 MET cc_start: 0.7804 (mtt) cc_final: 0.7321 (mtp) REVERT: A 235 GLU cc_start: 0.8405 (mt-10) cc_final: 0.8156 (mt-10) REVERT: A 251 MET cc_start: 0.8597 (mmt) cc_final: 0.8284 (mmt) REVERT: A 307 LYS cc_start: 0.8672 (tptt) cc_final: 0.8095 (mptt) REVERT: B 64 ILE cc_start: 0.8387 (mt) cc_final: 0.8107 (mm) REVERT: B 69 TYR cc_start: 0.9086 (p90) cc_final: 0.8526 (p90) REVERT: B 130 GLU cc_start: 0.8595 (tp30) cc_final: 0.8318 (tp30) REVERT: B 159 ASP cc_start: 0.8191 (t0) cc_final: 0.7872 (t0) REVERT: B 251 MET cc_start: 0.8176 (mmm) cc_final: 0.7896 (mtp) REVERT: B 274 ASP cc_start: 0.8309 (t0) cc_final: 0.8089 (t70) REVERT: B 277 ASP cc_start: 0.8296 (t0) cc_final: 0.7512 (t0) REVERT: B 296 GLU cc_start: 0.8315 (tp30) cc_final: 0.7568 (tp30) REVERT: B 307 LYS cc_start: 0.9225 (ttpp) cc_final: 0.8802 (tptt) REVERT: C 130 GLU cc_start: 0.8713 (mm-30) cc_final: 0.8315 (tp30) REVERT: C 324 GLU cc_start: 0.8485 (mm-30) cc_final: 0.7012 (pt0) REVERT: D 41 PHE cc_start: 0.7697 (m-80) cc_final: 0.7202 (m-80) REVERT: D 307 LYS cc_start: 0.8878 (tttm) cc_final: 0.7971 (mptt) REVERT: D 316 TYR cc_start: 0.8383 (OUTLIER) cc_final: 0.7447 (t80) REVERT: D 324 GLU cc_start: 0.8582 (mm-30) cc_final: 0.7033 (tt0) REVERT: E 15 ARG cc_start: 0.8395 (mtt-85) cc_final: 0.8189 (mtt-85) REVERT: E 60 GLN cc_start: 0.8477 (mt0) cc_final: 0.7680 (mm110) REVERT: E 111 ASP cc_start: 0.8853 (t0) cc_final: 0.8633 (m-30) REVERT: E 119 MET cc_start: 0.8645 (tmm) cc_final: 0.8431 (tmm) REVERT: E 176 MET cc_start: 0.8809 (mmm) cc_final: 0.8216 (mmm) REVERT: E 283 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.7603 (tpp) REVERT: F 69 TYR cc_start: 0.8212 (p90) cc_final: 0.7847 (p90) REVERT: F 130 GLU cc_start: 0.8201 (tp30) cc_final: 0.7839 (tp30) REVERT: F 178 MET cc_start: 0.8223 (mmt) cc_final: 0.7966 (mtt) REVERT: F 307 LYS cc_start: 0.8907 (tptp) cc_final: 0.8343 (mptt) REVERT: F 333 SER cc_start: 0.7987 (m) cc_final: 0.7647 (p) REVERT: G 64 ILE cc_start: 0.7595 (OUTLIER) cc_final: 0.7255 (pt) REVERT: G 75 LYS cc_start: 0.8599 (OUTLIER) cc_final: 0.8121 (mtpp) REVERT: G 213 VAL cc_start: 0.9262 (t) cc_final: 0.9027 (m) REVERT: G 289 MET cc_start: 0.8649 (tmm) cc_final: 0.8363 (ppp) REVERT: G 324 GLU cc_start: 0.8124 (mm-30) cc_final: 0.6848 (tt0) REVERT: G 333 SER cc_start: 0.8742 (m) cc_final: 0.8480 (p) REVERT: G 343 ASP cc_start: 0.8733 (t0) cc_final: 0.8394 (t0) REVERT: a 49 GLU cc_start: 0.8091 (mp0) cc_final: 0.7776 (mp0) REVERT: a 78 VAL cc_start: 0.9520 (t) cc_final: 0.9318 (p) REVERT: a 95 SER cc_start: 0.9467 (p) cc_final: 0.9198 (t) REVERT: b 137 ASN cc_start: 0.8310 (m-40) cc_final: 0.8100 (m-40) REVERT: c 36 ASP cc_start: 0.7103 (p0) cc_final: 0.6806 (m-30) REVERT: c 49 GLU cc_start: 0.8062 (mp0) cc_final: 0.7741 (mp0) REVERT: c 95 SER cc_start: 0.9218 (p) cc_final: 0.8920 (m) REVERT: c 132 ASN cc_start: 0.7652 (OUTLIER) cc_final: 0.7411 (t0) REVERT: c 138 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7545 (tp) REVERT: d 34 GLU cc_start: 0.5717 (mm-30) cc_final: 0.5384 (mm-30) REVERT: d 37 ILE cc_start: 0.8455 (mt) cc_final: 0.8245 (mt) REVERT: d 49 GLU cc_start: 0.8292 (mp0) cc_final: 0.7829 (mp0) REVERT: d 91 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8151 (mm110) REVERT: d 102 TYR cc_start: 0.8945 (m-80) cc_final: 0.8583 (m-80) REVERT: d 103 ILE cc_start: 0.8409 (OUTLIER) cc_final: 0.8146 (mp) REVERT: e 21 ASP cc_start: 0.9067 (p0) cc_final: 0.8789 (p0) REVERT: e 34 GLU cc_start: 0.4917 (mm-30) cc_final: 0.4623 (mm-30) REVERT: e 40 GLU cc_start: 0.5731 (OUTLIER) cc_final: 0.5077 (tt0) REVERT: e 91 GLN cc_start: 0.9092 (mm-40) cc_final: 0.8855 (mm-40) REVERT: f 30 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8006 (mp) REVERT: f 118 LEU cc_start: 0.9083 (tp) cc_final: 0.8647 (tt) REVERT: g 15 TYR cc_start: 0.8113 (m-80) cc_final: 0.7262 (m-80) outliers start: 92 outliers final: 63 residues processed: 724 average time/residue: 0.3288 time to fit residues: 387.3571 Evaluate side-chains 722 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 649 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 328 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 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 B residue 353 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 144 VAL Chi-restraints excluded: chain C residue 165 THR 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 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 315 ASP Chi-restraints excluded: chain E residue 316 TYR 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 G residue 39 ILE Chi-restraints excluded: chain G residue 64 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 300 CYS Chi-restraints excluded: chain G residue 316 TYR 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 103 ILE Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain c residue 138 LEU 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 119 ASP Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 119 ASP Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 82 GLN Chi-restraints excluded: chain f residue 103 ILE Chi-restraints excluded: chain f residue 108 ASN 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 278 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 chunk 224 optimal weight: 4.9990 chunk 277 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 154 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 27 optimal weight: 10.0000 chunk 188 optimal weight: 8.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 ** C 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 285 GLN G 70 ASN ** a 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 91 GLN ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 91 GLN ** 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** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.087992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.078300 restraints weight = 50048.745| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.67 r_work: 0.2887 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 26319 Z= 0.220 Angle : 0.646 12.635 35755 Z= 0.327 Chirality : 0.045 0.246 3876 Planarity : 0.004 0.045 4683 Dihedral : 5.656 59.737 3616 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.98 % Allowed : 21.73 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.15), residues: 3274 helix: 0.81 (0.22), residues: 600 sheet: -0.73 (0.18), residues: 871 loop : -0.96 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 27 HIS 0.008 0.001 HIS C 121 PHE 0.020 0.002 PHE g 31 TYR 0.017 0.002 TYR D 69 ARG 0.006 0.000 ARG E 264 Details of bonding type rmsd hydrogen bonds : bond 0.03861 ( 875) hydrogen bonds : angle 5.34418 ( 2469) covalent geometry : bond 0.00526 (26319) covalent geometry : angle 0.64648 (35755) *********************** 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 748 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 643 time to evaluate : 3.151 Fit side-chains revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8775 (p90) cc_final: 0.8415 (p90) REVERT: A 89 MET cc_start: 0.7927 (mtt) cc_final: 0.7438 (mtp) REVERT: A 207 ASP cc_start: 0.9074 (m-30) cc_final: 0.8814 (m-30) REVERT: A 227 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7870 (mtp) REVERT: A 235 GLU cc_start: 0.8711 (mt-10) cc_final: 0.8484 (mt-10) REVERT: A 268 ASN cc_start: 0.8937 (t0) cc_final: 0.8659 (t0) REVERT: A 296 GLU cc_start: 0.8963 (tp30) cc_final: 0.8674 (tp30) REVERT: A 307 LYS cc_start: 0.8809 (tptt) cc_final: 0.8298 (mppt) REVERT: B 64 ILE cc_start: 0.8583 (mt) cc_final: 0.8333 (mm) REVERT: B 159 ASP cc_start: 0.8399 (t0) cc_final: 0.8020 (t0) REVERT: B 251 MET cc_start: 0.8658 (mmm) cc_final: 0.8312 (mtp) REVERT: B 277 ASP cc_start: 0.8552 (t0) cc_final: 0.7718 (t0) REVERT: B 296 GLU cc_start: 0.8576 (tp30) cc_final: 0.7826 (tp30) REVERT: B 307 LYS cc_start: 0.9280 (ttpp) cc_final: 0.8836 (tptt) REVERT: C 130 GLU cc_start: 0.9013 (mm-30) cc_final: 0.8491 (tp30) REVERT: C 219 GLU cc_start: 0.8725 (mp0) cc_final: 0.8226 (mp0) REVERT: C 324 GLU cc_start: 0.8694 (mm-30) cc_final: 0.7070 (pt0) REVERT: D 58 ASN cc_start: 0.8531 (OUTLIER) cc_final: 0.8298 (m110) REVERT: D 296 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8399 (mm-30) REVERT: D 307 LYS cc_start: 0.8962 (tttm) cc_final: 0.8085 (mptt) REVERT: D 316 TYR cc_start: 0.8619 (OUTLIER) cc_final: 0.7490 (t80) REVERT: D 324 GLU cc_start: 0.8743 (mm-30) cc_final: 0.7102 (tt0) REVERT: E 15 ARG cc_start: 0.8458 (mtt-85) cc_final: 0.8256 (mtt-85) REVERT: E 60 GLN cc_start: 0.8712 (mt0) cc_final: 0.7663 (mm-40) REVERT: E 111 ASP cc_start: 0.9080 (t0) cc_final: 0.8775 (m-30) REVERT: E 119 MET cc_start: 0.8830 (tmm) cc_final: 0.8628 (tmm) REVERT: E 283 MET cc_start: 0.8966 (OUTLIER) cc_final: 0.7976 (tpp) REVERT: E 307 LYS cc_start: 0.6299 (mptt) cc_final: 0.5124 (mptt) REVERT: F 69 TYR cc_start: 0.8490 (p90) cc_final: 0.7899 (p90) REVERT: F 130 GLU cc_start: 0.8482 (tp30) cc_final: 0.8159 (tp30) REVERT: F 178 MET cc_start: 0.8414 (mmt) cc_final: 0.8099 (mtt) REVERT: F 209 TRP cc_start: 0.8842 (t-100) cc_final: 0.8164 (t-100) REVERT: F 246 GLU cc_start: 0.8228 (tp30) cc_final: 0.8005 (tp30) REVERT: F 251 MET cc_start: 0.8615 (mmt) cc_final: 0.7962 (mmt) REVERT: F 307 LYS cc_start: 0.8991 (tptp) cc_final: 0.8241 (mptt) REVERT: F 324 GLU cc_start: 0.8556 (mm-30) cc_final: 0.7412 (pt0) REVERT: F 333 SER cc_start: 0.8194 (m) cc_final: 0.7843 (p) REVERT: G 75 LYS cc_start: 0.8729 (OUTLIER) cc_final: 0.8419 (mtpp) REVERT: G 213 VAL cc_start: 0.9318 (t) cc_final: 0.9057 (m) REVERT: G 324 GLU cc_start: 0.8379 (mm-30) cc_final: 0.6998 (tt0) REVERT: G 333 SER cc_start: 0.8864 (m) cc_final: 0.8611 (p) REVERT: G 343 ASP cc_start: 0.8918 (t0) cc_final: 0.8589 (t0) REVERT: a 49 GLU cc_start: 0.8370 (mp0) cc_final: 0.8053 (mp0) REVERT: a 78 VAL cc_start: 0.9513 (t) cc_final: 0.9304 (p) REVERT: a 115 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.6731 (p90) REVERT: b 137 ASN cc_start: 0.8865 (m-40) cc_final: 0.8634 (m-40) REVERT: c 36 ASP cc_start: 0.7351 (p0) cc_final: 0.6867 (m-30) REVERT: c 49 GLU cc_start: 0.8398 (mp0) cc_final: 0.8092 (mp0) REVERT: c 95 SER cc_start: 0.9273 (p) cc_final: 0.9055 (t) REVERT: c 132 ASN cc_start: 0.8155 (OUTLIER) cc_final: 0.7820 (t0) REVERT: c 138 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7582 (tp) REVERT: d 37 ILE cc_start: 0.8633 (mt) cc_final: 0.8419 (mt) REVERT: d 49 GLU cc_start: 0.8517 (mp0) cc_final: 0.8016 (mp0) REVERT: d 91 GLN cc_start: 0.8855 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: d 103 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8226 (mp) REVERT: e 21 ASP cc_start: 0.9139 (p0) cc_final: 0.8815 (p0) REVERT: e 40 GLU cc_start: 0.6084 (OUTLIER) cc_final: 0.5538 (tt0) REVERT: e 91 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8940 (mm-40) REVERT: e 108 ASN cc_start: 0.8884 (t0) cc_final: 0.8511 (t0) REVERT: f 30 ILE cc_start: 0.8722 (OUTLIER) cc_final: 0.8228 (mp) REVERT: f 118 LEU cc_start: 0.9197 (tp) cc_final: 0.8828 (tp) outliers start: 105 outliers final: 81 residues processed: 697 average time/residue: 0.3314 time to fit residues: 376.8981 Evaluate side-chains 717 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 624 time to evaluate : 2.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LEU 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 289 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 101 THR 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 B residue 353 MET Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 66 GLU 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 D residue 10 LEU Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 193 SER Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain D residue 328 VAL Chi-restraints excluded: chain E residue 25 LEU 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 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 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 300 CYS 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 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 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 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 86 ILE Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain c residue 137 ASN Chi-restraints excluded: chain c residue 138 LEU 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 119 ASP Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 86 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 82 GLN Chi-restraints excluded: chain f residue 103 ILE Chi-restraints excluded: chain f residue 108 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 204 optimal weight: 1.9990 chunk 323 optimal weight: 0.9980 chunk 247 optimal weight: 7.9990 chunk 138 optimal weight: 2.9990 chunk 299 optimal weight: 5.9990 chunk 152 optimal weight: 9.9990 chunk 149 optimal weight: 0.0050 chunk 101 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 49 optimal weight: 7.9990 chunk 294 optimal weight: 9.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- 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 60 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 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN G 138 GLN ** 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.088879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.079227 restraints weight = 49708.801| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.68 r_work: 0.2915 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 26319 Z= 0.154 Angle : 0.626 14.252 35755 Z= 0.315 Chirality : 0.044 0.225 3876 Planarity : 0.004 0.046 4683 Dihedral : 5.555 58.270 3616 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.22 % Allowed : 22.57 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.15), residues: 3274 helix: 0.81 (0.22), residues: 602 sheet: -0.66 (0.18), residues: 817 loop : -0.92 (0.14), residues: 1855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 27 HIS 0.008 0.001 HIS a 109 PHE 0.019 0.001 PHE g 31 TYR 0.015 0.001 TYR A 250 ARG 0.005 0.000 ARG E 264 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 875) hydrogen bonds : angle 5.26300 ( 2469) covalent geometry : bond 0.00369 (26319) covalent geometry : angle 0.62590 (35755) ********************** 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 727 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 642 time to evaluate : 2.798 Fit side-chains REVERT: A 69 TYR cc_start: 0.8731 (p90) cc_final: 0.8382 (p90) REVERT: A 89 MET cc_start: 0.7948 (mtt) cc_final: 0.7462 (mtp) REVERT: A 130 GLU cc_start: 0.8760 (tp30) cc_final: 0.8552 (tp30) REVERT: A 235 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8422 (mt-10) REVERT: A 268 ASN cc_start: 0.8934 (t0) cc_final: 0.8662 (t0) REVERT: A 296 GLU cc_start: 0.8977 (tp30) cc_final: 0.8698 (tp30) REVERT: A 307 LYS cc_start: 0.8795 (tptt) cc_final: 0.8268 (mppt) REVERT: A 324 GLU cc_start: 0.8638 (mm-30) cc_final: 0.7527 (tt0) REVERT: B 64 ILE cc_start: 0.8563 (mt) cc_final: 0.8329 (mm) REVERT: B 69 TYR cc_start: 0.9135 (p90) cc_final: 0.8621 (p90) REVERT: B 159 ASP cc_start: 0.8386 (t0) cc_final: 0.8014 (t0) REVERT: B 251 MET cc_start: 0.8538 (mmm) cc_final: 0.8167 (mtp) REVERT: B 277 ASP cc_start: 0.8499 (t0) cc_final: 0.7733 (t0) REVERT: B 296 GLU cc_start: 0.8567 (tp30) cc_final: 0.7817 (tp30) REVERT: B 307 LYS cc_start: 0.9277 (ttpp) cc_final: 0.8825 (tptt) REVERT: C 41 PHE cc_start: 0.8303 (m-10) cc_final: 0.8075 (m-80) REVERT: C 130 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8461 (tp30) REVERT: C 219 GLU cc_start: 0.8732 (mp0) cc_final: 0.8526 (mp0) REVERT: C 249 GLN cc_start: 0.8344 (tp40) cc_final: 0.7980 (mt0) REVERT: C 251 MET cc_start: 0.8907 (mmt) cc_final: 0.8605 (mmp) REVERT: C 324 GLU cc_start: 0.8680 (mm-30) cc_final: 0.7087 (pt0) REVERT: D 58 ASN cc_start: 0.8443 (OUTLIER) cc_final: 0.8138 (m-40) REVERT: D 209 TRP cc_start: 0.8860 (t-100) cc_final: 0.8092 (t-100) REVERT: D 251 MET cc_start: 0.8230 (ttm) cc_final: 0.7593 (ttm) REVERT: D 296 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8383 (mm-30) REVERT: D 307 LYS cc_start: 0.8958 (tttm) cc_final: 0.8048 (mptt) REVERT: D 316 TYR cc_start: 0.8490 (OUTLIER) cc_final: 0.7968 (t80) REVERT: D 324 GLU cc_start: 0.8742 (mm-30) cc_final: 0.7121 (tt0) REVERT: E 15 ARG cc_start: 0.8373 (mtt-85) cc_final: 0.8157 (mtt-85) REVERT: E 60 GLN cc_start: 0.8554 (mt0) cc_final: 0.7573 (mm110) REVERT: E 111 ASP cc_start: 0.9058 (t0) cc_final: 0.8755 (m-30) REVERT: E 119 MET cc_start: 0.8816 (tmm) cc_final: 0.8613 (tmm) REVERT: E 176 MET cc_start: 0.8933 (mmm) cc_final: 0.8473 (mmm) REVERT: E 251 MET cc_start: 0.8428 (mmm) cc_final: 0.7511 (mmm) REVERT: E 283 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.7857 (tpp) REVERT: E 307 LYS cc_start: 0.6181 (mptt) cc_final: 0.4863 (mptt) REVERT: F 69 TYR cc_start: 0.8470 (p90) cc_final: 0.7774 (p90) REVERT: F 130 GLU cc_start: 0.8469 (tp30) cc_final: 0.8157 (tp30) REVERT: F 178 MET cc_start: 0.8392 (mmt) cc_final: 0.8098 (mtt) REVERT: F 209 TRP cc_start: 0.8824 (t-100) cc_final: 0.8161 (t-100) REVERT: F 251 MET cc_start: 0.8562 (mmt) cc_final: 0.8060 (mmt) REVERT: F 307 LYS cc_start: 0.8950 (tptp) cc_final: 0.8363 (mptt) REVERT: F 333 SER cc_start: 0.8114 (m) cc_final: 0.7776 (p) REVERT: G 75 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8400 (mtpp) REVERT: G 213 VAL cc_start: 0.9308 (t) cc_final: 0.9055 (m) REVERT: G 283 MET cc_start: 0.9038 (tpp) cc_final: 0.8672 (tpp) REVERT: G 289 MET cc_start: 0.8741 (tmm) cc_final: 0.8431 (ppp) REVERT: G 324 GLU cc_start: 0.8343 (mm-30) cc_final: 0.6937 (tt0) REVERT: G 333 SER cc_start: 0.8859 (m) cc_final: 0.8651 (p) REVERT: G 343 ASP cc_start: 0.8947 (t0) cc_final: 0.8706 (t0) REVERT: a 49 GLU cc_start: 0.8317 (mp0) cc_final: 0.8022 (mp0) REVERT: a 82 GLN cc_start: 0.8695 (pm20) cc_final: 0.8080 (pm20) REVERT: a 115 HIS cc_start: 0.7561 (OUTLIER) cc_final: 0.6767 (p90) REVERT: b 123 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8305 (mtmm) REVERT: c 36 ASP cc_start: 0.7255 (p0) cc_final: 0.6820 (m-30) REVERT: c 49 GLU cc_start: 0.8366 (mp0) cc_final: 0.8049 (mp0) REVERT: c 95 SER cc_start: 0.9260 (p) cc_final: 0.9045 (t) REVERT: c 132 ASN cc_start: 0.8111 (OUTLIER) cc_final: 0.7791 (t0) REVERT: c 138 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7510 (tp) REVERT: d 37 ILE cc_start: 0.8624 (mt) cc_final: 0.8416 (mt) REVERT: d 49 GLU cc_start: 0.8511 (mp0) cc_final: 0.8027 (mp0) REVERT: d 91 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.7946 (mp10) REVERT: d 103 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8187 (mp) REVERT: e 21 ASP cc_start: 0.9129 (p0) cc_final: 0.8820 (p0) REVERT: e 40 GLU cc_start: 0.6074 (OUTLIER) cc_final: 0.5460 (tt0) REVERT: e 91 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8758 (mm110) REVERT: e 108 ASN cc_start: 0.8789 (t0) cc_final: 0.8410 (t0) REVERT: f 30 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8171 (mp) REVERT: f 118 LEU cc_start: 0.9159 (tp) cc_final: 0.8802 (tp) outliers start: 85 outliers final: 71 residues processed: 689 average time/residue: 0.3343 time to fit residues: 376.4134 Evaluate side-chains 714 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 632 time to evaluate : 2.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 328 VAL 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 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 B residue 353 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 D residue 58 ASN 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 25 LEU 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 66 GLU Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 300 CYS 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 190 SER Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 316 TYR 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 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 86 ILE Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain c residue 137 ASN Chi-restraints excluded: chain c residue 138 LEU 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 119 ASP Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 86 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 82 GLN Chi-restraints excluded: chain f residue 103 ILE Chi-restraints excluded: chain f residue 108 ASN 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 74 optimal weight: 7.9990 chunk 193 optimal weight: 2.9990 chunk 294 optimal weight: 20.0000 chunk 165 optimal weight: 8.9990 chunk 128 optimal weight: 9.9990 chunk 214 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 67 optimal weight: 0.5980 chunk 225 optimal weight: 10.0000 chunk 120 optimal weight: 9.9990 chunk 306 optimal weight: 7.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- 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 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 GLN 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 ** 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 ** f 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 125 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.085026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.075311 restraints weight = 50743.593| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.68 r_work: 0.2838 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 26319 Z= 0.285 Angle : 0.704 13.766 35755 Z= 0.356 Chirality : 0.047 0.246 3876 Planarity : 0.005 0.045 4683 Dihedral : 5.884 56.289 3616 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 3.67 % Allowed : 22.53 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.14), residues: 3274 helix: 0.53 (0.21), residues: 608 sheet: -0.77 (0.18), residues: 834 loop : -1.09 (0.14), residues: 1832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 27 HIS 0.011 0.002 HIS C 121 PHE 0.019 0.002 PHE b 128 TYR 0.022 0.002 TYR D 69 ARG 0.006 0.001 ARG F 112 Details of bonding type rmsd hydrogen bonds : bond 0.04073 ( 875) hydrogen bonds : angle 5.50143 ( 2469) covalent geometry : bond 0.00681 (26319) covalent geometry : angle 0.70408 (35755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24968.21 seconds wall clock time: 431 minutes 7.93 seconds (25867.93 seconds total)