Starting phenix.real_space_refine on Sun Jun 22 05:31:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vji_43282/06_2025/8vji_43282.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vji_43282/06_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_43282/06_2025/8vji_43282.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vji_43282/06_2025/8vji_43282.map" model { file = "/net/cci-nas-00/data/ceres_data/8vji_43282/06_2025/8vji_43282.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vji_43282/06_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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 25.24, per 1000 atoms: 0.98 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: 6.70 Conformation dependent library (CDL) restraints added in 3.4 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: 3.76 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: 10.83 Time building geometry restraints manager: 7.92 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: 2065.440 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: 0.040 Extract box with map and model: 1.170 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 71.810 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.130 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:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 2143.390 ------------------------------------------------------------------------------- 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 : 2.811 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: 0.3613 time to fit residues: 462.1402 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 : 2.679 ------------------------------------------------------------------------------- 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 = 32)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.080277 restraints weight = 48822.540| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.68 r_work: 0.2937 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 3.60 % Allowed : 14.31 % 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 6.14610 ( 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 842 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 747 time to evaluate : 2.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8481 (ptpt) cc_final: 0.8214 (ptpp) REVERT: A 69 TYR cc_start: 0.8519 (p90) cc_final: 0.8158 (p90) REVERT: A 89 MET cc_start: 0.7531 (mtt) cc_final: 0.6931 (mtp) REVERT: A 263 MET cc_start: 0.8359 (mtm) cc_final: 0.8094 (mtp) REVERT: A 307 LYS cc_start: 0.8965 (tptt) cc_final: 0.8505 (mppt) REVERT: A 324 GLU cc_start: 0.8616 (mm-30) cc_final: 0.7580 (tt0) REVERT: A 329 GLU cc_start: 0.7862 (mt-10) cc_final: 0.7650 (tt0) REVERT: B 126 GLU cc_start: 0.8474 (tt0) cc_final: 0.8266 (mt-10) REVERT: B 130 GLU cc_start: 0.8555 (tp30) cc_final: 0.8272 (tp30) REVERT: B 147 GLN cc_start: 0.8575 (mt0) cc_final: 0.8321 (tt0) REVERT: B 159 ASP cc_start: 0.8264 (t0) cc_final: 0.8050 (t0) REVERT: B 186 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8049 (tm-30) REVERT: B 268 ASN cc_start: 0.8991 (t0) cc_final: 0.8459 (t0) REVERT: B 275 GLN cc_start: 0.8094 (mt0) cc_final: 0.7856 (mm-40) REVERT: B 277 ASP cc_start: 0.8470 (t0) cc_final: 0.7604 (t0) REVERT: B 296 GLU cc_start: 0.8055 (tp30) cc_final: 0.7356 (tp30) REVERT: B 307 LYS cc_start: 0.9275 (ttpp) cc_final: 0.8861 (tptt) REVERT: B 323 GLN cc_start: 0.8357 (tt0) cc_final: 0.7966 (tt0) REVERT: C 15 ARG cc_start: 0.8561 (mtp85) cc_final: 0.8321 (tpp80) REVERT: C 32 ILE cc_start: 0.9017 (tp) cc_final: 0.8810 (pt) REVERT: C 324 GLU cc_start: 0.8620 (mm-30) cc_final: 0.6939 (pt0) REVERT: D 58 ASN cc_start: 0.8387 (OUTLIER) cc_final: 0.8072 (m110) REVERT: D 219 GLU cc_start: 0.8527 (mp0) cc_final: 0.8272 (mp0) REVERT: D 307 LYS cc_start: 0.9010 (tttm) cc_final: 0.8367 (mptt) REVERT: D 332 MET cc_start: 0.8696 (OUTLIER) cc_final: 0.8314 (ttm) REVERT: D 353 MET cc_start: 0.8706 (mtp) cc_final: 0.8445 (mtt) REVERT: E 30 ARG cc_start: 0.8135 (mtm110) cc_final: 0.7934 (mtm110) REVERT: E 60 GLN cc_start: 0.8609 (mt0) cc_final: 0.8058 (mm-40) REVERT: E 111 ASP cc_start: 0.8939 (t0) cc_final: 0.8641 (m-30) REVERT: E 130 GLU cc_start: 0.8456 (tp30) cc_final: 0.8204 (tp30) REVERT: E 329 GLU cc_start: 0.8556 (mp0) cc_final: 0.8313 (mt-10) REVERT: E 339 MET cc_start: 0.8297 (mmm) cc_final: 0.8010 (mmp) REVERT: F 130 GLU cc_start: 0.8198 (tp30) cc_final: 0.7799 (tp30) REVERT: F 178 MET cc_start: 0.8325 (mmt) cc_final: 0.7960 (mtt) REVERT: F 307 LYS cc_start: 0.8889 (tptp) cc_final: 0.8210 (mptt) REVERT: F 324 GLU cc_start: 0.8575 (mm-30) cc_final: 0.7220 (pt0) REVERT: G 15 ARG cc_start: 0.7568 (mtm180) cc_final: 0.6693 (tpt170) REVERT: G 75 LYS cc_start: 0.8545 (mtpt) cc_final: 0.8255 (mtpp) REVERT: G 147 GLN cc_start: 0.7904 (mt0) cc_final: 0.7235 (pt0) REVERT: G 213 VAL cc_start: 0.9377 (t) cc_final: 0.9136 (m) REVERT: G 241 LEU cc_start: 0.9027 (tt) cc_final: 0.8697 (tt) REVERT: G 262 ARG cc_start: 0.8229 (ptt-90) cc_final: 0.6874 (mmt180) REVERT: G 283 MET cc_start: 0.9078 (tpp) cc_final: 0.8389 (tpp) REVERT: G 324 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7297 (tt0) REVERT: G 333 SER cc_start: 0.8893 (m) cc_final: 0.8617 (p) REVERT: G 353 MET cc_start: 0.8082 (mmm) cc_final: 0.7750 (mmm) REVERT: a 49 GLU cc_start: 0.7871 (mp0) cc_final: 0.7575 (mp0) REVERT: a 62 MET cc_start: 0.8769 (mmp) cc_final: 0.8502 (mmt) REVERT: a 95 SER cc_start: 0.9509 (p) cc_final: 0.9243 (t) REVERT: a 133 ILE cc_start: 0.9089 (mt) cc_final: 0.8862 (mm) REVERT: b 36 ASP cc_start: 0.7203 (p0) cc_final: 0.6970 (p0) REVERT: b 91 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8213 (mm-40) REVERT: c 26 GLU cc_start: 0.8511 (pm20) cc_final: 0.8252 (mm-30) REVERT: c 34 GLU cc_start: 0.5964 (mm-30) cc_final: 0.5499 (mm-30) REVERT: c 36 ASP cc_start: 0.7124 (p0) cc_final: 0.6586 (p0) REVERT: c 49 GLU cc_start: 0.8040 (mp0) cc_final: 0.7699 (mp0) REVERT: c 123 LYS cc_start: 0.9095 (mttm) cc_final: 0.8875 (mtpt) REVERT: c 132 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7127 (t0) REVERT: d 29 GLN cc_start: 0.7356 (mt0) cc_final: 0.6974 (mm-40) REVERT: d 37 ILE cc_start: 0.8567 (mt) cc_final: 0.8306 (mt) REVERT: d 49 GLU cc_start: 0.8257 (mp0) cc_final: 0.7925 (mp0) REVERT: d 62 MET cc_start: 0.8491 (mmm) cc_final: 0.8111 (mmt) REVERT: d 91 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8310 (mm-40) REVERT: e 21 ASP cc_start: 0.9074 (p0) cc_final: 0.8781 (p0) REVERT: e 103 ILE cc_start: 0.8597 (tp) cc_final: 0.8263 (tp) REVERT: f 34 GLU cc_start: 0.6114 (mm-30) cc_final: 0.5751 (tp30) REVERT: f 36 ASP cc_start: 0.7632 (p0) cc_final: 0.7426 (p0) REVERT: f 95 SER cc_start: 0.9132 (p) cc_final: 0.8916 (t) REVERT: f 118 LEU cc_start: 0.8985 (tp) cc_final: 0.8654 (tt) REVERT: g 15 TYR cc_start: 0.8327 (m-80) cc_final: 0.7660 (m-80) REVERT: g 84 VAL cc_start: 0.9295 (p) cc_final: 0.9031 (m) REVERT: g 119 ASP cc_start: 0.9140 (OUTLIER) cc_final: 0.8906 (p0) REVERT: g 138 LEU cc_start: 0.9324 (mt) cc_final: 0.9057 (mt) outliers start: 95 outliers final: 59 residues processed: 796 average time/residue: 0.3673 time to fit residues: 477.5600 Evaluate side-chains 716 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 650 time to evaluate : 4.265 ------------------------------------------------------------------------------- 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 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: 10.0000 chunk 141 optimal weight: 9.9990 chunk 310 optimal weight: 3.9990 chunk 317 optimal weight: 5.9990 chunk 40 optimal weight: 0.0770 chunk 198 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 318 optimal weight: 10.0000 chunk 265 optimal weight: 9.9990 chunk 321 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 overall best weight: 2.7944 ------------------------------------------------------------------------------- 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 ** 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 = 0.3199 r_free = 0.3199 target = 0.088916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.079091 restraints weight = 49138.181| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.67 r_work: 0.2927 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 26319 Z= 0.169 Angle : 0.606 10.444 35755 Z= 0.320 Chirality : 0.045 0.230 3876 Planarity : 0.004 0.052 4683 Dihedral : 6.316 59.093 3625 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.73 % Allowed : 15.68 % Favored : 79.59 % 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: 0.61 (0.21), residues: 606 sheet: -0.53 (0.17), residues: 895 loop : -0.92 (0.14), residues: 1773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 221 HIS 0.006 0.001 HIS e 109 PHE 0.018 0.001 PHE b 128 TYR 0.016 0.001 TYR D 69 ARG 0.005 0.000 ARG E 15 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 875) hydrogen bonds : angle 5.71741 ( 2469) covalent geometry : bond 0.00400 (26319) covalent geometry : angle 0.60625 (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 805 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 680 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LYS cc_start: 0.8542 (ptpt) cc_final: 0.7011 (mmtt) REVERT: A 69 TYR cc_start: 0.8600 (p90) cc_final: 0.8207 (p90) REVERT: A 89 MET cc_start: 0.7605 (mtt) cc_final: 0.7008 (mtp) REVERT: A 207 ASP cc_start: 0.9101 (m-30) cc_final: 0.8845 (m-30) REVERT: A 235 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8482 (mt-10) REVERT: A 263 MET cc_start: 0.8543 (mtm) cc_final: 0.8291 (mtp) REVERT: A 304 ILE cc_start: 0.8647 (mm) cc_final: 0.8436 (mt) REVERT: A 307 LYS cc_start: 0.8950 (tptt) cc_final: 0.8414 (mppt) REVERT: B 126 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8544 (mt-10) REVERT: B 130 GLU cc_start: 0.8762 (tp30) cc_final: 0.8492 (tp30) REVERT: B 147 GLN cc_start: 0.8644 (mt0) cc_final: 0.8441 (tt0) REVERT: B 159 ASP cc_start: 0.8386 (t0) cc_final: 0.8079 (t0) REVERT: B 268 ASN cc_start: 0.9071 (t0) cc_final: 0.8452 (t0) REVERT: B 274 ASP cc_start: 0.8123 (t70) cc_final: 0.7894 (t0) REVERT: B 275 GLN cc_start: 0.8236 (mt0) cc_final: 0.7935 (mm-40) REVERT: B 277 ASP cc_start: 0.8625 (t0) cc_final: 0.7803 (t0) REVERT: B 296 GLU cc_start: 0.8321 (tp30) cc_final: 0.7460 (tp30) REVERT: B 307 LYS cc_start: 0.9289 (ttpp) cc_final: 0.8886 (tptt) REVERT: B 323 GLN cc_start: 0.8448 (tt0) cc_final: 0.8097 (tt0) REVERT: C 15 ARG cc_start: 0.8667 (mtp85) cc_final: 0.8440 (tpp80) REVERT: C 36 GLU cc_start: 0.9258 (mp0) cc_final: 0.9032 (mp0) REVERT: C 130 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8542 (tp30) REVERT: C 324 GLU cc_start: 0.8619 (mm-30) cc_final: 0.6920 (pt0) REVERT: D 37 ASP cc_start: 0.8714 (t70) cc_final: 0.8381 (t0) REVERT: D 130 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8471 (mm-30) REVERT: D 219 GLU cc_start: 0.8800 (mp0) cc_final: 0.8553 (mp0) REVERT: D 274 ASP cc_start: 0.8357 (t70) cc_final: 0.8020 (t70) REVERT: D 307 LYS cc_start: 0.9025 (tttm) cc_final: 0.8258 (mptt) REVERT: D 324 GLU cc_start: 0.8676 (mm-30) cc_final: 0.7139 (tt0) REVERT: D 332 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8555 (ttm) REVERT: D 353 MET cc_start: 0.8906 (mtp) cc_final: 0.8659 (mtt) REVERT: E 60 GLN cc_start: 0.8832 (mt0) cc_final: 0.8054 (mm-40) REVERT: E 65 LYS cc_start: 0.5264 (mmtm) cc_final: 0.4760 (mmtm) REVERT: E 111 ASP cc_start: 0.9061 (t0) cc_final: 0.8765 (m-30) REVERT: E 329 GLU cc_start: 0.8797 (mp0) cc_final: 0.8580 (mt-10) REVERT: E 339 MET cc_start: 0.8334 (mmm) cc_final: 0.8059 (mmp) REVERT: F 130 GLU cc_start: 0.8442 (tp30) cc_final: 0.8083 (tp30) REVERT: F 178 MET cc_start: 0.8396 (mmt) cc_final: 0.8031 (mtt) REVERT: F 251 MET cc_start: 0.8349 (mmm) cc_final: 0.8097 (mmt) REVERT: F 307 LYS cc_start: 0.8957 (tptp) cc_final: 0.8456 (mptt) REVERT: F 324 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7258 (pt0) REVERT: G 75 LYS cc_start: 0.8691 (mtpt) cc_final: 0.8293 (mtpp) REVERT: G 130 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8272 (tm-30) REVERT: G 213 VAL cc_start: 0.9363 (t) cc_final: 0.9111 (m) REVERT: G 324 GLU cc_start: 0.8525 (mm-30) cc_final: 0.7156 (tt0) REVERT: G 333 SER cc_start: 0.8894 (m) cc_final: 0.8593 (p) REVERT: G 353 MET cc_start: 0.8152 (mmm) cc_final: 0.7811 (mmm) REVERT: a 40 GLU cc_start: 0.6447 (OUTLIER) cc_final: 0.5872 (tt0) REVERT: a 49 GLU cc_start: 0.8173 (mp0) cc_final: 0.7829 (mp0) REVERT: a 62 MET cc_start: 0.8894 (mmp) cc_final: 0.8584 (mmt) REVERT: a 95 SER cc_start: 0.9511 (p) cc_final: 0.9242 (t) REVERT: a 123 LYS cc_start: 0.8864 (mtmm) cc_final: 0.8391 (mttp) REVERT: a 133 ILE cc_start: 0.9171 (mt) cc_final: 0.8961 (mm) REVERT: b 91 GLN cc_start: 0.8645 (OUTLIER) cc_final: 0.8303 (mm-40) REVERT: c 26 GLU cc_start: 0.8636 (pm20) cc_final: 0.8272 (mm-30) REVERT: c 34 GLU cc_start: 0.6489 (mm-30) cc_final: 0.5888 (mm-30) REVERT: c 36 ASP cc_start: 0.7276 (p0) cc_final: 0.6694 (p0) REVERT: c 49 GLU cc_start: 0.8421 (mp0) cc_final: 0.8094 (mp0) REVERT: c 123 LYS cc_start: 0.9138 (mttm) cc_final: 0.8931 (mtpt) REVERT: c 132 ASN cc_start: 0.7714 (OUTLIER) cc_final: 0.7278 (t0) REVERT: d 29 GLN cc_start: 0.7267 (mt0) cc_final: 0.6941 (mm-40) REVERT: d 36 ASP cc_start: 0.7486 (m-30) cc_final: 0.7278 (m-30) REVERT: d 37 ILE cc_start: 0.8664 (mt) cc_final: 0.8392 (mt) REVERT: d 49 GLU cc_start: 0.8477 (mp0) cc_final: 0.8096 (mp0) REVERT: d 91 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8307 (mm-40) REVERT: e 21 ASP cc_start: 0.9140 (p0) cc_final: 0.8836 (p0) REVERT: e 34 GLU cc_start: 0.5838 (mm-30) cc_final: 0.5512 (mm-30) REVERT: e 103 ILE cc_start: 0.8695 (tp) cc_final: 0.8423 (tp) REVERT: e 108 ASN cc_start: 0.8548 (t0) cc_final: 0.8285 (t0) REVERT: f 34 GLU cc_start: 0.6624 (mm-30) cc_final: 0.6121 (tp30) REVERT: f 36 ASP cc_start: 0.7632 (p0) cc_final: 0.7362 (p0) REVERT: f 95 SER cc_start: 0.9146 (p) cc_final: 0.8934 (t) REVERT: f 118 LEU cc_start: 0.9048 (tp) cc_final: 0.8736 (tt) REVERT: g 15 TYR cc_start: 0.8338 (m-80) cc_final: 0.7456 (m-80) REVERT: g 62 MET cc_start: 0.8626 (mmt) cc_final: 0.8371 (mmt) REVERT: g 66 ASP cc_start: 0.8936 (t0) cc_final: 0.8720 (t70) REVERT: g 84 VAL cc_start: 0.9295 (p) cc_final: 0.9036 (m) REVERT: g 119 ASP cc_start: 0.9295 (OUTLIER) cc_final: 0.9061 (p0) REVERT: g 138 LEU cc_start: 0.9301 (mt) cc_final: 0.9099 (mp) outliers start: 125 outliers final: 84 residues processed: 732 average time/residue: 0.3940 time to fit residues: 475.4831 Evaluate side-chains 720 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 629 time to evaluate : 2.915 ------------------------------------------------------------------------------- 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 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 99 LEU Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 39 ILE Chi-restraints excluded: chain C residue 69 TYR 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 70 ASN Chi-restraints excluded: chain D residue 142 VAL 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 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 44 VAL 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 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 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 123 LYS Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 82 GLN Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain c residue 119 ASP Chi-restraints excluded: chain c residue 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 86 ILE Chi-restraints excluded: chain e residue 119 ASP Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 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: 9.9990 chunk 164 optimal weight: 0.9990 chunk 319 optimal weight: 8.9990 chunk 320 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 233 optimal weight: 10.0000 chunk 286 optimal weight: 9.9990 chunk 152 optimal weight: 10.0000 chunk 145 optimal weight: 7.9990 chunk 58 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 345 ASN D 58 ASN ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 88 ASN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN G 125 HIS ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 211 GLN ** a 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 109 HIS f 125 GLN ** g 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.086031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.076266 restraints weight = 50563.071| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.68 r_work: 0.2852 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2728 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 26319 Z= 0.254 Angle : 0.642 8.463 35755 Z= 0.337 Chirality : 0.046 0.228 3876 Planarity : 0.004 0.047 4683 Dihedral : 6.349 59.081 3625 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 5.30 % Allowed : 17.46 % Favored : 77.24 % 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: -0.89 (0.14), residues: 3274 helix: 0.60 (0.21), residues: 600 sheet: -0.54 (0.18), residues: 867 loop : -1.01 (0.14), residues: 1807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 221 HIS 0.007 0.001 HIS C 121 PHE 0.020 0.002 PHE b 128 TYR 0.018 0.002 TYR D 69 ARG 0.007 0.001 ARG A 30 Details of bonding type rmsd hydrogen bonds : bond 0.04284 ( 875) hydrogen bonds : angle 5.70747 ( 2469) covalent geometry : bond 0.00606 (26319) covalent geometry : angle 0.64228 (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 766 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 140 poor density : 626 time to evaluate : 3.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8726 (p90) cc_final: 0.8369 (p90) REVERT: A 227 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7566 (mtp) REVERT: A 263 MET cc_start: 0.8668 (mtm) cc_final: 0.8362 (mtp) REVERT: A 304 ILE cc_start: 0.8685 (mm) cc_final: 0.8473 (mt) REVERT: A 307 LYS cc_start: 0.8936 (tptt) cc_final: 0.8382 (mppt) REVERT: B 126 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8600 (mt-10) REVERT: B 130 GLU cc_start: 0.8782 (tp30) cc_final: 0.8561 (tp30) REVERT: B 159 ASP cc_start: 0.8386 (t0) cc_final: 0.8035 (t0) REVERT: B 268 ASN cc_start: 0.9157 (t0) cc_final: 0.8527 (t0) REVERT: B 274 ASP cc_start: 0.8223 (t70) cc_final: 0.8005 (t0) REVERT: B 275 GLN cc_start: 0.8357 (mt0) cc_final: 0.8031 (mm-40) REVERT: B 277 ASP cc_start: 0.8640 (t0) cc_final: 0.7801 (t0) REVERT: B 296 GLU cc_start: 0.8410 (tp30) cc_final: 0.7548 (tp30) REVERT: B 315 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8387 (m-30) REVERT: B 323 GLN cc_start: 0.8472 (tt0) cc_final: 0.8079 (tt0) REVERT: C 15 ARG cc_start: 0.8704 (mtp85) cc_final: 0.8502 (tpp80) REVERT: C 130 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8564 (tp30) REVERT: C 324 GLU cc_start: 0.8727 (mm-30) cc_final: 0.7168 (pt0) REVERT: D 274 ASP cc_start: 0.8391 (t70) cc_final: 0.8005 (t70) REVERT: D 307 LYS cc_start: 0.9061 (tttm) cc_final: 0.8287 (mptt) REVERT: D 324 GLU cc_start: 0.8735 (mm-30) cc_final: 0.7038 (tt0) REVERT: E 15 ARG cc_start: 0.7971 (mtt-85) cc_final: 0.7714 (mtp180) REVERT: E 60 GLN cc_start: 0.8846 (mt0) cc_final: 0.7898 (mm-40) REVERT: E 65 LYS cc_start: 0.5408 (mmtm) cc_final: 0.5181 (mmtm) REVERT: E 111 ASP cc_start: 0.9094 (t0) cc_final: 0.8768 (m-30) REVERT: E 307 LYS cc_start: 0.6624 (mptt) cc_final: 0.5987 (mptt) REVERT: F 130 GLU cc_start: 0.8483 (tp30) cc_final: 0.8094 (tp30) REVERT: F 178 MET cc_start: 0.8442 (mmt) cc_final: 0.8029 (mtt) REVERT: F 283 MET cc_start: 0.9097 (tpt) cc_final: 0.8865 (tpt) REVERT: F 307 LYS cc_start: 0.9019 (tptp) cc_final: 0.8418 (mptt) REVERT: G 213 VAL cc_start: 0.9383 (t) cc_final: 0.9127 (m) REVERT: G 324 GLU cc_start: 0.8543 (mm-30) cc_final: 0.7235 (tt0) REVERT: G 333 SER cc_start: 0.8925 (m) cc_final: 0.8572 (p) REVERT: G 353 MET cc_start: 0.8142 (mmm) cc_final: 0.7839 (mmm) REVERT: a 40 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.5995 (tt0) REVERT: a 49 GLU cc_start: 0.8196 (mp0) cc_final: 0.7866 (mp0) REVERT: a 95 SER cc_start: 0.9495 (p) cc_final: 0.9257 (t) REVERT: a 125 GLN cc_start: 0.8874 (mm-40) cc_final: 0.8620 (mm-40) REVERT: a 133 ILE cc_start: 0.9233 (mt) cc_final: 0.9026 (mm) REVERT: b 91 GLN cc_start: 0.8653 (OUTLIER) cc_final: 0.8286 (mm-40) REVERT: b 123 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8482 (mtmm) REVERT: c 26 GLU cc_start: 0.8637 (pm20) cc_final: 0.8244 (mm-30) REVERT: c 36 ASP cc_start: 0.7253 (p0) cc_final: 0.6715 (m-30) REVERT: c 49 GLU cc_start: 0.8401 (mp0) cc_final: 0.8132 (mp0) REVERT: c 123 LYS cc_start: 0.9147 (mttm) cc_final: 0.8940 (mtpt) REVERT: c 132 ASN cc_start: 0.7881 (OUTLIER) cc_final: 0.7487 (t0) REVERT: d 29 GLN cc_start: 0.7255 (mt0) cc_final: 0.7036 (mm-40) REVERT: d 37 ILE cc_start: 0.8715 (mt) cc_final: 0.8445 (mt) REVERT: d 49 GLU cc_start: 0.8521 (mp0) cc_final: 0.8115 (mp0) REVERT: d 91 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.7911 (mp10) REVERT: e 21 ASP cc_start: 0.9100 (p0) cc_final: 0.8808 (p0) REVERT: e 40 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.5500 (tt0) REVERT: e 108 ASN cc_start: 0.8709 (t0) cc_final: 0.8339 (t0) REVERT: f 34 GLU cc_start: 0.6639 (mm-30) cc_final: 0.6420 (tp30) REVERT: f 36 ASP cc_start: 0.7769 (p0) cc_final: 0.7523 (p0) REVERT: f 95 SER cc_start: 0.9177 (p) cc_final: 0.8966 (t) REVERT: f 118 LEU cc_start: 0.9095 (tp) cc_final: 0.8677 (tt) REVERT: g 14 ASN cc_start: 0.9226 (t0) cc_final: 0.9016 (t0) REVERT: g 66 ASP cc_start: 0.9003 (t0) cc_final: 0.8690 (t70) REVERT: g 84 VAL cc_start: 0.9374 (p) cc_final: 0.9114 (m) REVERT: g 119 ASP cc_start: 0.9323 (OUTLIER) cc_final: 0.9099 (p0) outliers start: 140 outliers final: 103 residues processed: 702 average time/residue: 0.3325 time to fit residues: 383.1389 Evaluate side-chains 719 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 606 time to evaluate : 2.719 ------------------------------------------------------------------------------- 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 189 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 255 VAL Chi-restraints excluded: chain A residue 289 MET 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 101 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 69 TYR 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 165 THR Chi-restraints excluded: chain C residue 236 THR Chi-restraints excluded: chain C residue 243 ASP Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 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 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 37 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 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 137 ASN 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 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 131 THR 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 137 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 121 optimal weight: 9.9990 chunk 267 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 chunk 165 optimal weight: 9.9990 chunk 128 optimal weight: 10.0000 chunk 274 optimal weight: 6.9990 chunk 281 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 158 optimal weight: 10.0000 chunk 286 optimal weight: 2.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN 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** ** 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** ** g 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.086343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.076687 restraints weight = 50200.576| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 2.62 r_work: 0.2845 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 26319 Z= 0.219 Angle : 0.620 9.430 35755 Z= 0.323 Chirality : 0.045 0.219 3876 Planarity : 0.004 0.044 4683 Dihedral : 6.211 58.955 3625 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 5.38 % Allowed : 18.44 % Favored : 76.18 % 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: -0.90 (0.14), residues: 3274 helix: 0.67 (0.21), residues: 595 sheet: -0.56 (0.18), residues: 862 loop : -1.03 (0.14), residues: 1817 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 0.016 0.002 PHE b 128 TYR 0.016 0.002 TYR D 69 ARG 0.005 0.000 ARG G 262 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 875) hydrogen bonds : angle 5.60686 ( 2469) covalent geometry : bond 0.00520 (26319) covalent geometry : angle 0.62047 (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 780 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 638 time to evaluate : 2.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8699 (p90) cc_final: 0.8368 (p90) REVERT: A 89 MET cc_start: 0.7805 (mtt) cc_final: 0.7334 (mtp) REVERT: A 304 ILE cc_start: 0.8713 (mm) cc_final: 0.8510 (mt) REVERT: A 307 LYS cc_start: 0.8914 (tptt) cc_final: 0.8233 (mptt) REVERT: B 126 GLU cc_start: 0.8903 (OUTLIER) cc_final: 0.8616 (mt-10) REVERT: B 130 GLU cc_start: 0.8768 (tp30) cc_final: 0.8552 (tp30) REVERT: B 159 ASP cc_start: 0.8355 (t0) cc_final: 0.8017 (t0) REVERT: B 251 MET cc_start: 0.8659 (mmm) cc_final: 0.8303 (mtt) REVERT: B 268 ASN cc_start: 0.9132 (t0) cc_final: 0.8433 (t0) REVERT: B 274 ASP cc_start: 0.8290 (t70) cc_final: 0.8062 (t70) REVERT: B 275 GLN cc_start: 0.8417 (mt0) cc_final: 0.8183 (mm-40) REVERT: B 277 ASP cc_start: 0.8582 (t0) cc_final: 0.7775 (t0) REVERT: B 296 GLU cc_start: 0.8493 (tp30) cc_final: 0.7771 (tp30) REVERT: B 307 LYS cc_start: 0.9320 (ttpp) cc_final: 0.8891 (tptt) REVERT: B 315 ASP cc_start: 0.8779 (OUTLIER) cc_final: 0.8350 (m-30) REVERT: C 130 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8525 (tp30) REVERT: C 219 GLU cc_start: 0.8639 (mp0) cc_final: 0.8189 (mp0) REVERT: C 324 GLU cc_start: 0.8773 (mm-30) cc_final: 0.7079 (pt0) REVERT: D 274 ASP cc_start: 0.8475 (t70) cc_final: 0.8063 (t70) REVERT: D 307 LYS cc_start: 0.9025 (tttm) cc_final: 0.8309 (mptt) REVERT: D 324 GLU cc_start: 0.8741 (mm-30) cc_final: 0.7045 (tt0) REVERT: E 15 ARG cc_start: 0.7963 (mtt-85) cc_final: 0.7734 (mtp180) REVERT: E 60 GLN cc_start: 0.8830 (mt0) cc_final: 0.7999 (mm-40) REVERT: E 65 LYS cc_start: 0.5471 (mmtm) cc_final: 0.5223 (mmtm) REVERT: E 251 MET cc_start: 0.8520 (mmm) cc_final: 0.8087 (mmm) REVERT: E 283 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.7956 (tpp) REVERT: F 130 GLU cc_start: 0.8457 (tp30) cc_final: 0.8097 (tp30) REVERT: F 178 MET cc_start: 0.8460 (mmt) cc_final: 0.8028 (mtt) REVERT: F 283 MET cc_start: 0.9107 (tpt) cc_final: 0.8853 (tpt) REVERT: F 307 LYS cc_start: 0.9041 (tptp) cc_final: 0.8413 (mptt) REVERT: G 75 LYS cc_start: 0.8763 (OUTLIER) cc_final: 0.8330 (mtpp) REVERT: G 203 ILE cc_start: 0.9148 (OUTLIER) cc_final: 0.8922 (mt) REVERT: G 213 VAL cc_start: 0.9406 (t) cc_final: 0.9147 (m) REVERT: G 324 GLU cc_start: 0.8529 (mm-30) cc_final: 0.7205 (tt0) REVERT: G 333 SER cc_start: 0.8933 (m) cc_final: 0.8665 (p) REVERT: a 40 GLU cc_start: 0.6575 (OUTLIER) cc_final: 0.5977 (tt0) REVERT: a 49 GLU cc_start: 0.8264 (mp0) cc_final: 0.7969 (mp0) REVERT: a 115 HIS cc_start: 0.7420 (OUTLIER) cc_final: 0.6608 (p90) REVERT: a 118 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8959 (tt) REVERT: a 133 ILE cc_start: 0.9250 (mt) cc_final: 0.9049 (mm) REVERT: b 108 ASN cc_start: 0.8824 (t0) cc_final: 0.8389 (t0) REVERT: c 26 GLU cc_start: 0.8647 (pm20) cc_final: 0.8313 (mm-30) REVERT: c 36 ASP cc_start: 0.7141 (p0) cc_final: 0.6547 (m-30) REVERT: c 49 GLU cc_start: 0.8401 (mp0) cc_final: 0.8128 (mp0) REVERT: c 132 ASN cc_start: 0.8093 (OUTLIER) cc_final: 0.7794 (t0) REVERT: d 37 ILE cc_start: 0.8761 (mt) cc_final: 0.8513 (mt) REVERT: d 49 GLU cc_start: 0.8545 (mp0) cc_final: 0.8139 (mp0) REVERT: d 91 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7967 (mp10) REVERT: e 21 ASP cc_start: 0.9078 (p0) cc_final: 0.8770 (p0) REVERT: e 34 GLU cc_start: 0.5412 (mm-30) cc_final: 0.5115 (mm-30) REVERT: e 40 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5559 (tt0) REVERT: e 82 GLN cc_start: 0.8444 (mp10) cc_final: 0.8227 (pm20) REVERT: e 91 GLN cc_start: 0.9222 (mm-40) cc_final: 0.8888 (mm-40) REVERT: e 94 LYS cc_start: 0.9086 (mmtt) cc_final: 0.8823 (mmtm) REVERT: e 108 ASN cc_start: 0.8748 (t0) cc_final: 0.8452 (t0) REVERT: e 123 LYS cc_start: 0.9425 (mtpp) cc_final: 0.9210 (mtmm) REVERT: f 36 ASP cc_start: 0.7650 (p0) cc_final: 0.7337 (p0) REVERT: f 95 SER cc_start: 0.9172 (p) cc_final: 0.8965 (t) REVERT: f 118 LEU cc_start: 0.9093 (tp) cc_final: 0.8792 (tp) REVERT: g 84 VAL cc_start: 0.9507 (p) cc_final: 0.9237 (m) REVERT: g 119 ASP cc_start: 0.9326 (OUTLIER) cc_final: 0.9094 (p0) outliers start: 142 outliers final: 107 residues processed: 715 average time/residue: 0.3303 time to fit residues: 389.1794 Evaluate side-chains 735 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 616 time to evaluate : 2.652 ------------------------------------------------------------------------------- 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 248 VAL Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 MET 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 101 THR Chi-restraints excluded: chain B residue 126 GLU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 69 TYR 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 C residue 331 LEU Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 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 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 236 THR Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 316 TYR Chi-restraints excluded: chain F residue 37 ASP Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 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 300 CYS Chi-restraints excluded: chain F residue 320 MET 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 203 ILE Chi-restraints excluded: chain G residue 243 ASP 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 118 LEU Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 21 ASP Chi-restraints excluded: chain b residue 40 GLU Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 103 ILE Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 123 LYS Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain c residue 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 131 THR 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 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 123 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 249 optimal weight: 2.9990 chunk 286 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 222 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 205 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 16 optimal weight: 0.0770 chunk 149 optimal weight: 8.9990 chunk 192 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- 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 58 ASN C 60 GLN D 14 GLN ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN G 125 HIS ** 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 91 GLN b 109 HIS 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** ** g 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.089299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.079566 restraints weight = 49225.490| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.66 r_work: 0.2905 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2978 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= 0.141 Angle : 0.577 9.941 35755 Z= 0.299 Chirality : 0.044 0.184 3876 Planarity : 0.004 0.041 4683 Dihedral : 5.849 59.402 3622 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.35 % Allowed : 19.73 % Favored : 75.92 % 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: -0.81 (0.14), residues: 3274 helix: 0.80 (0.22), residues: 594 sheet: -0.65 (0.18), residues: 839 loop : -0.90 (0.14), residues: 1841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 221 HIS 0.006 0.001 HIS e 109 PHE 0.014 0.001 PHE b 128 TYR 0.015 0.001 TYR F 69 ARG 0.006 0.000 ARG E 15 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 875) hydrogen bonds : angle 5.40707 ( 2469) covalent geometry : bond 0.00335 (26319) covalent geometry : angle 0.57676 (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 780 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 665 time to evaluate : 3.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8645 (p90) cc_final: 0.8347 (p90) REVERT: A 89 MET cc_start: 0.7801 (mtt) cc_final: 0.7322 (mtp) REVERT: A 235 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8409 (mt-10) REVERT: A 307 LYS cc_start: 0.8781 (tptt) cc_final: 0.8151 (mptt) REVERT: B 87 PRO cc_start: 0.9033 (Cg_exo) cc_final: 0.8772 (Cg_endo) REVERT: B 126 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8586 (mt-10) REVERT: B 130 GLU cc_start: 0.8730 (tp30) cc_final: 0.8504 (tp30) REVERT: B 159 ASP cc_start: 0.8347 (t0) cc_final: 0.8022 (t0) REVERT: B 274 ASP cc_start: 0.8226 (t70) cc_final: 0.7990 (t70) REVERT: B 277 ASP cc_start: 0.8568 (t0) cc_final: 0.7744 (t0) REVERT: B 296 GLU cc_start: 0.8495 (tp30) cc_final: 0.7766 (tp30) REVERT: B 307 LYS cc_start: 0.9304 (ttpp) cc_final: 0.8850 (tptt) REVERT: B 315 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8341 (m-30) REVERT: C 130 GLU cc_start: 0.8969 (mm-30) cc_final: 0.8487 (tp30) REVERT: C 254 LEU cc_start: 0.8125 (mp) cc_final: 0.7851 (mt) REVERT: C 324 GLU cc_start: 0.8687 (mm-30) cc_final: 0.7060 (pt0) REVERT: D 41 PHE cc_start: 0.7692 (m-80) cc_final: 0.7381 (m-80) REVERT: D 58 ASN cc_start: 0.8461 (OUTLIER) cc_final: 0.8249 (m110) REVERT: D 125 HIS cc_start: 0.8328 (m-70) cc_final: 0.7992 (m170) REVERT: D 274 ASP cc_start: 0.8433 (t70) cc_final: 0.8043 (t70) REVERT: D 307 LYS cc_start: 0.8998 (tttm) cc_final: 0.8139 (mptt) REVERT: D 316 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.7796 (t80) REVERT: D 324 GLU cc_start: 0.8717 (mm-30) cc_final: 0.7098 (tt0) REVERT: E 60 GLN cc_start: 0.8780 (mt0) cc_final: 0.7877 (mm110) REVERT: E 111 ASP cc_start: 0.8896 (t0) cc_final: 0.8678 (m-30) REVERT: E 119 MET cc_start: 0.8812 (tmm) cc_final: 0.8603 (tmm) REVERT: E 274 ASP cc_start: 0.8639 (t70) cc_final: 0.7821 (p0) REVERT: F 130 GLU cc_start: 0.8441 (tp30) cc_final: 0.8061 (tp30) REVERT: F 178 MET cc_start: 0.8395 (mmt) cc_final: 0.8077 (mtt) REVERT: F 251 MET cc_start: 0.8646 (mmt) cc_final: 0.8150 (mmt) REVERT: F 307 LYS cc_start: 0.9007 (tptp) cc_final: 0.8381 (mptt) REVERT: G 75 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8179 (mtpp) REVERT: G 203 ILE cc_start: 0.9133 (OUTLIER) cc_final: 0.8901 (mt) REVERT: G 213 VAL cc_start: 0.9363 (t) cc_final: 0.9105 (m) REVERT: G 242 TRP cc_start: 0.8723 (m100) cc_final: 0.8468 (m100) REVERT: G 324 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7210 (tt0) REVERT: G 333 SER cc_start: 0.8868 (m) cc_final: 0.8616 (p) REVERT: a 49 GLU cc_start: 0.8234 (mp0) cc_final: 0.7937 (mp0) REVERT: a 95 SER cc_start: 0.9493 (p) cc_final: 0.9249 (t) REVERT: a 115 HIS cc_start: 0.7588 (OUTLIER) cc_final: 0.6739 (p90) REVERT: a 118 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8928 (tt) REVERT: c 26 GLU cc_start: 0.8627 (pm20) cc_final: 0.8309 (mm-30) REVERT: c 36 ASP cc_start: 0.7197 (p0) cc_final: 0.6590 (m-30) REVERT: c 49 GLU cc_start: 0.8343 (mp0) cc_final: 0.8064 (mp0) REVERT: c 95 SER cc_start: 0.9299 (p) cc_final: 0.9060 (t) REVERT: c 130 ARG cc_start: 0.7674 (tpp-160) cc_final: 0.5368 (mmm160) REVERT: c 132 ASN cc_start: 0.7913 (OUTLIER) cc_final: 0.7616 (t0) REVERT: d 37 ILE cc_start: 0.8662 (mt) cc_final: 0.8428 (mt) REVERT: d 49 GLU cc_start: 0.8519 (mp0) cc_final: 0.8091 (mp0) REVERT: d 91 GLN cc_start: 0.8898 (OUTLIER) cc_final: 0.8005 (mp10) REVERT: d 103 ILE cc_start: 0.8534 (OUTLIER) cc_final: 0.8178 (mp) REVERT: e 21 ASP cc_start: 0.9100 (p0) cc_final: 0.8817 (p0) REVERT: e 34 GLU cc_start: 0.5416 (mm-30) cc_final: 0.5078 (mm-30) REVERT: e 40 GLU cc_start: 0.6236 (OUTLIER) cc_final: 0.5337 (tt0) REVERT: e 91 GLN cc_start: 0.9242 (mm-40) cc_final: 0.8980 (mm-40) REVERT: e 94 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8809 (mmtm) REVERT: e 123 LYS cc_start: 0.9417 (mtpp) cc_final: 0.9213 (mtmm) REVERT: f 36 ASP cc_start: 0.7569 (p0) cc_final: 0.7222 (p0) REVERT: f 95 SER cc_start: 0.9140 (p) cc_final: 0.8936 (t) REVERT: f 118 LEU cc_start: 0.9106 (tp) cc_final: 0.8796 (tp) REVERT: g 84 VAL cc_start: 0.9463 (p) cc_final: 0.9172 (m) REVERT: g 98 ASN cc_start: 0.8908 (m110) cc_final: 0.8626 (m-40) REVERT: g 119 ASP cc_start: 0.9351 (OUTLIER) cc_final: 0.9144 (p0) outliers start: 115 outliers final: 89 residues processed: 721 average time/residue: 0.3402 time to fit residues: 400.4317 Evaluate side-chains 728 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 626 time to evaluate : 2.806 ------------------------------------------------------------------------------- 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 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 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 126 GLU 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 69 TYR 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 236 THR Chi-restraints excluded: chain C residue 243 ASP 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 25 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 316 TYR Chi-restraints excluded: chain F residue 37 ASP 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 300 CYS 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 203 ILE Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain a residue 115 HIS Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 40 GLU Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 123 LYS Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 82 GLN Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 119 ASP Chi-restraints excluded: chain c residue 131 THR Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain d residue 39 THR Chi-restraints excluded: chain d residue 78 VAL Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 119 ASP Chi-restraints excluded: chain d residue 137 ASN Chi-restraints excluded: chain e residue 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 108 ASN Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 119 ASP Chi-restraints excluded: chain g residue 123 LYS Chi-restraints excluded: chain g residue 137 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 313 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 254 optimal weight: 6.9990 chunk 227 optimal weight: 0.5980 chunk 255 optimal weight: 0.0470 chunk 121 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 307 optimal weight: 0.0570 chunk 152 optimal weight: 8.9990 chunk 218 optimal weight: 4.9990 chunk 260 optimal weight: 7.9990 overall best weight: 1.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 249 GLN D 33 ASN ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 285 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN ** G 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 91 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 ** f 97 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 = 0.3245 r_free = 0.3245 target = 0.091433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.081814 restraints weight = 49230.281| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.66 r_work: 0.2994 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 26319 Z= 0.119 Angle : 0.574 11.578 35755 Z= 0.294 Chirality : 0.043 0.184 3876 Planarity : 0.004 0.042 4683 Dihedral : 5.591 58.576 3620 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.98 % Allowed : 20.60 % Favored : 75.43 % 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: -0.72 (0.15), residues: 3274 helix: 0.93 (0.22), residues: 594 sheet: -0.61 (0.17), residues: 867 loop : -0.85 (0.15), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 221 HIS 0.008 0.001 HIS a 109 PHE 0.014 0.001 PHE b 128 TYR 0.015 0.001 TYR B 250 ARG 0.009 0.000 ARG E 15 Details of bonding type rmsd hydrogen bonds : bond 0.03643 ( 875) hydrogen bonds : angle 5.23996 ( 2469) covalent geometry : bond 0.00280 (26319) covalent geometry : angle 0.57374 (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 770 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 665 time to evaluate : 2.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8680 (p90) cc_final: 0.8265 (p90) REVERT: A 89 MET cc_start: 0.8024 (mtt) cc_final: 0.7541 (mtp) REVERT: A 235 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8430 (mt-10) REVERT: A 307 LYS cc_start: 0.8686 (tptt) cc_final: 0.8022 (mptt) REVERT: B 87 PRO cc_start: 0.9018 (Cg_exo) cc_final: 0.8737 (Cg_endo) REVERT: B 126 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.8487 (mt-10) REVERT: B 130 GLU cc_start: 0.8738 (tp30) cc_final: 0.7969 (tp30) REVERT: B 159 ASP cc_start: 0.8323 (t0) cc_final: 0.8003 (t0) REVERT: B 274 ASP cc_start: 0.8158 (t70) cc_final: 0.7949 (t70) REVERT: B 277 ASP cc_start: 0.8480 (t0) cc_final: 0.7743 (t0) REVERT: B 307 LYS cc_start: 0.9247 (ttpp) cc_final: 0.8823 (tttt) REVERT: C 130 GLU cc_start: 0.8911 (mm-30) cc_final: 0.8518 (tp30) REVERT: C 324 GLU cc_start: 0.8563 (mm-30) cc_final: 0.7039 (pt0) REVERT: D 41 PHE cc_start: 0.7617 (m-80) cc_final: 0.7172 (m-80) REVERT: D 307 LYS cc_start: 0.8972 (tttm) cc_final: 0.8078 (mptt) REVERT: D 316 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.7726 (t80) REVERT: D 324 GLU cc_start: 0.8675 (mm-30) cc_final: 0.7087 (tt0) REVERT: E 60 GLN cc_start: 0.8718 (mt0) cc_final: 0.7749 (mm110) REVERT: E 65 LYS cc_start: 0.5018 (mmtm) cc_final: 0.4305 (mmtm) REVERT: E 111 ASP cc_start: 0.8883 (t0) cc_final: 0.8665 (m-30) REVERT: E 119 MET cc_start: 0.8824 (tmm) cc_final: 0.8617 (tmm) REVERT: E 251 MET cc_start: 0.8254 (mmm) cc_final: 0.7194 (mmm) REVERT: E 274 ASP cc_start: 0.8596 (t70) cc_final: 0.7758 (p0) REVERT: E 283 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.7763 (tpp) REVERT: F 69 TYR cc_start: 0.8255 (p90) cc_final: 0.7811 (p90) REVERT: F 130 GLU cc_start: 0.8495 (tp30) cc_final: 0.8126 (tp30) REVERT: F 178 MET cc_start: 0.8413 (mmt) cc_final: 0.8105 (mtt) REVERT: F 283 MET cc_start: 0.9082 (tpt) cc_final: 0.8769 (tpt) REVERT: F 307 LYS cc_start: 0.8994 (tptp) cc_final: 0.8361 (mptt) REVERT: G 75 LYS cc_start: 0.8621 (OUTLIER) cc_final: 0.8122 (mtpp) REVERT: G 213 VAL cc_start: 0.9284 (t) cc_final: 0.9028 (m) REVERT: G 242 TRP cc_start: 0.8703 (m100) cc_final: 0.8442 (m100) REVERT: G 324 GLU cc_start: 0.8292 (mm-30) cc_final: 0.7048 (tt0) REVERT: G 333 SER cc_start: 0.8820 (m) cc_final: 0.8591 (p) REVERT: G 353 MET cc_start: 0.7905 (mpp) cc_final: 0.7552 (mpp) REVERT: a 49 GLU cc_start: 0.8270 (mp0) cc_final: 0.7954 (mp0) REVERT: a 78 VAL cc_start: 0.9527 (t) cc_final: 0.9311 (p) REVERT: a 95 SER cc_start: 0.9477 (p) cc_final: 0.9223 (t) REVERT: a 115 HIS cc_start: 0.7424 (OUTLIER) cc_final: 0.6606 (p90) REVERT: a 118 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8910 (tt) REVERT: b 108 ASN cc_start: 0.8769 (t0) cc_final: 0.8473 (t0) REVERT: b 137 ASN cc_start: 0.8513 (m-40) cc_final: 0.8306 (m-40) REVERT: c 26 GLU cc_start: 0.8589 (pm20) cc_final: 0.8266 (mm-30) REVERT: c 36 ASP cc_start: 0.7194 (p0) cc_final: 0.6597 (m-30) REVERT: c 49 GLU cc_start: 0.8254 (mp0) cc_final: 0.7953 (mp0) REVERT: c 95 SER cc_start: 0.9250 (p) cc_final: 0.8943 (m) REVERT: c 132 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7522 (t0) REVERT: d 34 GLU cc_start: 0.5981 (mm-30) cc_final: 0.5527 (mm-30) REVERT: d 37 ILE cc_start: 0.8622 (mt) cc_final: 0.8384 (mt) REVERT: d 49 GLU cc_start: 0.8445 (mp0) cc_final: 0.8016 (mp0) REVERT: d 91 GLN cc_start: 0.8930 (OUTLIER) cc_final: 0.8049 (mp10) REVERT: d 103 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.8246 (mp) REVERT: e 21 ASP cc_start: 0.9121 (p0) cc_final: 0.8832 (p0) REVERT: e 40 GLU cc_start: 0.6124 (OUTLIER) cc_final: 0.5248 (tt0) REVERT: e 91 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8957 (mm-40) REVERT: e 94 LYS cc_start: 0.9039 (mmtt) cc_final: 0.8753 (mmtm) REVERT: e 123 LYS cc_start: 0.9412 (mtpp) cc_final: 0.9205 (mtmm) REVERT: f 30 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8045 (mp) REVERT: f 36 ASP cc_start: 0.7597 (p0) cc_final: 0.7394 (p0) REVERT: g 84 VAL cc_start: 0.9435 (p) cc_final: 0.9136 (m) REVERT: g 98 ASN cc_start: 0.8857 (m110) cc_final: 0.8549 (m-40) REVERT: g 119 ASP cc_start: 0.9318 (OUTLIER) cc_final: 0.9117 (p0) outliers start: 105 outliers final: 76 residues processed: 718 average time/residue: 0.3455 time to fit residues: 404.3632 Evaluate side-chains 725 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 637 time to evaluate : 3.174 ------------------------------------------------------------------------------- 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 248 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 126 GLU 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 69 TYR Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 114 ILE Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 144 VAL Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 316 TYR Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain E residue 25 LEU 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 315 ASP Chi-restraints excluded: chain E residue 316 TYR Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 114 ILE Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain a residue 115 HIS Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 21 ASP Chi-restraints excluded: chain b residue 40 GLU Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 123 LYS Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 82 GLN Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 119 ASP Chi-restraints excluded: chain c residue 131 THR 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 119 ASP Chi-restraints excluded: chain e residue 40 GLU Chi-restraints excluded: chain e residue 63 VAL 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 108 ASN Chi-restraints excluded: chain f residue 133 ILE 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 123 LYS 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: 7.9990 chunk 58 optimal weight: 9.9990 chunk 284 optimal weight: 0.0040 chunk 180 optimal weight: 7.9990 chunk 261 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 320 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 290 optimal weight: 0.0570 chunk 280 optimal weight: 10.0000 chunk 219 optimal weight: 0.7980 overall best weight: 1.1712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** D 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 GLN G 70 ASN G 138 GLN ** a 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.092821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.083354 restraints weight = 48876.137| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.61 r_work: 0.3029 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 26319 Z= 0.115 Angle : 0.581 11.896 35755 Z= 0.295 Chirality : 0.043 0.162 3876 Planarity : 0.004 0.043 4683 Dihedral : 5.427 58.269 3618 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.45 % Allowed : 21.81 % Favored : 74.74 % 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: -0.66 (0.15), residues: 3274 helix: 0.94 (0.22), residues: 600 sheet: -0.57 (0.18), residues: 862 loop : -0.80 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 27 HIS 0.009 0.001 HIS a 109 PHE 0.014 0.001 PHE a 128 TYR 0.013 0.001 TYR A 250 ARG 0.008 0.000 ARG D 264 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 875) hydrogen bonds : angle 5.13747 ( 2469) covalent geometry : bond 0.00268 (26319) covalent geometry : angle 0.58059 (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 754 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 663 time to evaluate : 2.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8644 (p90) cc_final: 0.8203 (p90) REVERT: A 89 MET cc_start: 0.7976 (mtt) cc_final: 0.7496 (mtp) REVERT: A 207 ASP cc_start: 0.9057 (m-30) cc_final: 0.8788 (m-30) REVERT: A 227 MET cc_start: 0.7941 (OUTLIER) cc_final: 0.7508 (mtp) REVERT: A 235 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8430 (mt-10) REVERT: A 307 LYS cc_start: 0.8692 (tptt) cc_final: 0.8098 (mptt) REVERT: B 64 ILE cc_start: 0.8664 (mt) cc_final: 0.8409 (mm) REVERT: B 69 TYR cc_start: 0.9120 (p90) cc_final: 0.8713 (p90) REVERT: B 130 GLU cc_start: 0.8744 (tp30) cc_final: 0.8538 (tp30) REVERT: B 159 ASP cc_start: 0.8325 (t0) cc_final: 0.7983 (t0) REVERT: B 227 MET cc_start: 0.7786 (mmm) cc_final: 0.7361 (mmm) REVERT: B 277 ASP cc_start: 0.8437 (t0) cc_final: 0.7948 (t0) REVERT: B 296 GLU cc_start: 0.8482 (tp30) cc_final: 0.7684 (tp30) REVERT: B 307 LYS cc_start: 0.9215 (ttpp) cc_final: 0.8737 (tptt) REVERT: C 130 GLU cc_start: 0.8878 (mm-30) cc_final: 0.8495 (tp30) REVERT: C 324 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7035 (pt0) REVERT: D 41 PHE cc_start: 0.7598 (m-80) cc_final: 0.7182 (m-80) REVERT: D 307 LYS cc_start: 0.8901 (tttm) cc_final: 0.7982 (mptt) REVERT: D 316 TYR cc_start: 0.8441 (OUTLIER) cc_final: 0.7668 (t80) REVERT: D 324 GLU cc_start: 0.8649 (mm-30) cc_final: 0.7077 (tt0) REVERT: E 60 GLN cc_start: 0.8612 (mt0) cc_final: 0.7717 (mm110) REVERT: E 65 LYS cc_start: 0.5360 (mmtm) cc_final: 0.4676 (mmtm) REVERT: E 111 ASP cc_start: 0.8891 (t0) cc_final: 0.8657 (m-30) REVERT: E 119 MET cc_start: 0.8809 (tmm) cc_final: 0.8599 (tmm) REVERT: E 176 MET cc_start: 0.8854 (mmm) cc_final: 0.8414 (mmm) REVERT: E 274 ASP cc_start: 0.8559 (t70) cc_final: 0.7720 (p0) REVERT: E 283 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.7895 (tpp) REVERT: F 69 TYR cc_start: 0.8252 (p90) cc_final: 0.7478 (p90) REVERT: F 130 GLU cc_start: 0.8480 (tp30) cc_final: 0.8112 (tp30) REVERT: F 164 MET cc_start: 0.8778 (mtp) cc_final: 0.8539 (mtm) REVERT: F 178 MET cc_start: 0.8390 (mmt) cc_final: 0.8101 (mtt) REVERT: F 264 ARG cc_start: 0.7878 (mtt90) cc_final: 0.7659 (mtt-85) REVERT: F 307 LYS cc_start: 0.8964 (tptp) cc_final: 0.8187 (mptt) REVERT: G 75 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8224 (mtpp) REVERT: G 130 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8327 (tm-30) REVERT: G 213 VAL cc_start: 0.9254 (t) cc_final: 0.9008 (m) REVERT: G 324 GLU cc_start: 0.8175 (mm-30) cc_final: 0.6932 (tt0) REVERT: G 333 SER cc_start: 0.8836 (m) cc_final: 0.8635 (p) REVERT: a 49 GLU cc_start: 0.8229 (mp0) cc_final: 0.7930 (mp0) REVERT: a 95 SER cc_start: 0.9448 (p) cc_final: 0.9183 (t) REVERT: a 115 HIS cc_start: 0.7330 (OUTLIER) cc_final: 0.6496 (p90) REVERT: a 118 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8873 (tt) REVERT: c 26 GLU cc_start: 0.8583 (pm20) cc_final: 0.8271 (mm-30) REVERT: c 36 ASP cc_start: 0.7058 (p0) cc_final: 0.6498 (m-30) REVERT: c 49 GLU cc_start: 0.8236 (mp0) cc_final: 0.7911 (mp0) REVERT: c 95 SER cc_start: 0.9209 (p) cc_final: 0.8956 (m) REVERT: c 132 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7499 (t0) REVERT: d 34 GLU cc_start: 0.5945 (mm-30) cc_final: 0.5441 (mm-30) REVERT: d 37 ILE cc_start: 0.8542 (mt) cc_final: 0.8324 (mt) REVERT: d 49 GLU cc_start: 0.8423 (mp0) cc_final: 0.7936 (mp0) REVERT: d 56 LYS cc_start: 0.9072 (mtmt) cc_final: 0.8840 (mtpp) REVERT: d 91 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8018 (mp10) REVERT: d 102 TYR cc_start: 0.9003 (m-80) cc_final: 0.8626 (m-80) REVERT: d 103 ILE cc_start: 0.8464 (OUTLIER) cc_final: 0.8177 (mp) REVERT: e 21 ASP cc_start: 0.9123 (p0) cc_final: 0.8843 (p0) REVERT: e 91 GLN cc_start: 0.9185 (mm-40) cc_final: 0.8941 (mm-40) REVERT: e 94 LYS cc_start: 0.9047 (mmtt) cc_final: 0.8771 (mmtm) REVERT: f 30 ILE cc_start: 0.8545 (OUTLIER) cc_final: 0.8044 (mp) REVERT: f 118 LEU cc_start: 0.9033 (tp) cc_final: 0.8673 (tt) REVERT: g 84 VAL cc_start: 0.9398 (p) cc_final: 0.9091 (m) REVERT: g 98 ASN cc_start: 0.8836 (m110) cc_final: 0.8513 (m-40) REVERT: g 125 GLN cc_start: 0.8416 (mt0) cc_final: 0.8143 (mt0) outliers start: 91 outliers final: 68 residues processed: 711 average time/residue: 0.3400 time to fit residues: 394.3564 Evaluate side-chains 714 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 636 time to evaluate : 2.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 148 ASP Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 193 SER Chi-restraints excluded: chain A residue 198 VAL Chi-restraints excluded: chain A residue 227 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 69 TYR 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 42 ASP Chi-restraints excluded: chain D residue 70 ASN 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 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 G residue 39 ILE Chi-restraints excluded: chain G residue 66 GLU Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 105 SER Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 152 VAL Chi-restraints excluded: chain G residue 244 ASP Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain a residue 115 HIS Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 40 GLU Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain b residue 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 103 ILE Chi-restraints excluded: chain c residue 119 ASP Chi-restraints excluded: chain c residue 131 THR Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 119 ASP Chi-restraints excluded: chain e residue 63 VAL 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 108 ASN Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 137 ASN 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: 10.0000 chunk 224 optimal weight: 0.9980 chunk 277 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 154 optimal weight: 0.9990 chunk 98 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 188 optimal weight: 8.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 285 GLN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN G 138 GLN ** a 91 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** ** a 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 98 ASN ** d 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 125 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.093273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.083772 restraints weight = 49099.393| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.66 r_work: 0.3077 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 26319 Z= 0.113 Angle : 0.581 12.668 35755 Z= 0.295 Chirality : 0.043 0.281 3876 Planarity : 0.004 0.044 4683 Dihedral : 5.306 58.177 3616 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 3.41 % Allowed : 22.19 % Favored : 74.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.61 (0.15), residues: 3274 helix: 0.99 (0.22), residues: 602 sheet: -0.51 (0.18), residues: 854 loop : -0.80 (0.15), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 27 HIS 0.010 0.001 HIS a 109 PHE 0.013 0.001 PHE a 128 TYR 0.013 0.001 TYR F 69 ARG 0.008 0.000 ARG E 15 Details of bonding type rmsd hydrogen bonds : bond 0.03469 ( 875) hydrogen bonds : angle 5.08182 ( 2469) covalent geometry : bond 0.00265 (26319) covalent geometry : angle 0.58087 (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 751 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 661 time to evaluate : 2.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8620 (p90) cc_final: 0.8179 (p90) REVERT: A 89 MET cc_start: 0.8104 (mtt) cc_final: 0.7625 (mtp) REVERT: A 207 ASP cc_start: 0.9060 (m-30) cc_final: 0.8787 (m-30) REVERT: A 227 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7576 (mtp) REVERT: A 307 LYS cc_start: 0.8693 (tptt) cc_final: 0.8189 (mptt) REVERT: B 64 ILE cc_start: 0.8595 (mt) cc_final: 0.8338 (mm) REVERT: B 69 TYR cc_start: 0.9113 (p90) cc_final: 0.8812 (p90) REVERT: B 130 GLU cc_start: 0.8745 (tp30) cc_final: 0.8539 (tp30) REVERT: B 159 ASP cc_start: 0.8298 (t0) cc_final: 0.7957 (t0) REVERT: B 277 ASP cc_start: 0.8372 (t0) cc_final: 0.7716 (t0) REVERT: B 296 GLU cc_start: 0.8484 (tp30) cc_final: 0.7584 (tp30) REVERT: B 307 LYS cc_start: 0.9195 (ttpp) cc_final: 0.8745 (tptt) REVERT: C 130 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8507 (tp30) REVERT: C 324 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7031 (pt0) REVERT: D 125 HIS cc_start: 0.8181 (m-70) cc_final: 0.7778 (m170) REVERT: D 164 MET cc_start: 0.9171 (ptp) cc_final: 0.8798 (pmm) REVERT: D 307 LYS cc_start: 0.8899 (tttm) cc_final: 0.7984 (mptt) REVERT: D 316 TYR cc_start: 0.8408 (OUTLIER) cc_final: 0.7449 (t80) REVERT: D 324 GLU cc_start: 0.8649 (mm-30) cc_final: 0.6956 (tt0) REVERT: E 60 GLN cc_start: 0.8587 (mt0) cc_final: 0.7639 (mm110) REVERT: E 65 LYS cc_start: 0.5464 (mmtm) cc_final: 0.4812 (mmtm) REVERT: E 111 ASP cc_start: 0.8871 (t0) cc_final: 0.8647 (m-30) REVERT: E 119 MET cc_start: 0.8819 (tmm) cc_final: 0.8613 (tmm) REVERT: E 176 MET cc_start: 0.8845 (mmm) cc_final: 0.8325 (mmm) REVERT: E 251 MET cc_start: 0.8253 (mmm) cc_final: 0.7134 (mmm) REVERT: E 274 ASP cc_start: 0.8537 (t70) cc_final: 0.7713 (p0) REVERT: E 283 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.7965 (tpp) REVERT: F 69 TYR cc_start: 0.8244 (p90) cc_final: 0.7361 (p90) REVERT: F 130 GLU cc_start: 0.8472 (tp30) cc_final: 0.8079 (tp30) REVERT: F 178 MET cc_start: 0.8336 (mmt) cc_final: 0.8071 (mtt) REVERT: F 209 TRP cc_start: 0.8798 (t-100) cc_final: 0.8109 (t-100) REVERT: F 251 MET cc_start: 0.8456 (mmt) cc_final: 0.7923 (mmt) REVERT: F 264 ARG cc_start: 0.7894 (mtt90) cc_final: 0.7687 (mtt-85) REVERT: F 307 LYS cc_start: 0.8960 (tptp) cc_final: 0.8306 (mptt) REVERT: F 324 GLU cc_start: 0.8477 (mm-30) cc_final: 0.7434 (pt0) REVERT: G 15 ARG cc_start: 0.7426 (mtm180) cc_final: 0.6593 (tpt170) REVERT: G 64 ILE cc_start: 0.7729 (OUTLIER) cc_final: 0.7480 (pp) REVERT: G 75 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8355 (mtpp) REVERT: G 213 VAL cc_start: 0.9231 (t) cc_final: 0.8998 (m) REVERT: G 324 GLU cc_start: 0.8149 (mm-30) cc_final: 0.6912 (tt0) REVERT: a 49 GLU cc_start: 0.8231 (mp0) cc_final: 0.7948 (mp0) REVERT: a 62 MET cc_start: 0.8902 (mmt) cc_final: 0.8624 (mmt) REVERT: a 91 GLN cc_start: 0.9444 (mm-40) cc_final: 0.9169 (mm110) REVERT: a 95 SER cc_start: 0.9437 (p) cc_final: 0.9161 (t) REVERT: a 115 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.6518 (p90) REVERT: a 118 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8837 (tt) REVERT: c 26 GLU cc_start: 0.8565 (pm20) cc_final: 0.8275 (mm-30) REVERT: c 36 ASP cc_start: 0.7209 (p0) cc_final: 0.6839 (m-30) REVERT: c 49 GLU cc_start: 0.8229 (mp0) cc_final: 0.7898 (mp0) REVERT: c 132 ASN cc_start: 0.7750 (OUTLIER) cc_final: 0.7522 (t0) REVERT: d 37 ILE cc_start: 0.8520 (mt) cc_final: 0.8307 (mt) REVERT: d 49 GLU cc_start: 0.8428 (mp0) cc_final: 0.7944 (mp0) REVERT: d 91 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8074 (mp10) REVERT: d 102 TYR cc_start: 0.9000 (m-80) cc_final: 0.8650 (m-80) REVERT: d 103 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8185 (mp) REVERT: e 21 ASP cc_start: 0.9117 (p0) cc_final: 0.8846 (p0) REVERT: e 91 GLN cc_start: 0.9177 (mm-40) cc_final: 0.8939 (mm-40) REVERT: e 94 LYS cc_start: 0.9032 (mmtt) cc_final: 0.8751 (mmtm) REVERT: e 108 ASN cc_start: 0.8695 (t0) cc_final: 0.8426 (t0) REVERT: f 30 ILE cc_start: 0.8535 (OUTLIER) cc_final: 0.8035 (mt) REVERT: f 118 LEU cc_start: 0.9064 (tp) cc_final: 0.8704 (tt) REVERT: g 125 GLN cc_start: 0.8370 (mt0) cc_final: 0.8110 (mt0) outliers start: 90 outliers final: 67 residues processed: 708 average time/residue: 0.3314 time to fit residues: 382.6752 Evaluate side-chains 717 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 639 time to evaluate : 2.749 ------------------------------------------------------------------------------- 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 227 MET Chi-restraints excluded: chain A residue 328 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 63 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 142 VAL Chi-restraints excluded: chain B residue 148 ASP Chi-restraints excluded: chain B residue 198 VAL Chi-restraints excluded: chain B residue 316 TYR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 69 TYR 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 D residue 42 ASP Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 316 TYR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 132 MET Chi-restraints excluded: chain E residue 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 63 VAL Chi-restraints excluded: chain F residue 66 GLU Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 300 CYS 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 114 ILE Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 144 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 298 VAL Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain a residue 115 HIS Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 40 GLU Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 86 ILE Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 131 THR Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain d residue 22 LEU Chi-restraints excluded: chain d residue 39 THR 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 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 86 ILE Chi-restraints excluded: chain f residue 108 ASN Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 137 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 204 optimal weight: 9.9990 chunk 323 optimal weight: 3.9990 chunk 247 optimal weight: 5.9990 chunk 138 optimal weight: 9.9990 chunk 299 optimal weight: 2.9990 chunk 152 optimal weight: 10.0000 chunk 149 optimal weight: 0.0030 chunk 101 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 294 optimal weight: 5.9990 overall best weight: 3.7998 ------------------------------------------------------------------------------- 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 ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 70 ASN G 138 GLN ** a 91 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** c 98 ASN ** d 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 125 GLN ** g 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 98 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.088663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.078995 restraints weight = 50010.296| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.67 r_work: 0.2946 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 26319 Z= 0.205 Angle : 0.646 13.278 35755 Z= 0.326 Chirality : 0.045 0.336 3876 Planarity : 0.004 0.045 4683 Dihedral : 5.549 58.217 3616 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.63 % Allowed : 21.92 % Favored : 74.44 % 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: -0.74 (0.15), residues: 3274 helix: 0.90 (0.22), residues: 600 sheet: -0.55 (0.18), residues: 849 loop : -0.91 (0.14), residues: 1825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 27 HIS 0.009 0.001 HIS a 109 PHE 0.016 0.002 PHE b 128 TYR 0.017 0.001 TYR F 69 ARG 0.008 0.000 ARG D 264 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 875) hydrogen bonds : angle 5.27676 ( 2469) covalent geometry : bond 0.00490 (26319) covalent geometry : angle 0.64581 (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 719 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 623 time to evaluate : 3.121 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.8741 (p90) cc_final: 0.8362 (p90) REVERT: A 89 MET cc_start: 0.8010 (mtt) cc_final: 0.7526 (mtp) REVERT: A 268 ASN cc_start: 0.8962 (t0) cc_final: 0.8682 (t0) REVERT: A 296 GLU cc_start: 0.8941 (tp30) cc_final: 0.8665 (tp30) REVERT: A 307 LYS cc_start: 0.8810 (tptt) cc_final: 0.8324 (mppt) REVERT: B 69 TYR cc_start: 0.9133 (p90) cc_final: 0.8557 (p90) REVERT: B 130 GLU cc_start: 0.8769 (tp30) cc_final: 0.8559 (tp30) REVERT: B 159 ASP cc_start: 0.8388 (t0) cc_final: 0.8025 (t0) REVERT: B 277 ASP cc_start: 0.8467 (t0) cc_final: 0.7782 (t0) REVERT: B 296 GLU cc_start: 0.8566 (tp30) cc_final: 0.7798 (tp30) REVERT: B 307 LYS cc_start: 0.9250 (ttpp) cc_final: 0.8835 (tttt) REVERT: C 130 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8522 (tp30) REVERT: C 324 GLU cc_start: 0.8576 (mm-30) cc_final: 0.7052 (pt0) REVERT: D 307 LYS cc_start: 0.8981 (tttm) cc_final: 0.8097 (mptt) REVERT: D 316 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.7881 (t80) REVERT: D 324 GLU cc_start: 0.8751 (mm-30) cc_final: 0.7174 (tt0) REVERT: E 60 GLN cc_start: 0.8646 (mt0) cc_final: 0.7591 (mm110) REVERT: E 65 LYS cc_start: 0.5769 (mmtm) cc_final: 0.5137 (mmtp) REVERT: E 111 ASP cc_start: 0.8944 (t0) cc_final: 0.8679 (m-30) REVERT: E 119 MET cc_start: 0.8852 (tmm) cc_final: 0.8633 (tmm) REVERT: E 251 MET cc_start: 0.8531 (mmm) cc_final: 0.7442 (mmm) REVERT: E 274 ASP cc_start: 0.8622 (t70) cc_final: 0.7779 (p0) REVERT: E 283 MET cc_start: 0.8904 (OUTLIER) cc_final: 0.7967 (tpp) REVERT: F 69 TYR cc_start: 0.8344 (p90) cc_final: 0.7750 (p90) REVERT: F 130 GLU cc_start: 0.8510 (tp30) cc_final: 0.8164 (tp30) REVERT: F 178 MET cc_start: 0.8442 (mmt) cc_final: 0.8110 (mtt) REVERT: F 209 TRP cc_start: 0.8828 (t-100) cc_final: 0.8187 (t-100) REVERT: F 251 MET cc_start: 0.8558 (mmt) cc_final: 0.8009 (mmt) REVERT: F 307 LYS cc_start: 0.8989 (tptp) cc_final: 0.8336 (mptt) REVERT: G 64 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7562 (pp) REVERT: G 75 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8446 (mtpp) REVERT: G 213 VAL cc_start: 0.9283 (t) cc_final: 0.9036 (m) REVERT: G 324 GLU cc_start: 0.8273 (mm-30) cc_final: 0.6876 (tt0) REVERT: a 49 GLU cc_start: 0.8290 (mp0) cc_final: 0.7985 (mp0) REVERT: a 82 GLN cc_start: 0.8742 (pm20) cc_final: 0.8137 (pm20) REVERT: a 95 SER cc_start: 0.9499 (p) cc_final: 0.9238 (t) REVERT: a 115 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.6544 (p90) REVERT: a 118 LEU cc_start: 0.9165 (OUTLIER) cc_final: 0.8897 (tt) REVERT: c 26 GLU cc_start: 0.8638 (pm20) cc_final: 0.8348 (mm-30) REVERT: c 36 ASP cc_start: 0.7221 (p0) cc_final: 0.6579 (m-30) REVERT: c 49 GLU cc_start: 0.8299 (mp0) cc_final: 0.7993 (mp0) REVERT: c 95 SER cc_start: 0.9259 (p) cc_final: 0.9007 (m) REVERT: c 132 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7809 (t0) REVERT: d 37 ILE cc_start: 0.8617 (mt) cc_final: 0.8408 (mt) REVERT: d 49 GLU cc_start: 0.8460 (mp0) cc_final: 0.7990 (mp0) REVERT: d 91 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7958 (mp10) REVERT: d 103 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8198 (mp) REVERT: e 21 ASP cc_start: 0.9104 (p0) cc_final: 0.8826 (p0) REVERT: e 91 GLN cc_start: 0.9174 (mm-40) cc_final: 0.8853 (mm-40) REVERT: f 30 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8250 (mp) REVERT: g 125 GLN cc_start: 0.8427 (mt0) cc_final: 0.8177 (mt0) outliers start: 96 outliers final: 78 residues processed: 675 average time/residue: 0.3674 time to fit residues: 407.4643 Evaluate side-chains 702 residues out of total 2658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 614 time to evaluate : 5.851 ------------------------------------------------------------------------------- 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 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 316 TYR Chi-restraints excluded: chain B residue 320 MET Chi-restraints excluded: chain C residue 10 LEU Chi-restraints excluded: chain C residue 69 TYR 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 255 VAL Chi-restraints excluded: chain D residue 10 LEU Chi-restraints excluded: chain D residue 42 ASP Chi-restraints excluded: chain D residue 70 ASN Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 293 SER 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 236 THR Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 288 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 316 TYR Chi-restraints excluded: chain F residue 63 VAL Chi-restraints excluded: chain F residue 193 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 300 CYS Chi-restraints excluded: chain F residue 328 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 114 ILE Chi-restraints excluded: chain G residue 142 VAL Chi-restraints excluded: chain G residue 144 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 263 MET Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 316 TYR Chi-restraints excluded: chain a residue 115 HIS Chi-restraints excluded: chain a residue 118 LEU Chi-restraints excluded: chain a residue 120 THR Chi-restraints excluded: chain b residue 40 GLU Chi-restraints excluded: chain b residue 78 VAL Chi-restraints excluded: chain b residue 109 HIS Chi-restraints excluded: chain b residue 115 HIS Chi-restraints excluded: chain b residue 118 LEU Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain c residue 63 VAL Chi-restraints excluded: chain c residue 78 VAL Chi-restraints excluded: chain c residue 82 GLN Chi-restraints excluded: chain c residue 131 THR Chi-restraints excluded: chain c residue 132 ASN Chi-restraints excluded: chain d residue 22 LEU Chi-restraints excluded: chain d residue 91 GLN Chi-restraints excluded: chain d residue 103 ILE Chi-restraints excluded: chain d residue 119 ASP Chi-restraints excluded: chain e residue 14 ASN Chi-restraints excluded: chain e residue 109 HIS Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 119 ASP Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 38 VAL Chi-restraints excluded: chain f residue 82 GLN Chi-restraints excluded: chain f residue 108 ASN Chi-restraints excluded: chain f residue 133 ILE Chi-restraints excluded: chain g residue 54 ILE Chi-restraints excluded: chain g residue 78 VAL Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 137 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 327 random chunks: chunk 74 optimal weight: 0.9980 chunk 193 optimal weight: 10.0000 chunk 294 optimal weight: 1.9990 chunk 165 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 214 optimal weight: 0.9980 chunk 58 optimal weight: 10.0000 chunk 67 optimal weight: 2.9990 chunk 225 optimal weight: 9.9990 chunk 120 optimal weight: 1.9990 chunk 306 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN ** E 334 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN G 70 ASN G 138 GLN ** a 91 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** ** a 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 125 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.091159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.081566 restraints weight = 49250.046| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.67 r_work: 0.2994 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 26319 Z= 0.132 Angle : 0.607 13.318 35755 Z= 0.305 Chirality : 0.044 0.301 3876 Planarity : 0.004 0.046 4683 Dihedral : 5.402 59.757 3616 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.33 % Allowed : 22.38 % 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: -0.73 (0.15), residues: 3274 helix: 0.95 (0.22), residues: 600 sheet: -0.63 (0.18), residues: 865 loop : -0.86 (0.15), residues: 1809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 27 HIS 0.011 0.001 HIS a 109 PHE 0.016 0.001 PHE d 128 TYR 0.013 0.001 TYR F 69 ARG 0.008 0.000 ARG D 264 Details of bonding type rmsd hydrogen bonds : bond 0.03559 ( 875) hydrogen bonds : angle 5.14632 ( 2469) covalent geometry : bond 0.00314 (26319) covalent geometry : angle 0.60736 (35755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30340.54 seconds wall clock time: 527 minutes 20.34 seconds (31640.34 seconds total)