Starting phenix.real_space_refine on Tue Mar 19 10:05:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/03_2024/8i1v_35123.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/03_2024/8i1v_35123.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/03_2024/8i1v_35123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/03_2024/8i1v_35123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/03_2024/8i1v_35123.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/03_2024/8i1v_35123.pdb" } resolution = 2.6 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 ------------------------------------------------------------------------------- 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= 0.007 sd= 0.825 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 98 5.16 5 C 14961 2.51 5 N 4163 2.21 5 O 4648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 18": "OE1" <-> "OE2" Residue "G TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 54": "OE1" <-> "OE2" Residue "G ASP 62": "OD1" <-> "OD2" Residue "G GLU 72": "OE1" <-> "OE2" Residue "G TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 292": "OD1" <-> "OD2" Residue "A GLU 18": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A ASP 85": "OD1" <-> "OD2" Residue "A ASP 92": "OD1" <-> "OD2" Residue "A ASP 163": "OD1" <-> "OD2" Residue "A ASP 316": "OD1" <-> "OD2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "A TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 62": "OD1" <-> "OD2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B ASP 83": "OD1" <-> "OD2" Residue "B ASP 85": "OD1" <-> "OD2" Residue "B GLU 152": "OE1" <-> "OE2" Residue "B ASP 292": "OD1" <-> "OD2" Residue "B TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B ASP 356": "OD1" <-> "OD2" Residue "B ASP 397": "OD1" <-> "OD2" Residue "B TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F GLU 116": "OE1" <-> "OE2" Residue "F GLU 152": "OE1" <-> "OE2" Residue "F PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 186": "OD1" <-> "OD2" Residue "F ASP 244": "OD1" <-> "OD2" Residue "F ASP 302": "OD1" <-> "OD2" Residue "F TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 347": "OD1" <-> "OD2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C ASP 96": "OD1" <-> "OD2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 210": "OD1" <-> "OD2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "C GLU 323": "OE1" <-> "OE2" Residue "C ASP 397": "OD1" <-> "OD2" Residue "D GLU 5": "OE1" <-> "OE2" Residue "D GLU 15": "OE1" <-> "OE2" Residue "D TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D GLU 59": "OE1" <-> "OE2" Residue "D ASP 85": "OD1" <-> "OD2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "D GLU 153": "OE1" <-> "OE2" Residue "D TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 210": "OD1" <-> "OD2" Residue "D ASP 302": "OD1" <-> "OD2" Residue "D TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 336": "OD1" <-> "OD2" Residue "D ASP 397": "OD1" <-> "OD2" Residue "E ASP 14": "OD1" <-> "OD2" Residue "E TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 52": "OE1" <-> "OE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "E ASP 92": "OD1" <-> "OD2" Residue "E ASP 96": "OD1" <-> "OD2" Residue "E TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 186": "OD1" <-> "OD2" Residue "E ASP 302": "OD1" <-> "OD2" Residue "E GLU 323": "OE1" <-> "OE2" Residue "E ASP 336": "OD1" <-> "OD2" Residue "E PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 411": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23870 Number of models: 1 Model: "" Number of chains: 14 Chain: "G" Number of atoms: 3203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3203 Classifications: {'peptide': 420} Link IDs: {'PTRANS': 20, 'TRANS': 399} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "A" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3162 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 20, 'TRANS': 394} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 3156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 3156 Classifications: {'peptide': 414} Link IDs: {'PTRANS': 20, 'TRANS': 393} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3220 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 20, 'TRANS': 401} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 3220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3220 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 20, 'TRANS': 401} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3139 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 20, 'TRANS': 391} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 3139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 3139 Classifications: {'peptide': 412} Link IDs: {'PTRANS': 20, 'TRANS': 391} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "I" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "J" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "K" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "L" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "M" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "N" Number of atoms: 233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 233 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Time building chain proxies: 12.12, per 1000 atoms: 0.51 Number of scatterers: 23870 At special positions: 0 Unit cell: (102.82, 182.32, 161.12, 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 98 16.00 O 4648 8.00 N 4163 7.00 C 14961 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 - 3.50 Amino acid : False - 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: 8.81 Conformation dependent library (CDL) restraints added in 4.1 seconds 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5868 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 56 sheets defined 26.6% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.60 Creating SS restraints... Processing helix chain 'G' and resid 4 through 24 removed outlier: 3.656A pdb=" N THR G 24 " --> pdb=" O ILE G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 30 Processing helix chain 'G' and resid 96 through 127 removed outlier: 3.526A pdb=" N TYR G 100 " --> pdb=" O ASP G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 159 Processing helix chain 'G' and resid 171 through 178 Processing helix chain 'G' and resid 321 through 326 Processing helix chain 'G' and resid 417 through 419 No H-bonds generated for 'chain 'G' and resid 417 through 419' Processing helix chain 'A' and resid 4 through 23 Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.929A pdb=" N GLN A 28 " --> pdb=" O THR A 24 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 30 " --> pdb=" O MET A 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 24 through 30' Processing helix chain 'A' and resid 90 through 95 Processing helix chain 'A' and resid 96 through 126 removed outlier: 3.502A pdb=" N LYS A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 159 Processing helix chain 'A' and resid 171 through 178 Processing helix chain 'A' and resid 321 through 326 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' Processing helix chain 'B' and resid 4 through 23 Processing helix chain 'B' and resid 90 through 95 Processing helix chain 'B' and resid 96 through 127 Processing helix chain 'B' and resid 146 through 159 Processing helix chain 'B' and resid 171 through 178 Processing helix chain 'B' and resid 321 through 326 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' Processing helix chain 'F' and resid 4 through 23 removed outlier: 3.593A pdb=" N ALA F 12 " --> pdb=" O ILE F 8 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 95 Processing helix chain 'F' and resid 96 through 127 Processing helix chain 'F' and resid 146 through 159 Processing helix chain 'F' and resid 171 through 178 Processing helix chain 'F' and resid 202 through 207 Processing helix chain 'F' and resid 321 through 326 Processing helix chain 'F' and resid 417 through 419 No H-bonds generated for 'chain 'F' and resid 417 through 419' Processing helix chain 'C' and resid 4 through 23 Processing helix chain 'C' and resid 92 through 95 Processing helix chain 'C' and resid 96 through 127 Processing helix chain 'C' and resid 146 through 158 Processing helix chain 'C' and resid 171 through 178 Processing helix chain 'C' and resid 202 through 207 Processing helix chain 'C' and resid 321 through 326 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' Processing helix chain 'D' and resid 4 through 24 removed outlier: 3.718A pdb=" N ALA D 12 " --> pdb=" O ILE D 8 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR D 24 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 127 Processing helix chain 'D' and resid 146 through 158 Processing helix chain 'D' and resid 171 through 178 Processing helix chain 'D' and resid 186 through 190 removed outlier: 3.921A pdb=" N ARG D 190 " --> pdb=" O ILE D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 326 Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing helix chain 'E' and resid 4 through 23 Processing helix chain 'E' and resid 96 through 127 Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 171 through 179 removed outlier: 3.559A pdb=" N GLY E 179 " --> pdb=" O TYR E 175 " (cutoff:3.500A) Processing helix chain 'E' and resid 321 through 326 Processing helix chain 'E' and resid 417 through 419 No H-bonds generated for 'chain 'E' and resid 417 through 419' Processing helix chain 'H' and resid 272 through 287 Processing helix chain 'H' and resid 288 through 300 Processing helix chain 'I' and resid 272 through 287 Processing helix chain 'I' and resid 288 through 300 Processing helix chain 'J' and resid 272 through 287 Processing helix chain 'J' and resid 288 through 300 Processing helix chain 'K' and resid 272 through 287 Processing helix chain 'K' and resid 288 through 300 Processing helix chain 'L' and resid 272 through 287 Processing helix chain 'L' and resid 288 through 300 Processing helix chain 'M' and resid 272 through 287 Processing helix chain 'M' and resid 288 through 300 Processing helix chain 'N' and resid 272 through 287 Processing helix chain 'N' and resid 288 through 300 removed outlier: 3.848A pdb=" N TYR N 292 " --> pdb=" O ASP N 288 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 31 through 33 Processing sheet with id=AA2, first strand: chain 'G' and resid 47 through 51 removed outlier: 4.503A pdb=" N LEU G 73 " --> pdb=" O VAL G 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 83 through 89 removed outlier: 3.670A pdb=" N GLY G 403 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASN G 389 " --> pdb=" O TRP G 410 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 129 through 131 removed outlier: 5.746A pdb=" N LEU G 129 " --> pdb=" O VAL G 423 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N TYR G 168 " --> pdb=" O LEU G 212 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 136 through 137 removed outlier: 7.536A pdb=" N ALA G 136 " --> pdb=" O TRP G 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'G' and resid 219 through 220 removed outlier: 3.605A pdb=" N ALA G 348 " --> pdb=" O LEU G 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 241 through 243 Processing sheet with id=AA8, first strand: chain 'G' and resid 257 through 260 removed outlier: 4.070A pdb=" N ARG G 299 " --> pdb=" O GLU G 307 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 279 through 281 removed outlier: 4.343A pdb=" N PHE G 280 " --> pdb=" O LEU G 289 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 31 through 33 Processing sheet with id=AB2, first strand: chain 'A' and resid 46 through 50 Processing sheet with id=AB3, first strand: chain 'A' and resid 376 through 383 removed outlier: 3.942A pdb=" N LEU A 388 " --> pdb=" O ILE A 383 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASN A 389 " --> pdb=" O TRP A 410 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN F 58 " --> pdb=" O ASN A 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 129 through 133 Processing sheet with id=AB5, first strand: chain 'A' and resid 219 through 220 removed outlier: 3.760A pdb=" N ALA A 348 " --> pdb=" O LEU A 220 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 241 through 243 Processing sheet with id=AB7, first strand: chain 'A' and resid 257 through 260 removed outlier: 6.993A pdb=" N HIS A 305 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N VAL A 300 " --> pdb=" O HIS A 305 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU A 307 " --> pdb=" O VAL A 298 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 279 through 281 removed outlier: 6.420A pdb=" N GLN A 291 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.542A pdb=" N LYS B 31 " --> pdb=" O ILE B 361 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 46 through 50 Processing sheet with id=AC2, first strand: chain 'B' and resid 58 through 59 removed outlier: 4.604A pdb=" N GLN B 58 " --> pdb=" O ASN C 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 83 through 89 removed outlier: 3.516A pdb=" N ILE B 407 " --> pdb=" O ASP B 85 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ASN B 389 " --> pdb=" O TRP B 410 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 129 through 133 removed outlier: 6.210A pdb=" N LEU B 129 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LEU B 425 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ILE B 131 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 219 through 220 removed outlier: 3.725A pdb=" N ALA B 348 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 241 through 243 Processing sheet with id=AC7, first strand: chain 'B' and resid 257 through 260 removed outlier: 7.309A pdb=" N HIS B 305 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N VAL B 300 " --> pdb=" O HIS B 305 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU B 307 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU B 289 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LYS B 279 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N GLN B 291 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 9.468A pdb=" N GLY B 277 " --> pdb=" O GLN B 291 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ALA B 293 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N PHE B 275 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 31 through 33 removed outlier: 6.271A pdb=" N LYS F 31 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N SER F 363 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N TYR F 33 " --> pdb=" O SER F 363 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN F 389 " --> pdb=" O TRP F 410 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 31 through 33 removed outlier: 6.271A pdb=" N LYS F 31 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N SER F 363 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N TYR F 33 " --> pdb=" O SER F 363 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY F 403 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLN E 58 " --> pdb=" O ASN F 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 47 through 51 removed outlier: 4.488A pdb=" N LEU F 73 " --> pdb=" O VAL F 51 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 129 through 133 removed outlier: 3.500A pdb=" N SER F 133 " --> pdb=" O LEU F 425 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR F 166 " --> pdb=" O ASP F 210 " (cutoff:3.500A) removed outlier: 7.470A pdb=" N LEU F 212 " --> pdb=" O THR F 166 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR F 168 " --> pdb=" O LEU F 212 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 219 through 220 removed outlier: 3.578A pdb=" N ALA F 348 " --> pdb=" O LEU F 220 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 241 through 243 Processing sheet with id=AD5, first strand: chain 'F' and resid 257 through 260 removed outlier: 6.950A pdb=" N GLU F 307 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N LEU F 289 " --> pdb=" O LYS F 279 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N LYS F 279 " --> pdb=" O LEU F 289 " (cutoff:3.500A) removed outlier: 10.145A pdb=" N GLN F 291 " --> pdb=" O GLY F 277 " (cutoff:3.500A) removed outlier: 9.365A pdb=" N GLY F 277 " --> pdb=" O GLN F 291 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N ALA F 293 " --> pdb=" O PHE F 275 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N PHE F 275 " --> pdb=" O ALA F 293 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 31 through 33 removed outlier: 6.471A pdb=" N LYS C 31 " --> pdb=" O ILE C 361 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 47 through 50 Processing sheet with id=AD8, first strand: chain 'C' and resid 86 through 89 removed outlier: 3.808A pdb=" N GLY C 403 " --> pdb=" O LEU C 89 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN C 389 " --> pdb=" O TRP C 410 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 131 through 133 removed outlier: 3.525A pdb=" N SER C 133 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 219 through 220 removed outlier: 3.623A pdb=" N ALA C 348 " --> pdb=" O LEU C 220 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 242 through 243 Processing sheet with id=AE3, first strand: chain 'C' and resid 257 through 260 removed outlier: 6.963A pdb=" N HIS C 305 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL C 300 " --> pdb=" O HIS C 305 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLU C 307 " --> pdb=" O VAL C 298 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 279 through 281 removed outlier: 4.563A pdb=" N PHE C 280 " --> pdb=" O LEU C 289 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 31 through 33 removed outlier: 6.593A pdb=" N LYS D 31 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N SER D 363 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR D 33 " --> pdb=" O SER D 363 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY D 403 " --> pdb=" O LEU D 89 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 31 through 33 removed outlier: 6.593A pdb=" N LYS D 31 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N SER D 363 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N TYR D 33 " --> pdb=" O SER D 363 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN D 389 " --> pdb=" O TRP D 410 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 47 through 50 Processing sheet with id=AE8, first strand: chain 'D' and resid 58 through 59 removed outlier: 4.425A pdb=" N GLN D 58 " --> pdb=" O ASN E 84 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY E 403 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ASN E 389 " --> pdb=" O TRP E 410 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 129 through 133 Processing sheet with id=AF1, first strand: chain 'D' and resid 219 through 220 removed outlier: 3.564A pdb=" N ALA D 348 " --> pdb=" O LEU D 220 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 241 through 243 Processing sheet with id=AF3, first strand: chain 'D' and resid 257 through 260 removed outlier: 6.781A pdb=" N GLU D 307 " --> pdb=" O VAL D 298 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 279 through 281 removed outlier: 4.894A pdb=" N PHE D 280 " --> pdb=" O LEU D 289 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 31 through 33 removed outlier: 6.275A pdb=" N LYS E 31 " --> pdb=" O ILE E 361 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 47 through 50 Processing sheet with id=AF7, first strand: chain 'E' and resid 129 through 133 removed outlier: 3.545A pdb=" N SER E 133 " --> pdb=" O LEU E 425 " (cutoff:3.500A) removed outlier: 7.867A pdb=" N LEU E 212 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N TYR E 168 " --> pdb=" O LEU E 212 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 219 through 220 removed outlier: 3.540A pdb=" N ALA E 348 " --> pdb=" O LEU E 220 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 241 through 243 Processing sheet with id=AG1, first strand: chain 'E' and resid 257 through 260 removed outlier: 6.896A pdb=" N GLU E 307 " --> pdb=" O VAL E 298 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'E' and resid 279 through 281 removed outlier: 6.468A pdb=" N GLN E 291 " --> pdb=" O PHE E 280 " (cutoff:3.500A) 973 hydrogen bonds defined for protein. 2700 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: 7.75 Time building geometry restraints manager: 9.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4180 1.31 - 1.44: 5879 1.44 - 1.56: 14010 1.56 - 1.69: 1 1.69 - 1.81: 189 Bond restraints: 24259 Sorted by residual: bond pdb=" CA GLN B 395 " pdb=" C GLN B 395 " ideal model delta sigma weight residual 1.521 1.467 0.054 1.21e-02 6.83e+03 1.96e+01 bond pdb=" CA PRO A 25 " pdb=" CB PRO A 25 " ideal model delta sigma weight residual 1.533 1.475 0.058 1.42e-02 4.96e+03 1.68e+01 bond pdb=" C THR A 19 " pdb=" O THR A 19 " ideal model delta sigma weight residual 1.237 1.191 0.046 1.19e-02 7.06e+03 1.47e+01 bond pdb=" CA SER A 21 " pdb=" C SER A 21 " ideal model delta sigma weight residual 1.522 1.470 0.052 1.39e-02 5.18e+03 1.40e+01 bond pdb=" C GLN B 395 " pdb=" O GLN B 395 " ideal model delta sigma weight residual 1.234 1.191 0.043 1.20e-02 6.94e+03 1.28e+01 ... (remaining 24254 not shown) Histogram of bond angle deviations from ideal: 97.01 - 104.42: 419 104.42 - 111.83: 11996 111.83 - 119.24: 8110 119.24 - 126.65: 12067 126.65 - 134.06: 313 Bond angle restraints: 32905 Sorted by residual: angle pdb=" C SER A 44 " pdb=" CA SER A 44 " pdb=" CB SER A 44 " ideal model delta sigma weight residual 116.54 111.02 5.52 1.15e+00 7.56e-01 2.30e+01 angle pdb=" N ALA A 22 " pdb=" CA ALA A 22 " pdb=" C ALA A 22 " ideal model delta sigma weight residual 112.04 118.81 -6.77 1.44e+00 4.82e-01 2.21e+01 angle pdb=" C PRO A 25 " pdb=" CA PRO A 25 " pdb=" CB PRO A 25 " ideal model delta sigma weight residual 111.56 104.19 7.37 1.65e+00 3.67e-01 2.00e+01 angle pdb=" N MET A 164 " pdb=" CA MET A 164 " pdb=" C MET A 164 " ideal model delta sigma weight residual 114.75 109.84 4.91 1.26e+00 6.30e-01 1.52e+01 angle pdb=" N SER B 399 " pdb=" CA SER B 399 " pdb=" C SER B 399 " ideal model delta sigma weight residual 113.18 108.57 4.61 1.21e+00 6.83e-01 1.45e+01 ... (remaining 32900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13594 17.98 - 35.96: 1011 35.96 - 53.94: 159 53.94 - 71.92: 31 71.92 - 89.90: 14 Dihedral angle restraints: 14809 sinusoidal: 5779 harmonic: 9030 Sorted by residual: dihedral pdb=" CA ARG A 162 " pdb=" C ARG A 162 " pdb=" N ASP A 163 " pdb=" CA ASP A 163 " ideal model delta harmonic sigma weight residual 180.00 -150.41 -29.59 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA ARG B 162 " pdb=" C ARG B 162 " pdb=" N ASP B 163 " pdb=" CA ASP B 163 " ideal model delta harmonic sigma weight residual 180.00 -152.40 -27.60 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA TRP G 145 " pdb=" C TRP G 145 " pdb=" N ASN G 146 " pdb=" CA ASN G 146 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 14806 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 3379 0.068 - 0.137: 418 0.137 - 0.205: 10 0.205 - 0.273: 5 0.273 - 0.341: 2 Chirality restraints: 3814 Sorted by residual: chirality pdb=" CA ALA A 22 " pdb=" N ALA A 22 " pdb=" C ALA A 22 " pdb=" CB ALA A 22 " both_signs ideal model delta sigma weight residual False 2.48 2.14 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA ILE A 20 " pdb=" N ILE A 20 " pdb=" C ILE A 20 " pdb=" CB ILE A 20 " both_signs ideal model delta sigma weight residual False 2.43 2.15 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CA ASN E 161 " pdb=" N ASN E 161 " pdb=" C ASN E 161 " pdb=" CB ASN E 161 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.41e+00 ... (remaining 3811 not shown) Planarity restraints: 4303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 410 " 0.027 2.00e-02 2.50e+03 2.15e-02 1.16e+01 pdb=" CG TRP F 410 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP F 410 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP F 410 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP F 410 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP F 410 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 410 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 410 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 410 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP F 410 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER G 55 " 0.045 5.00e-02 4.00e+02 6.69e-02 7.16e+00 pdb=" N PRO G 56 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO G 56 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO G 56 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 24 " -0.043 5.00e-02 4.00e+02 6.54e-02 6.84e+00 pdb=" N PRO D 25 " 0.113 5.00e-02 4.00e+02 pdb=" CA PRO D 25 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 25 " -0.036 5.00e-02 4.00e+02 ... (remaining 4300 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 257 2.63 - 3.19: 21241 3.19 - 3.76: 35498 3.76 - 4.33: 51339 4.33 - 4.90: 87002 Nonbonded interactions: 195337 Sorted by model distance: nonbonded pdb=" O ASN E 161 " pdb=" ND2 ASN E 161 " model vdw 2.058 2.520 nonbonded pdb=" OE1 GLU B 52 " pdb=" NH2 ARG C 109 " model vdw 2.196 2.520 nonbonded pdb=" NH2 ARG C 158 " pdb=" OE1 GLN C 283 " model vdw 2.214 2.520 nonbonded pdb=" NH2 ARG F 213 " pdb=" OE2 GLU E 152 " model vdw 2.222 2.520 nonbonded pdb=" OE2 GLU A 152 " pdb=" NH2 ARG B 213 " model vdw 2.225 2.520 ... (remaining 195332 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 192 or resid 210 through 430)) selection = (chain 'B' and (resid 2 through 192 or resid 210 through 430)) selection = (chain 'C' and (resid 2 through 192 or resid 210 through 430)) selection = chain 'D' selection = chain 'E' selection = (chain 'F' and (resid 2 through 192 or resid 210 through 430)) selection = (chain 'G' and (resid 2 through 192 or resid 210 through 430)) } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 1.920 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: 0.020 Extract box with map and model: 8.290 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 59.440 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.150 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:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 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 : 0.005 0.070 24259 Z= 0.344 Angle : 0.623 10.373 32905 Z= 0.345 Chirality : 0.044 0.341 3814 Planarity : 0.004 0.067 4303 Dihedral : 13.195 89.903 8941 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.04 % Allowed : 0.51 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.33 (0.14), residues: 3085 helix: 1.97 (0.18), residues: 747 sheet: -0.61 (0.19), residues: 725 loop : -1.09 (0.14), residues: 1613 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP F 410 HIS 0.002 0.001 HIS B 305 PHE 0.026 0.002 PHE E 86 TYR 0.014 0.002 TYR C 175 ARG 0.008 0.001 ARG G 185 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 368 time to evaluate : 3.012 Fit side-chains revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. REVERT: K 280 MET cc_start: 0.7667 (mtp) cc_final: 0.7424 (mtt) REVERT: M 280 MET cc_start: 0.8344 (mtm) cc_final: 0.8020 (mtm) outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 1.6137 time to fit residues: 665.2049 Evaluate side-chains 208 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 2.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 2.9990 chunk 235 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 159 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 243 optimal weight: 0.4980 chunk 94 optimal weight: 1.9990 chunk 148 optimal weight: 10.0000 chunk 181 optimal weight: 3.9990 chunk 282 optimal weight: 0.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 305 HIS A 121 ASN A 291 GLN F 41 GLN F 204 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 369 ASN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 88 GLN E 305 HIS E 364 GLN ** H 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 24259 Z= 0.180 Angle : 0.542 8.237 32905 Z= 0.284 Chirality : 0.041 0.202 3814 Planarity : 0.004 0.045 4303 Dihedral : 4.385 28.446 3319 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.08 % Allowed : 8.11 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.10 (0.14), residues: 3085 helix: 2.25 (0.18), residues: 764 sheet: -0.30 (0.19), residues: 723 loop : -1.14 (0.14), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP F 410 HIS 0.008 0.001 HIS C 370 PHE 0.016 0.001 PHE E 170 TYR 0.020 0.001 TYR E 411 ARG 0.008 0.000 ARG F 185 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 223 time to evaluate : 2.820 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. REVERT: A 267 MET cc_start: 0.7141 (mmm) cc_final: 0.6826 (mtm) REVERT: C 284 MET cc_start: 0.6709 (OUTLIER) cc_final: 0.6298 (mtp) REVERT: E 54 GLU cc_start: 0.7198 (OUTLIER) cc_final: 0.6987 (mt-10) REVERT: K 280 MET cc_start: 0.7537 (mtp) cc_final: 0.7204 (mtt) REVERT: M 280 MET cc_start: 0.8353 (mtm) cc_final: 0.8085 (mtm) outliers start: 53 outliers final: 15 residues processed: 248 average time/residue: 1.6210 time to fit residues: 453.5960 Evaluate side-chains 215 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 198 time to evaluate : 2.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 301 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 3.9990 chunk 87 optimal weight: 4.9990 chunk 235 optimal weight: 9.9990 chunk 192 optimal weight: 0.9990 chunk 77 optimal weight: 20.0000 chunk 282 optimal weight: 6.9990 chunk 305 optimal weight: 1.9990 chunk 251 optimal weight: 0.0980 chunk 280 optimal weight: 2.9990 chunk 96 optimal weight: 8.9990 chunk 226 optimal weight: 7.9990 overall best weight: 2.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 305 HIS A 121 ASN ** A 341 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN B 105 GLN F 41 GLN F 53 GLN F 204 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN E 364 GLN ** H 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 24259 Z= 0.221 Angle : 0.522 8.251 32905 Z= 0.271 Chirality : 0.041 0.196 3814 Planarity : 0.004 0.045 4303 Dihedral : 4.350 29.017 3319 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.19 % Allowed : 9.79 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.03 (0.15), residues: 3085 helix: 2.24 (0.18), residues: 781 sheet: -0.29 (0.19), residues: 703 loop : -1.07 (0.14), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP F 410 HIS 0.003 0.001 HIS F 370 PHE 0.016 0.001 PHE A 86 TYR 0.015 0.001 TYR E 411 ARG 0.005 0.000 ARG F 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 206 time to evaluate : 3.002 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.4022 (mm-30) cc_final: 0.3538 (mm-30) REVERT: G 81 GLU cc_start: 0.5526 (tm-30) cc_final: 0.4382 (tt0) REVERT: A 267 MET cc_start: 0.7167 (mmm) cc_final: 0.6830 (mtm) REVERT: A 364 GLN cc_start: 0.6878 (OUTLIER) cc_final: 0.6664 (pt0) REVERT: E 52 GLU cc_start: 0.6650 (OUTLIER) cc_final: 0.6431 (tm-30) REVERT: E 54 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6967 (mt-10) REVERT: K 280 MET cc_start: 0.7586 (mtp) cc_final: 0.7264 (mtt) REVERT: M 280 MET cc_start: 0.8315 (mtm) cc_final: 0.8035 (mtm) outliers start: 56 outliers final: 25 residues processed: 237 average time/residue: 1.5655 time to fit residues: 419.8925 Evaluate side-chains 221 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 193 time to evaluate : 2.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 102 ARG Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 364 GLN Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 280 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 7.9990 chunk 212 optimal weight: 0.0870 chunk 146 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 135 optimal weight: 7.9990 chunk 189 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 chunk 300 optimal weight: 0.8980 chunk 148 optimal weight: 0.6980 chunk 269 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 overall best weight: 1.0760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** A 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN F 204 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 GLN ** H 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24259 Z= 0.164 Angle : 0.497 10.285 32905 Z= 0.256 Chirality : 0.040 0.182 3814 Planarity : 0.003 0.041 4303 Dihedral : 4.211 27.443 3319 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.68 % Allowed : 11.48 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.01 (0.15), residues: 3085 helix: 2.32 (0.18), residues: 782 sheet: -0.29 (0.19), residues: 710 loop : -1.06 (0.14), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 145 HIS 0.002 0.000 HIS A 305 PHE 0.013 0.001 PHE E 170 TYR 0.012 0.001 TYR D 168 ARG 0.004 0.000 ARG F 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 209 time to evaluate : 2.758 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.3916 (mm-30) cc_final: 0.3434 (mm-30) REVERT: G 81 GLU cc_start: 0.5221 (tm-30) cc_final: 0.4200 (tt0) REVERT: A 267 MET cc_start: 0.7204 (mmm) cc_final: 0.6895 (mtm) REVERT: M 280 MET cc_start: 0.8238 (mtm) cc_final: 0.7953 (mtm) outliers start: 43 outliers final: 23 residues processed: 231 average time/residue: 1.5352 time to fit residues: 401.2508 Evaluate side-chains 214 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 371 GLU Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 279 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 223 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 256 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 0.0670 chunk 269 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN F 41 GLN F 204 GLN F 283 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 ASN ** E 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24259 Z= 0.248 Angle : 0.525 11.384 32905 Z= 0.269 Chirality : 0.041 0.192 3814 Planarity : 0.003 0.045 4303 Dihedral : 4.299 27.780 3319 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.47 % Allowed : 11.91 % Favored : 85.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.03 (0.14), residues: 3085 helix: 2.34 (0.18), residues: 783 sheet: -0.24 (0.19), residues: 694 loop : -1.06 (0.14), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 410 HIS 0.003 0.001 HIS C 305 PHE 0.015 0.001 PHE D 86 TYR 0.011 0.001 TYR F 33 ARG 0.007 0.000 ARG A 185 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 195 time to evaluate : 2.957 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.4217 (mm-30) cc_final: 0.3114 (mm-30) REVERT: G 81 GLU cc_start: 0.5415 (tm-30) cc_final: 0.3730 (tt0) REVERT: A 267 MET cc_start: 0.7266 (mmm) cc_final: 0.6943 (mtm) REVERT: F 122 MET cc_start: 0.6853 (OUTLIER) cc_final: 0.6425 (ttm) REVERT: E 52 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6450 (tm-30) REVERT: M 280 MET cc_start: 0.8249 (mtm) cc_final: 0.7952 (mtm) outliers start: 63 outliers final: 33 residues processed: 235 average time/residue: 1.5432 time to fit residues: 411.8813 Evaluate side-chains 218 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 132 THR Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain A residue 8 ILE Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 307 GLU Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 139 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 280 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 7.9990 chunk 270 optimal weight: 0.4980 chunk 59 optimal weight: 8.9990 chunk 176 optimal weight: 9.9990 chunk 74 optimal weight: 6.9990 chunk 300 optimal weight: 1.9990 chunk 249 optimal weight: 8.9990 chunk 139 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 99 optimal weight: 20.0000 chunk 157 optimal weight: 10.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN F 283 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 ASN ** E 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 24259 Z= 0.325 Angle : 0.562 9.404 32905 Z= 0.289 Chirality : 0.042 0.213 3814 Planarity : 0.004 0.049 4303 Dihedral : 4.503 27.828 3319 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.55 % Allowed : 12.38 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.04 (0.14), residues: 3085 helix: 2.27 (0.18), residues: 784 sheet: -0.28 (0.19), residues: 694 loop : -1.11 (0.14), residues: 1607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 145 HIS 0.004 0.001 HIS C 305 PHE 0.019 0.002 PHE D 86 TYR 0.010 0.001 TYR A 180 ARG 0.008 0.000 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 194 time to evaluate : 3.159 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.3809 (mm-30) cc_final: 0.2851 (mm-30) REVERT: G 81 GLU cc_start: 0.5389 (tm-30) cc_final: 0.3642 (tt0) REVERT: A 267 MET cc_start: 0.7358 (mmm) cc_final: 0.7105 (mtm) REVERT: E 52 GLU cc_start: 0.6728 (OUTLIER) cc_final: 0.6466 (tm-30) REVERT: E 54 GLU cc_start: 0.7242 (OUTLIER) cc_final: 0.6981 (mt-10) REVERT: M 280 MET cc_start: 0.8266 (mtm) cc_final: 0.7981 (mtm) outliers start: 65 outliers final: 32 residues processed: 234 average time/residue: 1.5413 time to fit residues: 409.8205 Evaluate side-chains 218 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 184 time to evaluate : 4.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 297 VAL Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 371 GLU Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 54 GLU Chi-restraints excluded: chain E residue 118 LYS Chi-restraints excluded: chain E residue 226 THR Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 279 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 171 optimal weight: 6.9990 chunk 219 optimal weight: 0.7980 chunk 170 optimal weight: 0.9980 chunk 253 optimal weight: 0.5980 chunk 168 optimal weight: 7.9990 chunk 299 optimal weight: 10.0000 chunk 187 optimal weight: 10.0000 chunk 182 optimal weight: 6.9990 chunk 138 optimal weight: 4.9990 overall best weight: 2.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 171 ASN D 351 ASN ** E 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 24259 Z= 0.265 Angle : 0.541 12.766 32905 Z= 0.278 Chirality : 0.041 0.199 3814 Planarity : 0.003 0.050 4303 Dihedral : 4.457 27.008 3319 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.31 % Allowed : 12.93 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.08 (0.14), residues: 3085 helix: 2.22 (0.17), residues: 795 sheet: -0.28 (0.19), residues: 689 loop : -1.15 (0.14), residues: 1601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 145 HIS 0.002 0.001 HIS C 305 PHE 0.015 0.001 PHE D 86 TYR 0.013 0.001 TYR D 168 ARG 0.011 0.000 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 196 time to evaluate : 2.758 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.4086 (mm-30) cc_final: 0.3015 (tp30) REVERT: G 81 GLU cc_start: 0.5380 (OUTLIER) cc_final: 0.3527 (tt0) REVERT: A 267 MET cc_start: 0.7382 (mmm) cc_final: 0.7095 (mtm) REVERT: C 284 MET cc_start: 0.6954 (OUTLIER) cc_final: 0.6526 (mtp) REVERT: E 52 GLU cc_start: 0.6734 (OUTLIER) cc_final: 0.6491 (tm-30) REVERT: M 280 MET cc_start: 0.8291 (mtm) cc_final: 0.7982 (mtm) outliers start: 59 outliers final: 35 residues processed: 236 average time/residue: 1.4796 time to fit residues: 396.6905 Evaluate side-chains 222 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 184 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 280 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 4.9990 chunk 119 optimal weight: 5.9990 chunk 179 optimal weight: 8.9990 chunk 90 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 190 optimal weight: 5.9990 chunk 204 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 27 optimal weight: 10.0000 chunk 235 optimal weight: 7.9990 chunk 272 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 389 ASN ** G 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN F 41 GLN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN F 305 HIS ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 364 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 ASN ** E 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 24259 Z= 0.457 Angle : 0.619 14.100 32905 Z= 0.318 Chirality : 0.043 0.228 3814 Planarity : 0.004 0.049 4303 Dihedral : 4.739 26.879 3319 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.55 % Allowed : 13.08 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.22 (0.14), residues: 3085 helix: 2.06 (0.18), residues: 795 sheet: -0.31 (0.19), residues: 685 loop : -1.24 (0.13), residues: 1605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP G 145 HIS 0.005 0.001 HIS C 305 PHE 0.024 0.002 PHE D 86 TYR 0.013 0.002 TYR A 180 ARG 0.012 0.001 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 176 time to evaluate : 3.003 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 81 GLU cc_start: 0.5593 (OUTLIER) cc_final: 0.3520 (tt0) REVERT: A 52 GLU cc_start: 0.6381 (mt-10) cc_final: 0.5482 (mt-10) REVERT: A 267 MET cc_start: 0.7441 (mmm) cc_final: 0.7191 (mtm) REVERT: C 284 MET cc_start: 0.6981 (OUTLIER) cc_final: 0.6538 (mtp) REVERT: E 40 MET cc_start: 0.4152 (OUTLIER) cc_final: 0.3718 (tmt) REVERT: E 52 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6521 (tm-30) REVERT: M 280 MET cc_start: 0.8288 (mtm) cc_final: 0.7987 (mtm) outliers start: 65 outliers final: 41 residues processed: 217 average time/residue: 1.5675 time to fit residues: 391.7185 Evaluate side-chains 217 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 172 time to evaluate : 2.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 210 ASP Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 61 TRP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 330 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain I residue 290 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 2.9990 chunk 262 optimal weight: 6.9990 chunk 279 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 219 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 chunk 264 optimal weight: 0.9990 chunk 278 optimal weight: 0.8980 chunk 183 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 ASN F 204 GLN F 351 ASN F 364 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24259 Z= 0.178 Angle : 0.524 13.000 32905 Z= 0.269 Chirality : 0.041 0.192 3814 Planarity : 0.003 0.052 4303 Dihedral : 4.425 29.126 3319 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.96 % Allowed : 13.79 % Favored : 84.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.12 (0.14), residues: 3085 helix: 2.14 (0.17), residues: 801 sheet: -0.27 (0.18), residues: 724 loop : -1.20 (0.14), residues: 1560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 354 HIS 0.002 0.000 HIS A 305 PHE 0.012 0.001 PHE F 170 TYR 0.008 0.001 TYR A 100 ARG 0.013 0.000 ARG F 203 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 195 time to evaluate : 2.666 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 59 GLU cc_start: 0.3952 (mm-30) cc_final: 0.2752 (mm-30) REVERT: G 81 GLU cc_start: 0.5193 (OUTLIER) cc_final: 0.3459 (tt0) REVERT: A 267 MET cc_start: 0.7379 (mmm) cc_final: 0.7134 (mtm) REVERT: C 284 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6562 (mtp) REVERT: E 52 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6526 (tm-30) REVERT: K 280 MET cc_start: 0.7746 (tpp) cc_final: 0.7400 (mtt) REVERT: M 280 MET cc_start: 0.8259 (mtm) cc_final: 0.7954 (mtm) outliers start: 50 outliers final: 34 residues processed: 229 average time/residue: 1.5144 time to fit residues: 392.3839 Evaluate side-chains 223 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 186 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 84 ASN Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 152 GLU Chi-restraints excluded: chain C residue 284 MET Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 61 TRP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain H residue 280 MET Chi-restraints excluded: chain I residue 290 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 295 optimal weight: 7.9990 chunk 180 optimal weight: 7.9990 chunk 140 optimal weight: 6.9990 chunk 205 optimal weight: 4.9990 chunk 309 optimal weight: 50.0000 chunk 285 optimal weight: 2.9990 chunk 246 optimal weight: 10.0000 chunk 25 optimal weight: 7.9990 chunk 190 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 195 optimal weight: 9.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 251 ASN B 41 GLN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 GLN F 204 GLN F 364 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 24259 Z= 0.468 Angle : 0.629 13.013 32905 Z= 0.322 Chirality : 0.043 0.225 3814 Planarity : 0.004 0.060 4303 Dihedral : 4.718 28.067 3319 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.00 % Allowed : 14.02 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.20 (0.14), residues: 3085 helix: 2.10 (0.18), residues: 795 sheet: -0.33 (0.18), residues: 720 loop : -1.25 (0.14), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 145 HIS 0.004 0.001 HIS C 305 PHE 0.022 0.002 PHE D 86 TYR 0.015 0.002 TYR D 168 ARG 0.013 0.001 ARG F 203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6170 Ramachandran restraints generated. 3085 Oldfield, 0 Emsley, 3085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 172 time to evaluate : 2.557 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: G 81 GLU cc_start: 0.5572 (OUTLIER) cc_final: 0.3583 (tt0) REVERT: A 267 MET cc_start: 0.7445 (mmm) cc_final: 0.7213 (mtm) REVERT: E 40 MET cc_start: 0.4055 (OUTLIER) cc_final: 0.3364 (mmp) REVERT: E 52 GLU cc_start: 0.6773 (OUTLIER) cc_final: 0.6569 (tm-30) REVERT: M 280 MET cc_start: 0.8297 (mtm) cc_final: 0.7999 (mtm) outliers start: 51 outliers final: 39 residues processed: 209 average time/residue: 1.5932 time to fit residues: 376.2989 Evaluate side-chains 212 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 170 time to evaluate : 2.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 81 GLU Chi-restraints excluded: chain G residue 84 ASN Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 298 VAL Chi-restraints excluded: chain G residue 309 THR Chi-restraints excluded: chain G residue 423 VAL Chi-restraints excluded: chain A residue 126 MET Chi-restraints excluded: chain A residue 155 MET Chi-restraints excluded: chain A residue 210 ASP Chi-restraints excluded: chain A residue 306 VAL Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 57 THR Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain B residue 235 SER Chi-restraints excluded: chain B residue 302 ASP Chi-restraints excluded: chain B residue 356 ASP Chi-restraints excluded: chain B residue 357 ASP Chi-restraints excluded: chain B residue 385 ASP Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 297 VAL Chi-restraints excluded: chain F residue 301 VAL Chi-restraints excluded: chain F residue 306 VAL Chi-restraints excluded: chain F residue 338 MET Chi-restraints excluded: chain C residue 297 VAL Chi-restraints excluded: chain C residue 306 VAL Chi-restraints excluded: chain C residue 416 THR Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 224 THR Chi-restraints excluded: chain D residue 369 ASN Chi-restraints excluded: chain D residue 376 MET Chi-restraints excluded: chain E residue 40 MET Chi-restraints excluded: chain E residue 52 GLU Chi-restraints excluded: chain E residue 61 TRP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 313 VAL Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain H residue 279 GLN Chi-restraints excluded: chain I residue 290 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 227 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 247 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 253 optimal weight: 0.4980 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 chunk 216 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 41 GLN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 GLN F 364 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.089823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.068333 restraints weight = 52025.970| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.63 r_work: 0.2902 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 24259 Z= 0.210 Angle : 0.546 13.543 32905 Z= 0.279 Chirality : 0.041 0.218 3814 Planarity : 0.003 0.056 4303 Dihedral : 4.469 26.756 3319 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 1.68 % Allowed : 14.18 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.16 (0.14), residues: 3085 helix: 2.09 (0.17), residues: 807 sheet: -0.29 (0.18), residues: 727 loop : -1.23 (0.14), residues: 1551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 145 HIS 0.002 0.001 HIS A 305 PHE 0.012 0.001 PHE B 170 TYR 0.013 0.001 TYR D 168 ARG 0.013 0.000 ARG F 203 =============================================================================== Job complete usr+sys time: 7440.80 seconds wall clock time: 133 minutes 16.07 seconds (7996.07 seconds total)