Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 22:44:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/04_2023/8i1v_35123.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/04_2023/8i1v_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_35123/04_2023/8i1v_35123.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/04_2023/8i1v_35123.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/04_2023/8i1v_35123.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1v_35123/04_2023/8i1v_35123.pdb" } resolution = 2.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 12.85, per 1000 atoms: 0.54 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: 9.56 Conformation dependent library (CDL) restraints added in 3.7 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: 1.69 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: 9.52 Time building geometry restraints manager: 10.19 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: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 9.220 Check model and map are aligned: 0.360 Set scattering table: 0.190 Process input model: 62.690 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.170 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:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.010 Total: 89.870 ------------------------------------------------------------------------------- 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 % 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 *********************** 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 : 2.857 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. outliers start: 1 outliers final: 0 residues processed: 368 average time/residue: 1.6885 time to fit residues: 694.8300 Evaluate side-chains 208 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 2.989 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 3.8134 ------------------------------------------------------------------------------- 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 ** H 279 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 24259 Z= 0.177 Angle : 0.547 8.320 32905 Z= 0.286 Chirality : 0.041 0.195 3814 Planarity : 0.004 0.044 4303 Dihedral : 4.391 28.352 3319 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 2.12 % 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: -0.11 (0.14), residues: 3085 helix: 2.20 (0.18), residues: 764 sheet: -0.26 (0.19), residues: 716 loop : -1.14 (0.14), residues: 1605 *********************** 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 281 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 227 time to evaluate : 2.958 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASP E 357 " (corrupted residue). Skipping it. revert: symmetry clash outliers start: 54 outliers final: 15 residues processed: 254 average time/residue: 1.7061 time to fit residues: 487.6738 Evaluate side-chains 216 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 201 time to evaluate : 2.656 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 6 average time/residue: 1.2854 time to fit residues: 12.6160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 156 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 235 optimal weight: 10.0000 chunk 192 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 282 optimal weight: 0.9980 chunk 305 optimal weight: 0.9980 chunk 251 optimal weight: 3.9990 chunk 280 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 226 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 305 HIS ** G 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN A 341 ASN A 364 GLN B 105 GLN F 41 GLN F 53 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 41 GLN E 364 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 24259 Z= 0.207 Angle : 0.518 8.179 32905 Z= 0.268 Chirality : 0.041 0.191 3814 Planarity : 0.003 0.046 4303 Dihedral : 4.313 29.244 3319 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer Outliers : 2.31 % 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: -0.27 (0.19), residues: 708 loop : -1.08 (0.14), residues: 1596 *********************** 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 271 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 212 time to evaluate : 2.847 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 outliers start: 59 outliers final: 26 residues processed: 243 average time/residue: 1.5776 time to fit residues: 433.4208 Evaluate side-chains 215 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 189 time to evaluate : 3.029 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. outliers start: 26 outliers final: 16 residues processed: 11 average time/residue: 0.8322 time to fit residues: 15.2167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 279 optimal weight: 3.9990 chunk 212 optimal weight: 1.9990 chunk 146 optimal weight: 0.0000 chunk 31 optimal weight: 2.9990 chunk 135 optimal weight: 7.9990 chunk 189 optimal weight: 1.9990 chunk 283 optimal weight: 2.9990 chunk 300 optimal weight: 9.9990 chunk 148 optimal weight: 9.9990 chunk 269 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 overall best weight: 1.9992 ------------------------------------------------------------------------------- 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 F 41 GLN F 204 GLN F 283 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 ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2055 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= 0.217 Angle : 0.516 10.883 32905 Z= 0.265 Chirality : 0.041 0.191 3814 Planarity : 0.003 0.041 4303 Dihedral : 4.295 28.489 3319 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer Outliers : 2.35 % 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 (0.14), residues: 3085 helix: 2.31 (0.18), residues: 782 sheet: -0.26 (0.19), residues: 706 loop : -1.07 (0.14), residues: 1597 *********************** 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 257 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 197 time to evaluate : 2.873 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 outliers start: 60 outliers final: 27 residues processed: 233 average time/residue: 1.6133 time to fit residues: 426.4672 Evaluate side-chains 212 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 185 time to evaluate : 2.829 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. outliers start: 27 outliers final: 21 residues processed: 7 average time/residue: 0.3978 time to fit residues: 8.1343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 250 optimal weight: 3.9990 chunk 170 optimal weight: 5.9990 chunk 4 optimal weight: 0.0670 chunk 223 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 256 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 0.2980 chunk 269 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 overall best weight: 1.8724 ------------------------------------------------------------------------------- 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** F 41 GLN F 204 GLN F 283 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 78 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 364 GLN ** E 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 24259 Z= 0.207 Angle : 0.513 11.508 32905 Z= 0.263 Chirality : 0.040 0.187 3814 Planarity : 0.003 0.045 4303 Dihedral : 4.264 27.777 3319 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 2.23 % 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: 0.02 (0.14), residues: 3085 helix: 2.31 (0.17), residues: 783 sheet: -0.23 (0.19), residues: 697 loop : -1.06 (0.14), residues: 1605 *********************** 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 250 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 193 time to evaluate : 2.851 Fit side-chains TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. outliers start: 57 outliers final: 28 residues processed: 230 average time/residue: 1.5215 time to fit residues: 398.1647 Evaluate side-chains 213 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 2.943 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. outliers start: 28 outliers final: 22 residues processed: 9 average time/residue: 0.4969 time to fit residues: 10.0390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 101 optimal weight: 3.9990 chunk 270 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 176 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 300 optimal weight: 10.0000 chunk 249 optimal weight: 8.9990 chunk 139 optimal weight: 0.7980 chunk 25 optimal weight: 0.0000 chunk 99 optimal weight: 9.9990 chunk 157 optimal weight: 10.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 364 GLN ** G 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 ASN F 41 GLN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 204 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 24259 Z= 0.168 Angle : 0.501 11.042 32905 Z= 0.256 Chirality : 0.040 0.178 3814 Planarity : 0.003 0.046 4303 Dihedral : 4.148 26.908 3319 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 2.12 % 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: 2.25 (0.17), residues: 801 sheet: -0.16 (0.19), residues: 677 loop : -1.09 (0.14), residues: 1607 *********************** 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 255 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 201 time to evaluate : 2.849 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. outliers start: 54 outliers final: 29 residues processed: 231 average time/residue: 1.6621 time to fit residues: 439.1559 Evaluate side-chains 218 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 189 time to evaluate : 2.823 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. outliers start: 29 outliers final: 22 residues processed: 9 average time/residue: 0.7809 time to fit residues: 12.7891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 290 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 171 optimal weight: 7.9990 chunk 219 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 chunk 253 optimal weight: 1.9990 chunk 168 optimal weight: 0.5980 chunk 299 optimal weight: 30.0000 chunk 187 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 138 optimal weight: 4.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 364 GLN ** G 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 41 GLN F 84 ASN F 204 GLN F 305 HIS ** F 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 53 GLN ** 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** ** E 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.056 24259 Z= 0.297 Angle : 0.552 9.234 32905 Z= 0.284 Chirality : 0.041 0.200 3814 Planarity : 0.004 0.048 4303 Dihedral : 4.427 27.318 3319 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer Outliers : 2.27 % 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: -0.02 (0.14), residues: 3085 helix: 2.24 (0.18), residues: 801 sheet: -0.23 (0.19), residues: 700 loop : -1.13 (0.14), residues: 1584 *********************** 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 252 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 194 time to evaluate : 2.826 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. outliers start: 58 outliers final: 32 residues processed: 232 average time/residue: 1.6313 time to fit residues: 429.2602 Evaluate side-chains 215 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 183 time to evaluate : 2.989 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ASP B 357 " (corrupted residue). Skipping it. outliers start: 32 outliers final: 28 residues processed: 6 average time/residue: 0.7339 time to fit residues: 9.6405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 185 optimal weight: 3.9990 chunk 119 optimal weight: 0.5980 chunk 179 optimal weight: 8.9990 chunk 90 optimal weight: 5.9990 chunk 58 optimal weight: 6.9990 chunk 190 optimal weight: 3.9990 chunk 204 optimal weight: 8.9990 chunk 148 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 235 optimal weight: 5.9990 chunk 272 optimal weight: 6.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- 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 369 ASN ** 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** 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.061 24259 Z= 0.369 Angle : 0.590 12.809 32905 Z= 0.302 Chirality : 0.042 0.214 3814 Planarity : 0.004 0.051 4303 Dihedral : 4.640 27.615 3319 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer Outliers : 2.23 % 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: 2.17 (0.17), residues: 801 sheet: -0.26 (0.19), residues: 703 loop : -1.22 (0.14), residues: 1581 *********************** 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 237 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 180 time to evaluate : 2.840 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. outliers start: 57 outliers final: 36 residues processed: 222 average time/residue: 1.5650 time to fit residues: 393.8407 Evaluate side-chains 210 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 174 time to evaluate : 2.766 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 28 residues processed: 9 average time/residue: 0.7629 time to fit residues: 12.3362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 287 optimal weight: 0.8980 chunk 262 optimal weight: 7.9990 chunk 279 optimal weight: 4.9990 chunk 168 optimal weight: 6.9990 chunk 121 optimal weight: 8.9990 chunk 219 optimal weight: 7.9990 chunk 85 optimal weight: 0.5980 chunk 252 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 278 optimal weight: 2.9990 chunk 183 optimal weight: 0.3980 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 364 GLN ** G 414 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 7 GLN ** F 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.2602 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= 0.195 Angle : 0.526 13.660 32905 Z= 0.269 Chirality : 0.040 0.192 3814 Planarity : 0.003 0.051 4303 Dihedral : 4.392 25.559 3319 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer Outliers : 1.68 % 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: -0.09 (0.14), residues: 3085 helix: 2.18 (0.17), residues: 807 sheet: -0.26 (0.19), residues: 725 loop : -1.19 (0.14), residues: 1553 *********************** 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 233 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 190 time to evaluate : 2.630 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. outliers start: 43 outliers final: 33 residues processed: 224 average time/residue: 1.5209 time to fit residues: 390.0617 Evaluate side-chains 217 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 184 time to evaluate : 2.959 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 30 residues processed: 4 average time/residue: 0.6761 time to fit residues: 7.4516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 1.9990 chunk 309 optimal weight: 0.9990 chunk 285 optimal weight: 0.9990 chunk 246 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 151 optimal weight: 7.9990 chunk 195 optimal weight: 0.0470 overall best weight: 0.9684 ------------------------------------------------------------------------------- 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** F 84 ASN F 204 GLN F 364 GLN ** C 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 364 GLN 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** ** 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: 0.7858 moved from start: 0.2674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 24259 Z= 0.159 Angle : 0.512 14.191 32905 Z= 0.260 Chirality : 0.040 0.188 3814 Planarity : 0.003 0.044 4303 Dihedral : 4.203 25.166 3319 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 1.29 % 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: -0.00 (0.14), residues: 3085 helix: 2.20 (0.17), residues: 807 sheet: -0.16 (0.19), residues: 731 loop : -1.14 (0.14), residues: 1547 ********************** 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 230 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 197 time to evaluate : 3.037 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. outliers start: 33 outliers final: 27 residues processed: 228 average time/residue: 1.3588 time to fit residues: 353.9128 Evaluate side-chains 210 residues out of total 2553 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 183 time to evaluate : 3.006 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 27 residues processed: 0 time to fit residues: 4.2259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 311 random chunks: chunk 262 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 227 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 247 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 253 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 216 optimal weight: 6.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 84 ASN F 41 GLN F 84 ASN 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 41 GLN ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.090791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.069365 restraints weight = 52076.737| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.64 r_work: 0.2917 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 24259 Z= 0.216 Angle : 0.539 13.969 32905 Z= 0.274 Chirality : 0.041 0.183 3814 Planarity : 0.003 0.063 4303 Dihedral : 4.236 25.116 3319 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer Outliers : 1.53 % 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: -0.02 (0.14), residues: 3085 helix: 2.21 (0.17), residues: 807 sheet: -0.17 (0.19), residues: 719 loop : -1.16 (0.14), residues: 1559 =============================================================================== Job complete usr+sys time: 7577.89 seconds wall clock time: 135 minutes 57.50 seconds (8157.50 seconds total)