Starting phenix.real_space_refine on Tue Mar 19 02:42:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1t_35121/03_2024/8i1t_35121.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1t_35121/03_2024/8i1t_35121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1t_35121/03_2024/8i1t_35121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1t_35121/03_2024/8i1t_35121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1t_35121/03_2024/8i1t_35121.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i1t_35121/03_2024/8i1t_35121.pdb" } resolution = 2.8 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= 0.004 sd= 1.022 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 91 5.16 5 C 14371 2.51 5 N 3976 2.21 5 O 4501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G GLU 15": "OE1" <-> "OE2" Residue "G TYR 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 93": "OD1" <-> "OD2" Residue "G ASP 96": "OD1" <-> "OD2" Residue "G GLU 116": "OE1" <-> "OE2" Residue "G ASP 143": "OD1" <-> "OD2" Residue "G TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 193": "OE1" <-> "OE2" Residue "G PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 323": "OE1" <-> "OE2" Residue "G PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 385": "OD1" <-> "OD2" Residue "A GLU 18": "OE1" <-> "OE2" Residue "A GLU 52": "OE1" <-> "OE2" Residue "A ASP 96": "OD1" <-> "OD2" Residue "A TYR 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A ASP 244": "OD1" <-> "OD2" Residue "A ASP 302": "OD1" <-> "OD2" Residue "A ASP 385": "OD1" <-> "OD2" Residue "C GLU 18": "OE1" <-> "OE2" Residue "C GLU 97": "OE1" <-> "OE2" Residue "C ASP 150": "OD1" <-> "OD2" Residue "C ASP 246": "OD1" <-> "OD2" Residue "C ASP 302": "OD1" <-> "OD2" Residue "C GLU 307": "OE1" <-> "OE2" Residue "E GLU 54": "OE1" <-> "OE2" Residue "E ASP 85": "OD1" <-> "OD2" Residue "E ASP 93": "OD1" <-> "OD2" Residue "E PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 316": "OD1" <-> "OD2" Residue "E PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F ASP 96": "OD1" <-> "OD2" Residue "F ASP 174": "OD1" <-> "OD2" Residue "F TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 244": "OD1" <-> "OD2" Residue "F ASP 317": "OD1" <-> "OD2" Residue "F ASP 347": "OD1" <-> "OD2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 302": "OD1" <-> "OD2" Residue "B PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D GLU 54": "OE1" <-> "OE2" Residue "D PHE 392": "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: 22939 Number of models: 1 Model: "" Number of chains: 7 Chain: "G" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3277 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain: "A" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3277 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain: "C" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3277 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain: "E" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3277 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain: "F" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3277 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain: "B" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3277 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Chain: "D" Number of atoms: 3277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3277 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 20, 'TRANS': 408} Time building chain proxies: 12.52, per 1000 atoms: 0.55 Number of scatterers: 22939 At special positions: 0 Unit cell: (131.44, 178.08, 196.1, 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 91 16.00 O 4501 8.00 N 3976 7.00 C 14371 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: 8.91 Conformation dependent library (CDL) restraints added in 4.6 seconds 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5614 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 51 sheets defined 23.5% alpha, 24.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.71 Creating SS restraints... Processing helix chain 'G' and resid 24 through 29 removed outlier: 3.556A pdb=" N LYS G 29 " --> pdb=" O PRO G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 36 through 43 removed outlier: 3.619A pdb=" N ARG G 42 " --> pdb=" O ALA G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 95 Processing helix chain 'G' and resid 98 through 126 removed outlier: 3.660A pdb=" N ARG G 102 " --> pdb=" O THR G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 158 removed outlier: 3.860A pdb=" N ALA G 151 " --> pdb=" O PHE G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 185 removed outlier: 3.759A pdb=" N LYS G 177 " --> pdb=" O GLN G 173 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N TYR G 180 " --> pdb=" O LYS G 176 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ASP G 181 " --> pdb=" O LYS G 177 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LYS G 184 " --> pdb=" O TYR G 180 " (cutoff:3.500A) Processing helix chain 'G' and resid 192 through 199 Processing helix chain 'G' and resid 321 through 326 Processing helix chain 'A' and resid 24 through 30 removed outlier: 3.607A pdb=" N GLN A 28 " --> pdb=" O THR A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 36 through 43 removed outlier: 3.611A pdb=" N ARG A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 95 Processing helix chain 'A' and resid 97 through 127 Processing helix chain 'A' and resid 142 through 158 Processing helix chain 'A' and resid 171 through 184 Processing helix chain 'A' and resid 189 through 198 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 'C' and resid 24 through 30 Processing helix chain 'C' and resid 36 through 43 removed outlier: 3.686A pdb=" N ARG C 42 " --> pdb=" O ALA C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 95 removed outlier: 3.697A pdb=" N ARG C 95 " --> pdb=" O ASP C 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 92 through 95' Processing helix chain 'C' and resid 97 through 127 Processing helix chain 'C' and resid 142 through 158 removed outlier: 3.503A pdb=" N MET C 155 " --> pdb=" O ALA C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 184 Processing helix chain 'C' and resid 190 through 199 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 'E' and resid 24 through 30 removed outlier: 3.585A pdb=" N GLN E 28 " --> pdb=" O THR E 24 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS E 29 " --> pdb=" O PRO E 25 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA E 30 " --> pdb=" O MET E 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 24 through 30' Processing helix chain 'E' and resid 36 through 43 Processing helix chain 'E' and resid 92 through 95 removed outlier: 3.674A pdb=" N ARG E 95 " --> pdb=" O ASP E 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 92 through 95' Processing helix chain 'E' and resid 97 through 126 Processing helix chain 'E' and resid 142 through 158 Processing helix chain 'E' and resid 171 through 184 Processing helix chain 'E' and resid 189 through 199 Processing helix chain 'E' and resid 321 through 326 Processing helix chain 'E' and resid 417 through 420 Processing helix chain 'F' and resid 24 through 30 Processing helix chain 'F' and resid 36 through 43 Processing helix chain 'F' and resid 92 through 95 removed outlier: 4.013A pdb=" N ARG F 95 " --> pdb=" O ASP F 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 92 through 95' Processing helix chain 'F' and resid 97 through 127 Processing helix chain 'F' and resid 142 through 158 Processing helix chain 'F' and resid 171 through 184 Processing helix chain 'F' and resid 189 through 198 Processing helix chain 'F' and resid 245 through 247 No H-bonds generated for 'chain 'F' and resid 245 through 247' Processing helix chain 'F' and resid 321 through 326 Processing helix chain 'F' and resid 370 through 374 removed outlier: 3.514A pdb=" N ALA F 374 " --> pdb=" O GLU F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 419 No H-bonds generated for 'chain 'F' and resid 417 through 419' Processing helix chain 'B' and resid 24 through 30 removed outlier: 3.602A pdb=" N GLN B 28 " --> pdb=" O THR B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 36 through 43 removed outlier: 3.749A pdb=" N ARG B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 95 removed outlier: 3.652A pdb=" N ARG B 95 " --> pdb=" O ASP B 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 92 through 95' Processing helix chain 'B' and resid 97 through 126 Processing helix chain 'B' and resid 142 through 158 removed outlier: 3.563A pdb=" N ALA B 151 " --> pdb=" O PHE B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 171 through 184 Processing helix chain 'B' and resid 189 through 198 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 'D' and resid 24 through 30 removed outlier: 3.521A pdb=" N GLN D 28 " --> pdb=" O THR D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 36 through 43 Processing helix chain 'D' and resid 92 through 95 removed outlier: 4.027A pdb=" N ARG D 95 " --> pdb=" O ASP D 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 92 through 95' Processing helix chain 'D' and resid 97 through 126 Processing helix chain 'D' and resid 142 through 158 Processing helix chain 'D' and resid 171 through 184 Processing helix chain 'D' and resid 189 through 198 Processing helix chain 'D' and resid 321 through 326 Processing helix chain 'D' and resid 370 through 374 removed outlier: 3.750A pdb=" N ALA D 374 " --> pdb=" O GLU D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' Processing sheet with id=AA1, first strand: chain 'G' and resid 31 through 33 removed outlier: 6.413A pdb=" N LYS G 31 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N SER G 363 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR G 33 " --> pdb=" O SER G 363 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP G 410 " --> pdb=" O GLN G 364 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 31 through 33 removed outlier: 6.413A pdb=" N LYS G 31 " --> pdb=" O ILE G 361 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N SER G 363 " --> pdb=" O LYS G 31 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N TYR G 33 " --> pdb=" O SER G 363 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N TRP G 410 " --> pdb=" O GLN G 364 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER G 402 " --> pdb=" O ASP G 397 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TRP G 410 " --> pdb=" O ASN G 389 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ASN G 389 " --> pdb=" O TRP G 410 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 47 through 50 Processing sheet with id=AA4, first strand: chain 'G' and resid 70 through 71 removed outlier: 6.271A pdb=" N LEU G 70 " --> pdb=" O ASN B 4 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 129 through 132 removed outlier: 6.513A pdb=" N LEU G 129 " --> pdb=" O VAL G 423 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU G 425 " --> pdb=" O LEU G 129 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE G 131 " --> pdb=" O LEU G 425 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N THR G 166 " --> pdb=" O ASP G 210 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N LEU G 212 " --> pdb=" O THR G 166 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR G 168 " --> pdb=" O LEU G 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AA7, first strand: chain 'G' and resid 228 through 229 removed outlier: 4.800A pdb=" N ILE G 228 " --> pdb=" O VAL G 340 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ALA G 339 " --> pdb=" O ALA G 276 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N PHE G 275 " --> pdb=" O ALA G 293 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA G 293 " --> pdb=" O PHE G 275 " (cutoff:3.500A) removed outlier: 9.106A pdb=" N GLY G 277 " --> pdb=" O GLN G 291 " (cutoff:3.500A) removed outlier: 9.790A pdb=" N GLN G 291 " --> pdb=" O GLY G 277 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LYS G 279 " --> pdb=" O LEU G 289 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU G 289 " --> pdb=" O LYS G 279 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N GLU G 307 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N VAL G 300 " --> pdb=" O HIS G 305 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N HIS G 305 " --> pdb=" O VAL G 300 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 241 through 242 Processing sheet with id=AA9, first strand: chain 'A' and resid 31 through 33 Processing sheet with id=AB1, first strand: chain 'A' and resid 74 through 77 Processing sheet with id=AB2, first strand: chain 'A' and resid 58 through 59 removed outlier: 3.521A pdb=" N SER B 402 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 377 through 383 removed outlier: 4.691A pdb=" N LEU A 388 " --> pdb=" O ILE A 383 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 129 through 132 Processing sheet with id=AB5, first strand: chain 'A' and resid 219 through 220 Processing sheet with id=AB6, first strand: chain 'A' and resid 241 through 244 removed outlier: 3.809A pdb=" N ASN A 248 " --> pdb=" O ASP A 244 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 257 through 260 removed outlier: 7.840A pdb=" N HIS A 305 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 5.285A pdb=" N VAL A 300 " --> pdb=" O HIS A 305 " (cutoff:3.500A) removed outlier: 6.702A 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: 6.252A pdb=" N GLN A 291 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 31 through 33 removed outlier: 6.294A pdb=" N LYS C 31 " --> pdb=" O ILE C 361 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N SER C 363 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N TYR C 33 " --> pdb=" O SER C 363 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 74 through 77 Processing sheet with id=AC2, first strand: chain 'C' and resid 58 through 59 removed outlier: 6.212A pdb=" N LYS D 31 " --> pdb=" O ILE D 361 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N SER D 363 " --> pdb=" O LYS D 31 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N TYR D 33 " --> pdb=" O SER D 363 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 58 through 59 removed outlier: 5.041A pdb=" N TRP D 410 " --> pdb=" O ASN D 389 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ASN D 389 " --> pdb=" O TRP D 410 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 377 through 382 Processing sheet with id=AC5, first strand: chain 'C' and resid 129 through 132 removed outlier: 6.220A pdb=" N LEU C 129 " --> pdb=" O VAL C 423 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU C 425 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE C 131 " --> pdb=" O LEU C 425 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 219 through 220 Processing sheet with id=AC7, first strand: chain 'C' and resid 241 through 243 Processing sheet with id=AC8, first strand: chain 'C' and resid 257 through 260 removed outlier: 7.369A pdb=" N HIS C 305 " --> pdb=" O VAL C 300 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL C 300 " --> pdb=" O HIS C 305 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N GLU C 307 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU C 289 " --> pdb=" O LYS C 279 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N LYS C 279 " --> pdb=" O LEU C 289 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N GLN C 291 " --> pdb=" O GLY C 277 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N GLY C 277 " --> pdb=" O GLN C 291 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ALA C 293 " --> pdb=" O PHE C 275 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE C 275 " --> pdb=" O ALA C 293 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 31 through 33 removed outlier: 6.376A pdb=" N LYS E 31 " --> pdb=" O ILE E 361 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N SER E 363 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR E 33 " --> pdb=" O SER E 363 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 47 through 50 Processing sheet with id=AD2, first strand: chain 'E' and resid 58 through 59 removed outlier: 4.243A pdb=" N LEU F 388 " --> pdb=" O ILE F 383 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 377 through 383 removed outlier: 3.551A pdb=" N LEU E 388 " --> pdb=" O ILE E 383 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 129 through 132 removed outlier: 6.275A pdb=" N LEU E 129 " --> pdb=" O VAL E 423 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N LEU E 425 " --> pdb=" O LEU E 129 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE E 131 " --> pdb=" O LEU E 425 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 219 through 220 Processing sheet with id=AD6, first strand: chain 'E' and resid 241 through 243 Processing sheet with id=AD7, first strand: chain 'E' and resid 257 through 260 removed outlier: 7.669A pdb=" N HIS E 305 " --> pdb=" O VAL E 300 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N VAL E 300 " --> pdb=" O HIS E 305 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLU E 307 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N LEU E 289 " --> pdb=" O LYS E 279 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N LYS E 279 " --> pdb=" O LEU E 289 " (cutoff:3.500A) removed outlier: 8.939A pdb=" N GLN E 291 " --> pdb=" O GLY E 277 " (cutoff:3.500A) removed outlier: 8.745A pdb=" N GLY E 277 " --> pdb=" O GLN E 291 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ALA E 293 " --> pdb=" O PHE E 275 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N PHE E 275 " --> pdb=" O ALA E 293 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 31 through 33 removed outlier: 6.398A pdb=" N LYS F 31 " --> pdb=" O ILE F 361 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N SER F 363 " --> pdb=" O LYS F 31 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR F 33 " --> pdb=" O SER F 363 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'F' and resid 47 through 50 Processing sheet with id=AE1, first strand: chain 'F' and resid 129 through 132 removed outlier: 6.086A pdb=" N LEU F 129 " --> pdb=" O VAL F 423 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU F 425 " --> pdb=" O LEU F 129 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE F 131 " --> pdb=" O LEU F 425 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'F' and resid 219 through 220 Processing sheet with id=AE3, first strand: chain 'F' and resid 241 through 243 Processing sheet with id=AE4, first strand: chain 'F' and resid 257 through 260 removed outlier: 7.347A pdb=" N HIS F 305 " --> pdb=" O VAL F 300 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N VAL F 300 " --> pdb=" O HIS F 305 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU F 307 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N PHE F 280 " --> pdb=" O LEU F 289 " (cutoff:3.500A) removed outlier: 7.177A pdb=" N GLN F 291 " --> pdb=" O VAL F 278 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL F 278 " --> pdb=" O GLN F 291 " (cutoff:3.500A) removed outlier: 8.824A pdb=" N ALA F 293 " --> pdb=" O ALA F 276 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ALA F 276 " --> pdb=" O ALA F 293 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N PHE F 295 " --> pdb=" O SER F 274 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N SER F 274 " --> pdb=" O PHE F 295 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL F 297 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N LYS F 272 " --> pdb=" O VAL F 297 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.298A pdb=" N LYS B 31 " --> pdb=" O ILE B 361 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N SER B 363 " --> pdb=" O LYS B 31 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TYR B 33 " --> pdb=" O SER B 363 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'B' and resid 47 through 50 Processing sheet with id=AE7, first strand: chain 'B' and resid 129 through 132 removed outlier: 6.397A pdb=" N LEU B 129 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N LEU B 425 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ILE B 131 " --> pdb=" O LEU B 425 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 219 through 220 Processing sheet with id=AE9, first strand: chain 'B' and resid 241 through 243 Processing sheet with id=AF1, first strand: chain 'B' and resid 257 through 260 removed outlier: 7.180A pdb=" N HIS B 305 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL B 300 " --> pdb=" O HIS B 305 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU B 307 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N LEU B 289 " --> pdb=" O LYS B 279 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N LYS B 279 " --> pdb=" O LEU B 289 " (cutoff:3.500A) removed outlier: 9.210A pdb=" N GLN B 291 " --> pdb=" O GLY B 277 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N GLY B 277 " --> pdb=" O GLN B 291 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N ALA B 293 " --> pdb=" O PHE B 275 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N PHE B 275 " --> pdb=" O ALA B 293 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 47 through 50 Processing sheet with id=AF3, first strand: chain 'D' and resid 129 through 132 removed outlier: 6.248A pdb=" N LEU D 129 " --> pdb=" O VAL D 423 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N LEU D 425 " --> pdb=" O LEU D 129 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N ILE D 131 " --> pdb=" O LEU D 425 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP D 210 " --> pdb=" O THR D 166 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 219 through 220 Processing sheet with id=AF5, first strand: chain 'D' and resid 241 through 243 Processing sheet with id=AF6, first strand: chain 'D' and resid 257 through 260 removed outlier: 3.614A pdb=" N ARG D 299 " --> pdb=" O GLU D 307 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N PHE D 280 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N GLN D 291 " --> pdb=" O VAL D 278 " (cutoff:3.500A) removed outlier: 7.394A pdb=" N VAL D 278 " --> pdb=" O GLN D 291 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N ALA D 293 " --> pdb=" O ALA D 276 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ALA D 276 " --> pdb=" O ALA D 293 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N PHE D 295 " --> pdb=" O SER D 274 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N SER D 274 " --> pdb=" O PHE D 295 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N VAL D 297 " --> pdb=" O LYS D 272 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS D 272 " --> pdb=" O VAL D 297 " (cutoff:3.500A) 858 hydrogen bonds defined for protein. 2364 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: 7.97 Time building geometry restraints manager: 9.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4422 1.32 - 1.44: 5450 1.44 - 1.57: 13298 1.57 - 1.69: 0 1.69 - 1.81: 175 Bond restraints: 23345 Sorted by residual: bond pdb=" C GLU G 323 " pdb=" O GLU G 323 " ideal model delta sigma weight residual 1.237 1.201 0.036 1.17e-02 7.31e+03 9.29e+00 bond pdb=" C THR B 200 " pdb=" N ILE B 201 " ideal model delta sigma weight residual 1.332 1.293 0.039 1.73e-02 3.34e+03 5.17e+00 bond pdb=" C LEU G 320 " pdb=" O LEU G 320 " ideal model delta sigma weight residual 1.234 1.207 0.028 1.22e-02 6.72e+03 5.14e+00 bond pdb=" N GLU G 323 " pdb=" CA GLU G 323 " ideal model delta sigma weight residual 1.459 1.435 0.024 1.21e-02 6.83e+03 4.04e+00 bond pdb=" C PRO G 322 " pdb=" N GLU G 323 " ideal model delta sigma weight residual 1.335 1.311 0.024 1.31e-02 5.83e+03 3.26e+00 ... (remaining 23340 not shown) Histogram of bond angle deviations from ideal: 98.21 - 105.40: 491 105.40 - 112.59: 12481 112.59 - 119.78: 7605 119.78 - 126.98: 10928 126.98 - 134.17: 240 Bond angle restraints: 31745 Sorted by residual: angle pdb=" C ALA C 136 " pdb=" N ILE C 137 " pdb=" CA ILE C 137 " ideal model delta sigma weight residual 121.97 132.04 -10.07 1.80e+00 3.09e-01 3.13e+01 angle pdb=" N ILE B 201 " pdb=" CA ILE B 201 " pdb=" C ILE B 201 " ideal model delta sigma weight residual 110.05 105.16 4.89 1.09e+00 8.42e-01 2.01e+01 angle pdb=" C ASN G 140 " pdb=" CA ASN G 140 " pdb=" CB ASN G 140 " ideal model delta sigma weight residual 116.34 110.65 5.69 1.40e+00 5.10e-01 1.65e+01 angle pdb=" C SER G 321 " pdb=" N PRO G 322 " pdb=" CA PRO G 322 " ideal model delta sigma weight residual 118.85 114.78 4.07 1.09e+00 8.42e-01 1.39e+01 angle pdb=" N ILE C 137 " pdb=" CA ILE C 137 " pdb=" CB ILE C 137 " ideal model delta sigma weight residual 111.23 117.34 -6.11 1.65e+00 3.67e-01 1.37e+01 ... (remaining 31740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12865 17.98 - 35.96: 1060 35.96 - 53.94: 161 53.94 - 71.92: 43 71.92 - 89.89: 25 Dihedral angle restraints: 14154 sinusoidal: 5488 harmonic: 8666 Sorted by residual: dihedral pdb=" CA THR B 200 " pdb=" C THR B 200 " pdb=" N ILE B 201 " pdb=" CA ILE B 201 " ideal model delta harmonic sigma weight residual 180.00 153.33 26.67 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA ASN C 84 " pdb=" C ASN C 84 " pdb=" N ASP C 85 " pdb=" CA ASP C 85 " ideal model delta harmonic sigma weight residual 180.00 153.77 26.23 0 5.00e+00 4.00e-02 2.75e+01 dihedral pdb=" CA TRP F 354 " pdb=" C TRP F 354 " pdb=" N ALA F 355 " pdb=" CA ALA F 355 " ideal model delta harmonic sigma weight residual 180.00 154.03 25.97 0 5.00e+00 4.00e-02 2.70e+01 ... (remaining 14151 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2559 0.045 - 0.090: 794 0.090 - 0.135: 292 0.135 - 0.180: 16 0.180 - 0.224: 7 Chirality restraints: 3668 Sorted by residual: chirality pdb=" CA THR D 309 " pdb=" N THR D 309 " pdb=" C THR D 309 " pdb=" CB THR D 309 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA THR F 309 " pdb=" N THR F 309 " pdb=" C THR F 309 " pdb=" CB THR F 309 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CA THR E 309 " pdb=" N THR E 309 " pdb=" C THR E 309 " pdb=" CB THR E 309 " both_signs ideal model delta sigma weight residual False 2.53 2.30 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 3665 not shown) Planarity restraints: 4186 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP F 354 " -0.043 2.00e-02 2.50e+03 3.72e-02 3.46e+01 pdb=" CG TRP F 354 " 0.098 2.00e-02 2.50e+03 pdb=" CD1 TRP F 354 " -0.047 2.00e-02 2.50e+03 pdb=" CD2 TRP F 354 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP F 354 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP F 354 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP F 354 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP F 354 " -0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP F 354 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP F 354 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 354 " -0.041 2.00e-02 2.50e+03 3.71e-02 3.43e+01 pdb=" CG TRP C 354 " 0.097 2.00e-02 2.50e+03 pdb=" CD1 TRP C 354 " -0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP C 354 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP C 354 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP C 354 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP C 354 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 354 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 354 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP C 354 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 354 " 0.040 2.00e-02 2.50e+03 3.59e-02 3.22e+01 pdb=" CG TRP A 354 " -0.093 2.00e-02 2.50e+03 pdb=" CD1 TRP A 354 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP A 354 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP A 354 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP A 354 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 354 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 354 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 354 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 354 " 0.006 2.00e-02 2.50e+03 ... (remaining 4183 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2189 2.74 - 3.28: 22406 3.28 - 3.82: 39736 3.82 - 4.36: 49074 4.36 - 4.90: 82104 Nonbonded interactions: 195509 Sorted by model distance: nonbonded pdb=" O PRO A 134 " pdb=" OG1 THR A 429 " model vdw 2.196 2.440 nonbonded pdb=" NZ LYS E 176 " pdb=" OD1 ASN D 146 " model vdw 2.212 2.520 nonbonded pdb=" OG1 THR C 229 " pdb=" OG SER C 262 " model vdw 2.219 2.440 nonbonded pdb=" O LEU A 217 " pdb=" NH2 ARG A 349 " model vdw 2.237 2.520 nonbonded pdb=" O VAL F 13 " pdb=" NH2 ARG F 102 " model vdw 2.263 2.520 ... (remaining 195504 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.700 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: 11.540 Check model and map are aligned: 0.360 Set scattering table: 0.220 Process input model: 61.870 Find NCS groups from input model: 1.600 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: 0.000 Load rotamer database and sin/cos tables:10.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 89.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 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 : 0.007 0.054 23345 Z= 0.456 Angle : 0.696 10.068 31745 Z= 0.382 Chirality : 0.049 0.224 3668 Planarity : 0.005 0.060 4186 Dihedral : 14.073 89.894 8540 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.21 % Favored : 96.62 % Rotamer: Outliers : 0.08 % Allowed : 0.49 % Favored : 99.43 % 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: -1.01 (0.14), residues: 2989 helix: 0.27 (0.20), residues: 670 sheet: -0.20 (0.17), residues: 793 loop : -1.35 (0.14), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.005 TRP F 354 HIS 0.005 0.001 HIS C 370 PHE 0.054 0.003 PHE E 147 TYR 0.016 0.002 TYR D 100 ARG 0.007 0.001 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 168 time to evaluate : 2.757 Fit side-chains REVERT: G 185 ARG cc_start: 0.5234 (tpt170) cc_final: 0.5030 (tmt-80) REVERT: A 338 MET cc_start: 0.8274 (ttm) cc_final: 0.7735 (ttm) REVERT: B 338 MET cc_start: 0.8600 (ptp) cc_final: 0.8177 (ptp) outliers start: 2 outliers final: 0 residues processed: 170 average time/residue: 1.3614 time to fit residues: 265.5980 Evaluate side-chains 139 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 2.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 1.9990 chunk 222 optimal weight: 0.9980 chunk 123 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 150 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 230 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 140 optimal weight: 2.9990 chunk 171 optimal weight: 0.0470 chunk 266 optimal weight: 6.9990 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 28 GLN A 248 ASN E 53 GLN E 305 HIS B 161 ASN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.0954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23345 Z= 0.175 Angle : 0.527 8.470 31745 Z= 0.284 Chirality : 0.044 0.191 3668 Planarity : 0.004 0.050 4186 Dihedral : 5.041 27.775 3206 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.74 % Favored : 97.09 % Rotamer: Outliers : 1.02 % Allowed : 5.78 % Favored : 93.20 % 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: -0.63 (0.14), residues: 2989 helix: 0.87 (0.20), residues: 673 sheet: 0.00 (0.17), residues: 783 loop : -1.23 (0.14), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP C 354 HIS 0.003 0.001 HIS G 305 PHE 0.024 0.002 PHE A 147 TYR 0.014 0.001 TYR A 100 ARG 0.002 0.000 ARG C 360 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 2.690 Fit side-chains revert: symmetry clash REVERT: G 185 ARG cc_start: 0.4814 (tpt170) cc_final: 0.4500 (tmt-80) REVERT: A 338 MET cc_start: 0.8427 (ttm) cc_final: 0.7934 (ttm) REVERT: E 246 ASP cc_start: 0.7733 (m-30) cc_final: 0.7148 (t0) REVERT: E 316 ASP cc_start: 0.6939 (t70) cc_final: 0.6506 (t0) REVERT: F 194 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7448 (mt-10) REVERT: B 338 MET cc_start: 0.8613 (ptp) cc_final: 0.8223 (ptp) outliers start: 25 outliers final: 8 residues processed: 178 average time/residue: 1.3051 time to fit residues: 268.0440 Evaluate side-chains 156 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain D residue 301 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 181 optimal weight: 0.4980 chunk 73 optimal weight: 3.9990 chunk 267 optimal weight: 9.9990 chunk 288 optimal weight: 6.9990 chunk 238 optimal weight: 9.9990 chunk 265 optimal weight: 1.9990 chunk 91 optimal weight: 6.9990 chunk 214 optimal weight: 4.9990 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN B 248 ASN ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.0951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 23345 Z= 0.262 Angle : 0.550 7.895 31745 Z= 0.294 Chirality : 0.044 0.190 3668 Planarity : 0.004 0.050 4186 Dihedral : 5.094 26.930 3206 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.98 % Favored : 96.86 % Rotamer: Outliers : 1.79 % Allowed : 7.90 % Favored : 90.31 % 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: -0.66 (0.14), residues: 2989 helix: 0.89 (0.20), residues: 680 sheet: -0.12 (0.17), residues: 794 loop : -1.23 (0.14), residues: 1515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP F 354 HIS 0.003 0.001 HIS C 370 PHE 0.030 0.002 PHE G 208 TYR 0.015 0.001 TYR A 100 ARG 0.003 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 157 time to evaluate : 2.604 Fit side-chains REVERT: G 79 MET cc_start: 0.8560 (OUTLIER) cc_final: 0.7858 (mtm) REVERT: G 185 ARG cc_start: 0.4847 (tpt170) cc_final: 0.4504 (tmt-80) REVERT: A 242 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.8014 (pt0) REVERT: A 338 MET cc_start: 0.8382 (ttm) cc_final: 0.7953 (ttm) REVERT: C 307 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: E 246 ASP cc_start: 0.7692 (m-30) cc_final: 0.7133 (t0) REVERT: E 377 LYS cc_start: 0.6003 (OUTLIER) cc_final: 0.5538 (mptt) REVERT: F 203 ARG cc_start: 0.8153 (mmp80) cc_final: 0.7847 (mmp80) REVERT: F 212 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8535 (mt) REVERT: B 40 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8662 (tpt) REVERT: B 338 MET cc_start: 0.8588 (ptp) cc_final: 0.8215 (ptp) outliers start: 44 outliers final: 19 residues processed: 182 average time/residue: 1.2980 time to fit residues: 273.1701 Evaluate side-chains 169 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 144 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 126 MET Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 40 MET Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain B residue 248 ASN Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 5.9990 chunk 201 optimal weight: 10.0000 chunk 138 optimal weight: 4.9990 chunk 29 optimal weight: 7.9990 chunk 127 optimal weight: 9.9990 chunk 179 optimal weight: 8.9990 chunk 268 optimal weight: 7.9990 chunk 284 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 76 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 23345 Z= 0.577 Angle : 0.710 9.491 31745 Z= 0.377 Chirality : 0.051 0.249 3668 Planarity : 0.005 0.062 4186 Dihedral : 5.760 29.321 3206 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.28 % Favored : 96.55 % Rotamer: Outliers : 2.48 % Allowed : 9.52 % Favored : 87.99 % 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: -1.02 (0.14), residues: 2989 helix: 0.47 (0.19), residues: 678 sheet: -0.31 (0.17), residues: 778 loop : -1.40 (0.14), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP G 354 HIS 0.005 0.002 HIS C 370 PHE 0.032 0.003 PHE G 208 TYR 0.016 0.003 TYR G 175 ARG 0.007 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 146 time to evaluate : 2.352 Fit side-chains REVERT: G 79 MET cc_start: 0.8651 (OUTLIER) cc_final: 0.7930 (mtm) REVERT: G 152 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6847 (tp30) REVERT: G 185 ARG cc_start: 0.4998 (tpt170) cc_final: 0.4624 (tmt-80) REVERT: G 209 ASP cc_start: 0.8090 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: A 242 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.8119 (pt0) REVERT: A 338 MET cc_start: 0.8252 (ttm) cc_final: 0.7932 (ttm) REVERT: C 307 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: E 377 LYS cc_start: 0.6052 (OUTLIER) cc_final: 0.5465 (mptt) REVERT: F 203 ARG cc_start: 0.8159 (mmp80) cc_final: 0.7929 (mmp80) REVERT: B 338 MET cc_start: 0.8612 (ptp) cc_final: 0.8262 (ptp) outliers start: 61 outliers final: 27 residues processed: 183 average time/residue: 1.3073 time to fit residues: 275.9557 Evaluate side-chains 174 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 141 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 347 ASP Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 242 GLN Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 141 THR Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 423 VAL Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 5.9990 chunk 161 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 211 optimal weight: 2.9990 chunk 117 optimal weight: 7.9990 chunk 242 optimal weight: 0.9980 chunk 196 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 0.6980 chunk 255 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 242 GLN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 23345 Z= 0.157 Angle : 0.505 7.766 31745 Z= 0.270 Chirality : 0.043 0.188 3668 Planarity : 0.004 0.047 4186 Dihedral : 4.902 27.071 3206 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.64 % Favored : 97.19 % Rotamer: Outliers : 1.75 % Allowed : 11.11 % Favored : 87.14 % 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: -0.67 (0.14), residues: 2989 helix: 1.01 (0.20), residues: 674 sheet: -0.17 (0.17), residues: 796 loop : -1.27 (0.14), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 354 HIS 0.002 0.000 HIS F 305 PHE 0.015 0.001 PHE A 147 TYR 0.013 0.001 TYR D 100 ARG 0.002 0.000 ARG G 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 161 time to evaluate : 2.705 Fit side-chains REVERT: G 79 MET cc_start: 0.8547 (OUTLIER) cc_final: 0.7834 (mtm) REVERT: G 185 ARG cc_start: 0.4821 (tpt170) cc_final: 0.4472 (tmt-80) REVERT: G 271 ASP cc_start: 0.7517 (p0) cc_final: 0.7089 (m-30) REVERT: A 180 TYR cc_start: 0.8300 (t80) cc_final: 0.8048 (t80) REVERT: A 338 MET cc_start: 0.8431 (ttm) cc_final: 0.7959 (ttm) REVERT: C 307 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: E 246 ASP cc_start: 0.7677 (m-30) cc_final: 0.7117 (t0) REVERT: E 376 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8066 (ptm) REVERT: F 122 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.7683 (tpp) REVERT: F 203 ARG cc_start: 0.8079 (mmp80) cc_final: 0.7850 (mmp80) REVERT: B 338 MET cc_start: 0.8580 (ptp) cc_final: 0.8251 (ptp) outliers start: 43 outliers final: 15 residues processed: 188 average time/residue: 1.2505 time to fit residues: 273.1651 Evaluate side-chains 167 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 148 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 280 PHE Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain D residue 304 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 8.9990 chunk 255 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 284 optimal weight: 7.9990 chunk 236 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 149 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 23345 Z= 0.380 Angle : 0.606 7.621 31745 Z= 0.322 Chirality : 0.046 0.210 3668 Planarity : 0.004 0.053 4186 Dihedral : 5.340 28.267 3206 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.84 % Favored : 96.96 % Rotamer: Outliers : 2.48 % Allowed : 11.52 % Favored : 86.00 % 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: -0.88 (0.14), residues: 2989 helix: 0.76 (0.19), residues: 678 sheet: -0.32 (0.17), residues: 785 loop : -1.34 (0.14), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 354 HIS 0.004 0.001 HIS C 370 PHE 0.018 0.002 PHE B 87 TYR 0.016 0.002 TYR D 100 ARG 0.004 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 145 time to evaluate : 2.790 Fit side-chains REVERT: G 79 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7892 (mtm) REVERT: G 152 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6824 (tp30) REVERT: G 185 ARG cc_start: 0.4935 (tpt170) cc_final: 0.4540 (tmt-80) REVERT: G 209 ASP cc_start: 0.8093 (OUTLIER) cc_final: 0.7887 (m-30) REVERT: A 338 MET cc_start: 0.8362 (ttm) cc_final: 0.7950 (ttm) REVERT: C 307 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8078 (tt0) REVERT: E 246 ASP cc_start: 0.7671 (m-30) cc_final: 0.7094 (t0) REVERT: E 376 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8081 (ptm) REVERT: E 377 LYS cc_start: 0.6075 (OUTLIER) cc_final: 0.5558 (mptt) REVERT: F 122 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8080 (tpp) REVERT: B 338 MET cc_start: 0.8568 (ptp) cc_final: 0.8247 (ptp) outliers start: 61 outliers final: 34 residues processed: 185 average time/residue: 1.2594 time to fit residues: 270.2362 Evaluate side-chains 183 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 142 time to evaluate : 2.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 152 GLU Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 280 PHE Chi-restraints excluded: chain G residue 347 ASP Chi-restraints excluded: chain G residue 391 ILE Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 301 VAL Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 278 VAL Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 318 VAL Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 162 optimal weight: 6.9990 chunk 207 optimal weight: 4.9990 chunk 160 optimal weight: 6.9990 chunk 239 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 283 optimal weight: 2.9990 chunk 177 optimal weight: 6.9990 chunk 172 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 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 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23345 Z= 0.177 Angle : 0.509 7.774 31745 Z= 0.271 Chirality : 0.043 0.190 3668 Planarity : 0.004 0.047 4186 Dihedral : 4.828 26.406 3206 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.54 % Favored : 97.26 % Rotamer: Outliers : 2.12 % Allowed : 12.25 % Favored : 85.63 % 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: -0.66 (0.14), residues: 2989 helix: 1.06 (0.19), residues: 674 sheet: -0.22 (0.17), residues: 796 loop : -1.25 (0.14), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 354 HIS 0.001 0.000 HIS C 370 PHE 0.016 0.002 PHE A 147 TYR 0.013 0.001 TYR A 100 ARG 0.002 0.000 ARG F 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 154 time to evaluate : 2.646 Fit side-chains revert: symmetry clash REVERT: G 79 MET cc_start: 0.8535 (OUTLIER) cc_final: 0.7854 (mtm) REVERT: G 185 ARG cc_start: 0.4874 (tpt170) cc_final: 0.4483 (tmt-80) REVERT: G 209 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: G 271 ASP cc_start: 0.7523 (p0) cc_final: 0.7225 (m-30) REVERT: A 180 TYR cc_start: 0.8326 (t80) cc_final: 0.8064 (t80) REVERT: A 338 MET cc_start: 0.8424 (ttm) cc_final: 0.7960 (ttm) REVERT: C 307 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: E 246 ASP cc_start: 0.7677 (m-30) cc_final: 0.7104 (t0) REVERT: E 376 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8002 (ptm) REVERT: E 377 LYS cc_start: 0.6297 (OUTLIER) cc_final: 0.5738 (mttp) REVERT: F 122 MET cc_start: 0.8570 (OUTLIER) cc_final: 0.7681 (tpp) REVERT: F 203 ARG cc_start: 0.7950 (mmp80) cc_final: 0.7628 (mmp80) REVERT: B 338 MET cc_start: 0.8570 (ptp) cc_final: 0.8269 (ptp) outliers start: 52 outliers final: 26 residues processed: 194 average time/residue: 1.2269 time to fit residues: 277.5296 Evaluate side-chains 177 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 145 time to evaluate : 2.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 79 MET Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 209 ASP Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 280 PHE Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 164 MET Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 291 GLN Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 30.0000 chunk 113 optimal weight: 2.9990 chunk 169 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 55 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 180 optimal weight: 9.9990 chunk 193 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 222 optimal weight: 8.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 414 ASN ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 23345 Z= 0.423 Angle : 0.623 7.725 31745 Z= 0.331 Chirality : 0.047 0.211 3668 Planarity : 0.004 0.055 4186 Dihedral : 5.391 28.968 3206 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.04 % Favored : 96.75 % Rotamer: Outliers : 2.24 % Allowed : 12.62 % Favored : 85.14 % 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: -0.92 (0.14), residues: 2989 helix: 0.72 (0.19), residues: 678 sheet: -0.37 (0.17), residues: 785 loop : -1.35 (0.14), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP G 354 HIS 0.004 0.001 HIS C 370 PHE 0.019 0.002 PHE B 87 TYR 0.014 0.002 TYR A 100 ARG 0.005 0.001 ARG A 90 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 147 time to evaluate : 2.744 Fit side-chains REVERT: G 185 ARG cc_start: 0.4986 (tpt170) cc_final: 0.4593 (tmt-80) REVERT: G 271 ASP cc_start: 0.7704 (p0) cc_final: 0.7355 (m-30) REVERT: A 338 MET cc_start: 0.8294 (ttm) cc_final: 0.7865 (ttm) REVERT: C 307 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8053 (tt0) REVERT: E 246 ASP cc_start: 0.7667 (m-30) cc_final: 0.7085 (t0) REVERT: E 376 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8068 (ptm) REVERT: E 377 LYS cc_start: 0.6089 (OUTLIER) cc_final: 0.5593 (mttp) REVERT: F 122 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.8094 (tpp) REVERT: F 203 ARG cc_start: 0.8007 (mmp80) cc_final: 0.7669 (mmp80) REVERT: B 126 MET cc_start: 0.8445 (mmt) cc_final: 0.8193 (tpp) REVERT: B 338 MET cc_start: 0.8578 (ptp) cc_final: 0.8294 (ptp) outliers start: 55 outliers final: 31 residues processed: 187 average time/residue: 1.2825 time to fit residues: 278.3569 Evaluate side-chains 176 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 141 time to evaluate : 2.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 20 ILE Chi-restraints excluded: chain G residue 98 THR Chi-restraints excluded: chain G residue 135 ASP Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 280 PHE Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 163 ASP Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 307 GLU Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 122 MET Chi-restraints excluded: chain F residue 190 ARG Chi-restraints excluded: chain F residue 245 ASN Chi-restraints excluded: chain F residue 376 MET Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain D residue 198 ASP Chi-restraints excluded: chain D residue 301 VAL Chi-restraints excluded: chain D residue 304 THR Chi-restraints excluded: chain D residue 429 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 0.9980 chunk 271 optimal weight: 1.9990 chunk 247 optimal weight: 7.9990 chunk 264 optimal weight: 4.9990 chunk 158 optimal weight: 0.0010 chunk 115 optimal weight: 1.9990 chunk 207 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 238 optimal weight: 0.0010 chunk 249 optimal weight: 0.9990 chunk 263 optimal weight: 1.9990 overall best weight: 0.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 305 HIS F 84 ASN ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 23345 Z= 0.158 Angle : 0.501 7.802 31745 Z= 0.266 Chirality : 0.043 0.186 3668 Planarity : 0.004 0.048 4186 Dihedral : 4.723 25.983 3206 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.48 % Favored : 97.32 % Rotamer: Outliers : 1.67 % Allowed : 13.27 % Favored : 85.06 % 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: -0.66 (0.14), residues: 2989 helix: 1.04 (0.19), residues: 680 sheet: -0.22 (0.17), residues: 784 loop : -1.24 (0.14), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 354 HIS 0.001 0.000 HIS G 305 PHE 0.015 0.001 PHE A 147 TYR 0.013 0.001 TYR E 100 ARG 0.004 0.000 ARG D 203 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 153 time to evaluate : 2.807 Fit side-chains REVERT: G 185 ARG cc_start: 0.4846 (tpt170) cc_final: 0.4464 (tmt-80) REVERT: A 180 TYR cc_start: 0.8229 (t80) cc_final: 0.8018 (t80) REVERT: A 338 MET cc_start: 0.8441 (ttm) cc_final: 0.8000 (ttm) REVERT: E 246 ASP cc_start: 0.7652 (m-30) cc_final: 0.7065 (t0) REVERT: E 376 MET cc_start: 0.8674 (OUTLIER) cc_final: 0.7956 (ptm) REVERT: E 377 LYS cc_start: 0.6416 (OUTLIER) cc_final: 0.5850 (mttp) REVERT: F 203 ARG cc_start: 0.7953 (mmp80) cc_final: 0.7604 (mmp80) REVERT: B 338 MET cc_start: 0.8581 (ptp) cc_final: 0.8308 (ptp) outliers start: 41 outliers final: 21 residues processed: 182 average time/residue: 1.2638 time to fit residues: 267.4414 Evaluate side-chains 169 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 146 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 280 PHE Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 376 MET Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain D residue 301 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 0.0770 chunk 279 optimal weight: 5.9990 chunk 170 optimal weight: 7.9990 chunk 132 optimal weight: 0.3980 chunk 194 optimal weight: 8.9990 chunk 292 optimal weight: 9.9990 chunk 269 optimal weight: 3.9990 chunk 233 optimal weight: 0.4980 chunk 24 optimal weight: 7.9990 chunk 180 optimal weight: 10.0000 chunk 143 optimal weight: 2.9990 overall best weight: 1.5942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23345 Z= 0.197 Angle : 0.519 7.746 31745 Z= 0.275 Chirality : 0.043 0.180 3668 Planarity : 0.004 0.043 4186 Dihedral : 4.744 24.847 3206 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.74 % Favored : 97.06 % Rotamer: Outliers : 1.06 % Allowed : 13.88 % Favored : 85.06 % 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: -0.63 (0.14), residues: 2989 helix: 1.08 (0.19), residues: 680 sheet: -0.23 (0.17), residues: 784 loop : -1.21 (0.14), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 354 HIS 0.002 0.000 HIS C 370 PHE 0.015 0.002 PHE F 188 TYR 0.013 0.001 TYR D 100 ARG 0.003 0.000 ARG D 203 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5978 Ramachandran restraints generated. 2989 Oldfield, 0 Emsley, 2989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 2.655 Fit side-chains REVERT: G 185 ARG cc_start: 0.4858 (tpt170) cc_final: 0.4451 (tmt-80) REVERT: A 338 MET cc_start: 0.8421 (ttm) cc_final: 0.7953 (ttm) REVERT: E 246 ASP cc_start: 0.7561 (m-30) cc_final: 0.7053 (t0) REVERT: E 377 LYS cc_start: 0.6297 (OUTLIER) cc_final: 0.5763 (mttp) REVERT: F 203 ARG cc_start: 0.7999 (mmp80) cc_final: 0.7651 (mmp80) REVERT: B 338 MET cc_start: 0.8580 (ptp) cc_final: 0.8307 (ptp) outliers start: 26 outliers final: 23 residues processed: 166 average time/residue: 1.2910 time to fit residues: 247.9568 Evaluate side-chains 165 residues out of total 2457 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 141 time to evaluate : 2.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 259 VAL Chi-restraints excluded: chain G residue 280 PHE Chi-restraints excluded: chain A residue 49 MET Chi-restraints excluded: chain A residue 141 THR Chi-restraints excluded: chain A residue 301 VAL Chi-restraints excluded: chain A residue 309 THR Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 137 ILE Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 278 VAL Chi-restraints excluded: chain C residue 376 MET Chi-restraints excluded: chain E residue 84 ASN Chi-restraints excluded: chain E residue 94 LEU Chi-restraints excluded: chain E residue 135 ASP Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 301 VAL Chi-restraints excluded: chain E residue 377 LYS Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 84 ASN Chi-restraints excluded: chain F residue 416 THR Chi-restraints excluded: chain B residue 278 VAL Chi-restraints excluded: chain B residue 376 MET Chi-restraints excluded: chain D residue 301 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.9990 chunk 248 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 233 optimal weight: 0.0870 chunk 97 optimal weight: 4.9990 chunk 239 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 351 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 ASN ** E 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 ASN ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.084080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.075207 restraints weight = 44966.329| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.59 r_work: 0.2891 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.117 23345 Z= 0.220 Angle : 0.687 59.071 31745 Z= 0.392 Chirality : 0.045 0.670 3668 Planarity : 0.004 0.043 4186 Dihedral : 4.771 28.210 3206 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.20 % Allowed : 2.78 % Favored : 97.02 % Rotamer: Outliers : 1.14 % Allowed : 14.00 % Favored : 84.86 % Cbeta Deviations : 0.04 % 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: -0.63 (0.14), residues: 2989 helix: 1.08 (0.19), residues: 680 sheet: -0.24 (0.17), residues: 784 loop : -1.20 (0.14), residues: 1525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 354 HIS 0.001 0.000 HIS C 370 PHE 0.014 0.002 PHE B 87 TYR 0.013 0.001 TYR D 100 ARG 0.002 0.000 ARG F 102 =============================================================================== Job complete usr+sys time: 5948.39 seconds wall clock time: 107 minutes 0.17 seconds (6420.17 seconds total)