Starting phenix.real_space_refine on Tue Aug 6 21:04:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud5_42147/08_2024/8ud5_42147.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud5_42147/08_2024/8ud5_42147.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud5_42147/08_2024/8ud5_42147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud5_42147/08_2024/8ud5_42147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud5_42147/08_2024/8ud5_42147.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud5_42147/08_2024/8ud5_42147.cif" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.042 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: 5 Type Number sf(0) Gaussians P 53 5.49 5 S 60 5.16 5 C 11133 2.51 5 N 2880 2.21 5 O 3538 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F ASP 39": "OD1" <-> "OD2" Residue "F GLU 56": "OE1" <-> "OE2" Residue "F ASP 106": "OD1" <-> "OD2" Residue "F TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 239": "OD1" <-> "OD2" Residue "F PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 323": "OD1" <-> "OD2" Residue "D PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 16": "OD1" <-> "OD2" Residue "D ASP 36": "OD1" <-> "OD2" Residue "D GLU 56": "OE1" <-> "OE2" Residue "D PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 282": "OD1" <-> "OD2" Residue "D GLU 304": "OE1" <-> "OE2" Residue "E PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 16": "OD1" <-> "OD2" Residue "E ASP 39": "OD1" <-> "OD2" Residue "E ASP 128": "OD1" <-> "OD2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "E PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 233": "OE1" <-> "OE2" Residue "E TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 264": "OE1" <-> "OE2" Residue "E ASP 296": "OD1" <-> "OD2" Residue "B PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 16": "OD1" <-> "OD2" Residue "B ASP 36": "OD1" <-> "OD2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B ASP 91": "OD1" <-> "OD2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B GLU 220": "OE1" <-> "OE2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 239": "OD1" <-> "OD2" Residue "B GLU 264": "OE1" <-> "OE2" Residue "B TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 339": "OE1" <-> "OE2" Residue "B PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 16": "OD1" <-> "OD2" Residue "A GLU 68": "OE1" <-> "OE2" Residue "A ASP 91": "OD1" <-> "OD2" Residue "A GLU 202": "OE1" <-> "OE2" Residue "A PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 264": "OE1" <-> "OE2" Residue "A ASP 296": "OD1" <-> "OD2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "C GLU 3": "OE1" <-> "OE2" Residue "C PHE 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 21": "OE1" <-> "OE2" Residue "C ASP 39": "OD1" <-> "OD2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 68": "OE1" <-> "OE2" Residue "C ASP 78": "OD1" <-> "OD2" Residue "C GLU 113": "OE1" <-> "OE2" Residue "C GLU 170": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C PHE 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 228": "OE1" <-> "OE2" Residue "C PHE 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 260": "OE1" <-> "OE2" Residue "C PHE 263": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 272": "OD1" <-> "OD2" Residue "C ASP 296": "OD1" <-> "OD2" Residue "C TYR 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 326": "OE1" <-> "OE2" Residue "C PHE 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17664 Number of models: 1 Model: "" Number of chains: 8 Chain: "F" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "D" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "E" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "B" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "A" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "C" Number of atoms: 2755 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Conformer: "B" Number of residues, atoms: 346, 2731 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} bond proxies already assigned to first conformer: 2762 Chain: "G" Number of atoms: 542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 542 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna3p_pur': 2, 'rna3p_pyr': 25} Link IDs: {'rna3p': 26} Chain: "H" Number of atoms: 592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 592 Classifications: {'RNA': 27} Modifications used: {'rna3p_pur': 25, 'rna3p_pyr': 2} Link IDs: {'rna3p': 26} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N AILE F 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE F 27 " occ=0.48 residue: pdb=" N AASN F 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN F 28 " occ=0.48 residue: pdb=" N AASN F 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN F 29 " occ=0.48 residue: pdb=" N AILE D 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE D 27 " occ=0.48 residue: pdb=" N AASN D 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN D 28 " occ=0.48 residue: pdb=" N AASN D 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN D 29 " occ=0.48 residue: pdb=" N AILE E 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE E 27 " occ=0.48 residue: pdb=" N AASN E 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN E 28 " occ=0.48 residue: pdb=" N AASN E 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN E 29 " occ=0.48 residue: pdb=" N AILE B 27 " occ=0.52 ... (14 atoms not shown) pdb=" CD1BILE B 27 " occ=0.48 residue: pdb=" N AASN B 28 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN B 28 " occ=0.48 residue: pdb=" N AASN B 29 " occ=0.52 ... (14 atoms not shown) pdb=" ND2BASN B 29 " occ=0.48 ... (remaining 6 not shown) Time building chain proxies: 19.04, per 1000 atoms: 1.08 Number of scatterers: 17664 At special positions: 0 Unit cell: (115.92, 118.68, 129.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 60 16.00 P 53 15.00 O 3538 8.00 N 2880 7.00 C 11133 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: 7.42 Conformation dependent library (CDL) restraints added in 6.2 seconds 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3924 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 46 sheets defined 26.3% alpha, 24.0% beta 20 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 6.68 Creating SS restraints... Processing helix chain 'F' and resid 1 through 13 Processing helix chain 'F' and resid 50 through 60 Processing helix chain 'F' and resid 68 through 75 Processing helix chain 'F' and resid 113 through 117 Processing helix chain 'F' and resid 129 through 137 Processing helix chain 'F' and resid 207 through 216 Processing helix chain 'F' and resid 217 through 225 Processing helix chain 'F' and resid 231 through 236 Processing helix chain 'F' and resid 250 through 261 Processing helix chain 'F' and resid 298 through 308 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 50 through 60 Processing helix chain 'D' and resid 68 through 75 Processing helix chain 'D' and resid 129 through 137 Processing helix chain 'D' and resid 207 through 216 Processing helix chain 'D' and resid 217 through 225 Processing helix chain 'D' and resid 231 through 236 Processing helix chain 'D' and resid 250 through 261 removed outlier: 3.744A pdb=" N GLU D 260 " --> pdb=" O LYS D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 308 Processing helix chain 'E' and resid 2 through 13 Processing helix chain 'E' and resid 50 through 60 Processing helix chain 'E' and resid 68 through 75 Processing helix chain 'E' and resid 129 through 136 Processing helix chain 'E' and resid 207 through 216 Processing helix chain 'E' and resid 217 through 225 Processing helix chain 'E' and resid 231 through 236 removed outlier: 3.928A pdb=" N VAL E 236 " --> pdb=" O PHE E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 250 through 261 removed outlier: 3.766A pdb=" N GLU E 260 " --> pdb=" O LYS E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 308 Processing helix chain 'B' and resid 2 through 13 Processing helix chain 'B' and resid 50 through 60 Processing helix chain 'B' and resid 68 through 75 Processing helix chain 'B' and resid 113 through 117 Processing helix chain 'B' and resid 129 through 137 Processing helix chain 'B' and resid 207 through 216 Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 231 through 236 removed outlier: 3.531A pdb=" N VAL B 236 " --> pdb=" O PHE B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 261 removed outlier: 3.580A pdb=" N GLU B 260 " --> pdb=" O LYS B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 308 Processing helix chain 'A' and resid 2 through 13 Processing helix chain 'A' and resid 50 through 60 Processing helix chain 'A' and resid 68 through 75 Processing helix chain 'A' and resid 113 through 117 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'A' and resid 207 through 216 Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.520A pdb=" N VAL A 236 " --> pdb=" O PHE A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 261 removed outlier: 3.649A pdb=" N GLU A 260 " --> pdb=" O LYS A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 308 Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 50 through 60 Processing helix chain 'C' and resid 68 through 75 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'C' and resid 207 through 216 Processing helix chain 'C' and resid 217 through 225 Processing helix chain 'C' and resid 231 through 236 removed outlier: 3.624A pdb=" N VAL C 236 " --> pdb=" O PHE C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.631A pdb=" N GLU C 260 " --> pdb=" O LYS C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 308 Processing sheet with id=AA1, first strand: chain 'F' and resid 24 through 27 removed outlier: 6.632A pdb=" N VAL F 31 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 79 through 80 removed outlier: 7.268A pdb=" N ILE F 79 " --> pdb=" O PHE F 122 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N ASP F 124 " --> pdb=" O ILE F 79 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS F 180 " --> pdb=" O GLN F 187 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'F' and resid 86 through 87 Processing sheet with id=AA4, first strand: chain 'F' and resid 98 through 99 removed outlier: 8.208A pdb=" N THR F 98 " --> pdb=" O ILE F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 160 through 162 Processing sheet with id=AA6, first strand: chain 'F' and resid 264 through 266 removed outlier: 3.536A pdb=" N GLU F 266 " --> pdb=" O PHE F 279 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE F 280 " --> pdb=" O CYS F 290 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N CYS F 290 " --> pdb=" O ILE F 280 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 315 through 322 removed outlier: 7.357A pdb=" N SER F 328 " --> pdb=" O PRO F 343 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET F 330 " --> pdb=" O PHE F 341 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N PHE F 341 " --> pdb=" O MET F 330 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N TRP F 332 " --> pdb=" O GLU F 339 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 24 through 27 removed outlier: 6.684A pdb=" N VAL D 31 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 79 through 80 removed outlier: 7.190A pdb=" N ILE D 79 " --> pdb=" O PHE D 122 " (cutoff:3.500A) removed outlier: 8.574A pdb=" N ASP D 124 " --> pdb=" O ILE D 79 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N LYS D 180 " --> pdb=" O GLN D 187 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 86 through 87 Processing sheet with id=AB2, first strand: chain 'D' and resid 98 through 99 removed outlier: 8.236A pdb=" N THR D 98 " --> pdb=" O ILE D 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 160 through 162 Processing sheet with id=AB4, first strand: chain 'D' and resid 264 through 266 removed outlier: 4.869A pdb=" N ILE D 280 " --> pdb=" O CYS D 290 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N CYS D 290 " --> pdb=" O ILE D 280 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 315 through 322 removed outlier: 5.879A pdb=" N LYS D 334 " --> pdb=" O VAL D 338 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N VAL D 338 " --> pdb=" O LYS D 334 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 24 through 27 removed outlier: 6.658A pdb=" N VAL E 31 " --> pdb=" O LEU E 42 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.176A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 79 through 80 removed outlier: 7.176A pdb=" N ILE E 79 " --> pdb=" O PHE E 122 " (cutoff:3.500A) removed outlier: 8.567A pdb=" N ASP E 124 " --> pdb=" O ILE E 79 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N LYS E 180 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 86 through 87 Processing sheet with id=AC1, first strand: chain 'E' and resid 98 through 99 removed outlier: 8.306A pdb=" N THR E 98 " --> pdb=" O ILE E 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 160 through 162 Processing sheet with id=AC3, first strand: chain 'E' and resid 275 through 281 removed outlier: 4.915A pdb=" N ILE E 280 " --> pdb=" O CYS E 290 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N CYS E 290 " --> pdb=" O ILE E 280 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 315 through 322 removed outlier: 7.151A pdb=" N SER E 328 " --> pdb=" O PRO E 343 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N MET E 330 " --> pdb=" O PHE E 341 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE E 341 " --> pdb=" O MET E 330 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N TRP E 332 " --> pdb=" O GLU E 339 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 24 through 27 removed outlier: 6.698A pdb=" N VAL B 31 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.220A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 79 through 80 removed outlier: 7.220A pdb=" N ILE B 79 " --> pdb=" O PHE B 122 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N ASP B 124 " --> pdb=" O ILE B 79 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS B 180 " --> pdb=" O GLN B 187 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 86 through 87 Processing sheet with id=AC9, first strand: chain 'B' and resid 98 through 99 removed outlier: 8.108A pdb=" N THR B 98 " --> pdb=" O ILE B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 160 through 162 Processing sheet with id=AD2, first strand: chain 'B' and resid 264 through 266 removed outlier: 5.005A pdb=" N ILE B 280 " --> pdb=" O CYS B 290 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N CYS B 290 " --> pdb=" O ILE B 280 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 315 through 322 removed outlier: 6.677A pdb=" N TRP B 332 " --> pdb=" O GLU B 339 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'A' and resid 24 through 26 removed outlier: 6.685A pdb=" N VAL A 31 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.190A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'A' and resid 79 through 80 removed outlier: 7.190A pdb=" N ILE A 79 " --> pdb=" O PHE A 122 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N ASP A 124 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N LYS A 180 " --> pdb=" O GLN A 187 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'A' and resid 86 through 87 Processing sheet with id=AD8, first strand: chain 'A' and resid 98 through 99 removed outlier: 8.202A pdb=" N THR A 98 " --> pdb=" O ILE A 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'A' and resid 160 through 162 Processing sheet with id=AE1, first strand: chain 'A' and resid 264 through 266 removed outlier: 5.093A pdb=" N ILE A 280 " --> pdb=" O CYS A 290 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N CYS A 290 " --> pdb=" O ILE A 280 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'A' and resid 316 through 322 removed outlier: 7.255A pdb=" N SER A 328 " --> pdb=" O PRO A 343 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N MET A 330 " --> pdb=" O PHE A 341 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE A 341 " --> pdb=" O MET A 330 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TRP A 332 " --> pdb=" O GLU A 339 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 24 through 26 removed outlier: 6.634A pdb=" N VAL C 31 " --> pdb=" O LEU C 42 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.144A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 79 through 80 removed outlier: 7.144A pdb=" N ILE C 79 " --> pdb=" O PHE C 122 " (cutoff:3.500A) removed outlier: 8.501A pdb=" N ASP C 124 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LYS C 180 " --> pdb=" O GLN C 187 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 86 through 87 Processing sheet with id=AE7, first strand: chain 'C' and resid 98 through 99 removed outlier: 8.168A pdb=" N THR C 98 " --> pdb=" O ILE C 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'C' and resid 160 through 162 Processing sheet with id=AE9, first strand: chain 'C' and resid 264 through 266 removed outlier: 4.683A pdb=" N ILE C 280 " --> pdb=" O CYS C 290 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N CYS C 290 " --> pdb=" O ILE C 280 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 315 through 322 removed outlier: 3.547A pdb=" N THR C 340 " --> pdb=" O TRP C 332 " (cutoff:3.500A) removed outlier: 5.859A pdb=" N LYS C 334 " --> pdb=" O VAL C 338 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N VAL C 338 " --> pdb=" O LYS C 334 " (cutoff:3.500A) 630 hydrogen bonds defined for protein. 1632 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 43 hydrogen bonds 86 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 6.42 Time building geometry restraints manager: 8.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5443 1.34 - 1.45: 2718 1.45 - 1.57: 9783 1.57 - 1.69: 105 1.69 - 1.81: 90 Bond restraints: 18139 Sorted by residual: bond pdb=" CA LEU B 345 " pdb=" C LEU B 345 " ideal model delta sigma weight residual 1.526 1.496 0.030 1.29e-02 6.01e+03 5.49e+00 bond pdb=" O5' U G 7 " pdb=" C5' U G 7 " ideal model delta sigma weight residual 1.420 1.442 -0.022 1.50e-02 4.44e+03 2.16e+00 bond pdb=" CB PRO A 262 " pdb=" CG PRO A 262 " ideal model delta sigma weight residual 1.492 1.564 -0.072 5.00e-02 4.00e+02 2.09e+00 bond pdb=" O5' U G 5 " pdb=" C5' U G 5 " ideal model delta sigma weight residual 1.420 1.442 -0.022 1.50e-02 4.44e+03 2.08e+00 bond pdb=" O5' A H 29 " pdb=" C5' A H 29 " ideal model delta sigma weight residual 1.420 1.441 -0.021 1.50e-02 4.44e+03 2.01e+00 ... (remaining 18134 not shown) Histogram of bond angle deviations from ideal: 100.64 - 107.30: 784 107.30 - 113.97: 10428 113.97 - 120.64: 6910 120.64 - 127.30: 6496 127.30 - 133.97: 249 Bond angle restraints: 24867 Sorted by residual: angle pdb=" N LYS B 344 " pdb=" CA LYS B 344 " pdb=" C LYS B 344 " ideal model delta sigma weight residual 110.24 116.81 -6.57 1.30e+00 5.92e-01 2.55e+01 angle pdb=" C LYS C 344 " pdb=" N LEU C 345 " pdb=" CA LEU C 345 " ideal model delta sigma weight residual 121.54 128.71 -7.17 1.91e+00 2.74e-01 1.41e+01 angle pdb=" C4' U G 4 " pdb=" C3' U G 4 " pdb=" O3' U G 4 " ideal model delta sigma weight residual 113.00 107.58 5.42 1.50e+00 4.44e-01 1.30e+01 angle pdb=" C4' A H 26 " pdb=" C3' A H 26 " pdb=" O3' A H 26 " ideal model delta sigma weight residual 113.00 107.91 5.09 1.50e+00 4.44e-01 1.15e+01 angle pdb=" CA PRO A 262 " pdb=" N PRO A 262 " pdb=" CD PRO A 262 " ideal model delta sigma weight residual 112.00 107.30 4.70 1.40e+00 5.10e-01 1.13e+01 ... (remaining 24862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.40: 9478 19.40 - 38.80: 991 38.80 - 58.20: 301 58.20 - 77.60: 74 77.60 - 96.99: 25 Dihedral angle restraints: 10869 sinusoidal: 4785 harmonic: 6084 Sorted by residual: dihedral pdb=" C3' A H 27 " pdb=" C4' A H 27 " pdb=" O4' A H 27 " pdb=" C1' A H 27 " ideal model delta sinusoidal sigma weight residual 20.00 -10.12 30.12 1 8.00e+00 1.56e-02 2.03e+01 dihedral pdb=" C4' A H 27 " pdb=" O4' A H 27 " pdb=" C1' A H 27 " pdb=" C2' A H 27 " ideal model delta sinusoidal sigma weight residual 3.00 29.51 -26.51 1 8.00e+00 1.56e-02 1.58e+01 dihedral pdb=" C5' A H 27 " pdb=" C4' A H 27 " pdb=" C3' A H 27 " pdb=" O3' A H 27 " ideal model delta sinusoidal sigma weight residual 82.00 108.06 -26.06 1 8.00e+00 1.56e-02 1.53e+01 ... (remaining 10866 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2255 0.047 - 0.095: 427 0.095 - 0.142: 193 0.142 - 0.190: 23 0.190 - 0.237: 5 Chirality restraints: 2903 Sorted by residual: chirality pdb=" C3' A G 24 " pdb=" C4' A G 24 " pdb=" O3' A G 24 " pdb=" C2' A G 24 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" C3' A H 29 " pdb=" C4' A H 29 " pdb=" O3' A H 29 " pdb=" C2' A H 29 " both_signs ideal model delta sigma weight residual False -2.48 -2.71 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C3' A H 26 " pdb=" C4' A H 26 " pdb=" O3' A H 26 " pdb=" C2' A H 26 " both_signs ideal model delta sigma weight residual False -2.48 -2.69 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 2900 not shown) Planarity restraints: 3006 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER A 261 " -0.074 5.00e-02 4.00e+02 1.10e-01 1.95e+01 pdb=" N PRO A 262 " 0.191 5.00e-02 4.00e+02 pdb=" CA PRO A 262 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 262 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 261 " 0.066 5.00e-02 4.00e+02 9.89e-02 1.57e+01 pdb=" N PRO D 262 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO D 262 " 0.052 5.00e-02 4.00e+02 pdb=" CD PRO D 262 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS F 204 " 0.034 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO F 205 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO F 205 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO F 205 " 0.029 5.00e-02 4.00e+02 ... (remaining 3003 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2934 2.77 - 3.30: 16539 3.30 - 3.84: 30684 3.84 - 4.37: 37739 4.37 - 4.90: 63421 Nonbonded interactions: 151317 Sorted by model distance: nonbonded pdb=" O HIS A 242 " pdb=" OG SER A 287 " model vdw 2.238 3.040 nonbonded pdb=" O HIS E 242 " pdb=" OG SER E 287 " model vdw 2.240 3.040 nonbonded pdb=" OG1 THR B 195 " pdb=" OD2 ASP B 323 " model vdw 2.271 3.040 nonbonded pdb=" OH TYR A 193 " pdb=" OE2 GLU A 304 " model vdw 2.281 3.040 nonbonded pdb=" O HIS D 242 " pdb=" OG SER D 287 " model vdw 2.293 3.040 ... (remaining 151312 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'B' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'C' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'D' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'E' and (resid 1 through 26 or resid 30 through 346)) selection = (chain 'F' and (resid 1 through 26 or resid 30 through 346)) } 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=0.48 max=1.00 mean=0.99 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: 4.380 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: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 67.020 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 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 : 0.002 0.072 18139 Z= 0.138 Angle : 0.490 9.534 24867 Z= 0.283 Chirality : 0.046 0.237 2903 Planarity : 0.004 0.110 3006 Dihedral : 18.013 96.995 6945 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.27 % Allowed : 22.10 % Favored : 77.63 % 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: 0.54 (0.19), residues: 2094 helix: 0.73 (0.23), residues: 534 sheet: 0.54 (0.30), residues: 342 loop : 0.26 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 332 HIS 0.003 0.001 HIS B 337 PHE 0.027 0.001 PHE D 258 TYR 0.009 0.001 TYR A 342 ARG 0.004 0.000 ARG E 135 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 215 time to evaluate : 1.920 Fit side-chains REVERT: F 56 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8055 (mp0) REVERT: B 223 GLU cc_start: 0.8180 (tp30) cc_final: 0.7712 (tt0) REVERT: A 202 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7388 (tt0) outliers start: 5 outliers final: 2 residues processed: 219 average time/residue: 0.2903 time to fit residues: 97.4860 Evaluate side-chains 207 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 204 time to evaluate : 1.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 136 ASN Chi-restraints excluded: chain A residue 197 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 0.9990 chunk 157 optimal weight: 4.9990 chunk 87 optimal weight: 0.2980 chunk 53 optimal weight: 1.9990 chunk 106 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 163 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 99 optimal weight: 0.0770 chunk 121 optimal weight: 0.6980 chunk 188 optimal weight: 0.1980 overall best weight: 0.3938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 74 ASN B 187 GLN A 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18139 Z= 0.158 Angle : 0.494 10.183 24867 Z= 0.264 Chirality : 0.044 0.175 2903 Planarity : 0.004 0.085 3006 Dihedral : 12.035 88.787 2985 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.61 % Allowed : 21.40 % Favored : 76.99 % 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: 0.66 (0.19), residues: 2094 helix: 0.76 (0.23), residues: 546 sheet: 0.73 (0.30), residues: 342 loop : 0.33 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 332 HIS 0.003 0.001 HIS B 337 PHE 0.010 0.001 PHE B 7 TYR 0.011 0.001 TYR A 225 ARG 0.006 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 231 time to evaluate : 1.926 Fit side-chains revert: symmetry clash REVERT: F 228 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6523 (mp0) REVERT: F 264 GLU cc_start: 0.7639 (mp0) cc_final: 0.7322 (mt-10) REVERT: D 152 GLN cc_start: 0.7700 (pm20) cc_final: 0.7414 (tp40) REVERT: D 183 ASP cc_start: 0.7996 (m-30) cc_final: 0.7684 (m-30) REVERT: B 104 MET cc_start: 0.8848 (mmm) cc_final: 0.8523 (tpt) REVERT: B 223 GLU cc_start: 0.8189 (tp30) cc_final: 0.7771 (tt0) REVERT: B 277 ASN cc_start: 0.8637 (m-40) cc_final: 0.8400 (m-40) REVERT: A 163 ASN cc_start: 0.8464 (t0) cc_final: 0.8222 (t0) REVERT: A 288 SER cc_start: 0.8803 (p) cc_final: 0.8596 (t) REVERT: C 321 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8155 (m) outliers start: 29 outliers final: 15 residues processed: 241 average time/residue: 0.2880 time to fit residues: 105.5508 Evaluate side-chains 228 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 212 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 0.0870 chunk 58 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 128 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 189 optimal weight: 0.8980 chunk 204 optimal weight: 10.0000 chunk 168 optimal weight: 2.9990 chunk 187 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 151 optimal weight: 0.5980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN C 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18139 Z= 0.220 Angle : 0.501 9.137 24867 Z= 0.263 Chirality : 0.045 0.163 2903 Planarity : 0.004 0.078 3006 Dihedral : 11.764 92.796 2982 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.67 % Allowed : 21.51 % Favored : 76.83 % 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: 0.58 (0.19), residues: 2094 helix: 0.68 (0.23), residues: 546 sheet: 0.75 (0.30), residues: 342 loop : 0.26 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 332 HIS 0.003 0.001 HIS B 337 PHE 0.011 0.001 PHE F 134 TYR 0.014 0.001 TYR A 225 ARG 0.005 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 212 time to evaluate : 1.697 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 104 MET cc_start: 0.8801 (mmm) cc_final: 0.8192 (tpt) REVERT: D 138 ARG cc_start: 0.8330 (mtp180) cc_final: 0.8043 (ttp-170) REVERT: D 152 GLN cc_start: 0.7702 (pm20) cc_final: 0.7413 (tp40) REVERT: E 218 MET cc_start: 0.6740 (mtt) cc_final: 0.6035 (ttm) REVERT: B 104 MET cc_start: 0.8842 (mmm) cc_final: 0.8520 (tpt) REVERT: B 223 GLU cc_start: 0.8172 (tp30) cc_final: 0.7724 (tt0) REVERT: B 277 ASN cc_start: 0.8823 (m-40) cc_final: 0.8498 (m-40) REVERT: A 163 ASN cc_start: 0.8551 (t0) cc_final: 0.8247 (t0) REVERT: A 243 SER cc_start: 0.8844 (m) cc_final: 0.8592 (p) REVERT: A 345 LEU cc_start: 0.6931 (OUTLIER) cc_final: 0.6628 (tp) REVERT: C 321 THR cc_start: 0.8404 (OUTLIER) cc_final: 0.8189 (m) outliers start: 27 outliers final: 16 residues processed: 220 average time/residue: 0.2965 time to fit residues: 100.3486 Evaluate side-chains 217 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 199 time to evaluate : 1.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 155 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain D residue 344 LYS Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 0.7980 chunk 142 optimal weight: 0.0370 chunk 98 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 chunk 201 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18139 Z= 0.250 Angle : 0.508 8.737 24867 Z= 0.265 Chirality : 0.045 0.169 2903 Planarity : 0.004 0.073 3006 Dihedral : 11.654 92.569 2982 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.15 % Allowed : 21.13 % Favored : 76.72 % 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: 0.43 (0.19), residues: 2094 helix: 0.58 (0.23), residues: 546 sheet: 0.68 (0.30), residues: 342 loop : 0.14 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 PHE 0.024 0.002 PHE D 221 TYR 0.014 0.001 TYR A 225 ARG 0.007 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 1.961 Fit side-chains revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8426 (tp-100) cc_final: 0.8166 (tp-100) REVERT: D 138 ARG cc_start: 0.8327 (mtp180) cc_final: 0.8079 (ttp-170) REVERT: E 254 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7531 (mp) REVERT: B 104 MET cc_start: 0.8844 (mmm) cc_final: 0.8523 (tpt) REVERT: B 223 GLU cc_start: 0.8228 (tp30) cc_final: 0.7777 (tt0) REVERT: B 277 ASN cc_start: 0.8859 (m-40) cc_final: 0.8504 (m-40) REVERT: A 243 SER cc_start: 0.8866 (m) cc_final: 0.8613 (p) REVERT: A 345 LEU cc_start: 0.6927 (OUTLIER) cc_final: 0.6641 (tp) REVERT: C 264 GLU cc_start: 0.7082 (mt-10) cc_final: 0.6696 (mt-10) REVERT: C 321 THR cc_start: 0.8439 (OUTLIER) cc_final: 0.8235 (m) outliers start: 34 outliers final: 18 residues processed: 224 average time/residue: 0.2894 time to fit residues: 100.0091 Evaluate side-chains 224 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 203 time to evaluate : 1.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 321 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 167 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 82 optimal weight: 0.0470 chunk 171 optimal weight: 0.4980 chunk 138 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 180 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 overall best weight: 0.6280 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN E 136 ASN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN C 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18139 Z= 0.196 Angle : 0.496 8.415 24867 Z= 0.257 Chirality : 0.044 0.171 2903 Planarity : 0.004 0.069 3006 Dihedral : 11.533 92.567 2982 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.77 % Allowed : 21.45 % Favored : 76.77 % 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: 0.45 (0.19), residues: 2094 helix: 0.61 (0.23), residues: 546 sheet: 0.70 (0.30), residues: 342 loop : 0.14 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 PHE 0.030 0.001 PHE D 221 TYR 0.011 0.001 TYR A 225 ARG 0.006 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 207 time to evaluate : 1.816 Fit side-chains REVERT: F 208 GLN cc_start: 0.8441 (tp-100) cc_final: 0.8186 (tp-100) REVERT: D 109 LYS cc_start: 0.8669 (mmtm) cc_final: 0.8462 (mmtt) REVERT: D 296 ASP cc_start: 0.8242 (t0) cc_final: 0.7985 (t0) REVERT: B 104 MET cc_start: 0.8846 (mmm) cc_final: 0.8527 (tpt) REVERT: B 187 GLN cc_start: 0.7755 (mt0) cc_final: 0.7552 (mt0) REVERT: B 223 GLU cc_start: 0.8247 (tp30) cc_final: 0.7813 (tt0) REVERT: B 277 ASN cc_start: 0.8858 (m-40) cc_final: 0.8514 (m-40) REVERT: A 163 ASN cc_start: 0.8542 (t0) cc_final: 0.8329 (t0) REVERT: A 243 SER cc_start: 0.8834 (m) cc_final: 0.8625 (p) REVERT: A 345 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6661 (tp) REVERT: C 264 GLU cc_start: 0.7073 (mt-10) cc_final: 0.6822 (mt-10) REVERT: C 345 LEU cc_start: 0.3914 (OUTLIER) cc_final: 0.3698 (mt) outliers start: 27 outliers final: 18 residues processed: 220 average time/residue: 0.2884 time to fit residues: 97.1997 Evaluate side-chains 223 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 203 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 67 optimal weight: 9.9990 chunk 181 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 201 optimal weight: 6.9990 chunk 167 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 GLN A 136 ASN C 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 18139 Z= 0.238 Angle : 0.506 8.466 24867 Z= 0.262 Chirality : 0.045 0.172 2903 Planarity : 0.004 0.066 3006 Dihedral : 11.386 92.000 2979 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.88 % Allowed : 21.61 % Favored : 76.51 % 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: 0.38 (0.19), residues: 2094 helix: 0.57 (0.23), residues: 546 sheet: 0.68 (0.30), residues: 342 loop : 0.08 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 PHE 0.026 0.001 PHE D 221 TYR 0.012 0.001 TYR A 225 ARG 0.007 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 204 time to evaluate : 2.137 Fit side-chains revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8420 (tp-100) cc_final: 0.8155 (tp-100) REVERT: D 109 LYS cc_start: 0.8671 (mmtm) cc_final: 0.8455 (mmtt) REVERT: D 138 ARG cc_start: 0.8345 (mtp180) cc_final: 0.8129 (ttp-170) REVERT: D 296 ASP cc_start: 0.8258 (t0) cc_final: 0.8007 (t0) REVERT: E 204 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7430 (mtpp) REVERT: E 254 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7521 (mp) REVERT: B 104 MET cc_start: 0.8846 (mmm) cc_final: 0.8526 (tpt) REVERT: B 223 GLU cc_start: 0.8255 (tp30) cc_final: 0.7853 (tt0) REVERT: A 163 ASN cc_start: 0.8590 (t0) cc_final: 0.8361 (t0) REVERT: A 243 SER cc_start: 0.8831 (m) cc_final: 0.8615 (p) REVERT: A 345 LEU cc_start: 0.6967 (OUTLIER) cc_final: 0.6679 (tp) REVERT: C 345 LEU cc_start: 0.3906 (OUTLIER) cc_final: 0.3687 (mt) outliers start: 29 outliers final: 21 residues processed: 219 average time/residue: 0.2981 time to fit residues: 100.1333 Evaluate side-chains 220 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 195 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 146 optimal weight: 0.0980 chunk 113 optimal weight: 0.9980 chunk 169 optimal weight: 0.9990 chunk 112 optimal weight: 0.2980 chunk 200 optimal weight: 0.9990 chunk 125 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN A 187 GLN C 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18139 Z= 0.170 Angle : 0.486 8.408 24867 Z= 0.251 Chirality : 0.044 0.174 2903 Planarity : 0.004 0.065 3006 Dihedral : 11.256 90.945 2979 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.99 % Allowed : 21.34 % Favored : 76.67 % 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: 0.47 (0.19), residues: 2094 helix: 0.67 (0.23), residues: 546 sheet: 0.71 (0.30), residues: 342 loop : 0.13 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 86 HIS 0.004 0.001 HIS B 337 PHE 0.030 0.001 PHE D 221 TYR 0.008 0.001 TYR B 278 ARG 0.006 0.000 ARG B 224 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 209 time to evaluate : 1.889 Fit side-chains revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8420 (tp-100) cc_final: 0.8153 (tp-100) REVERT: D 296 ASP cc_start: 0.8235 (t0) cc_final: 0.7975 (t0) REVERT: B 223 GLU cc_start: 0.8228 (tp30) cc_final: 0.7823 (tt0) REVERT: A 163 ASN cc_start: 0.8579 (t0) cc_final: 0.8359 (t0) REVERT: A 170 GLU cc_start: 0.8379 (OUTLIER) cc_final: 0.7857 (mt-10) REVERT: C 264 GLU cc_start: 0.7141 (mt-10) cc_final: 0.6927 (mt-10) REVERT: C 345 LEU cc_start: 0.3938 (OUTLIER) cc_final: 0.3730 (mt) outliers start: 31 outliers final: 24 residues processed: 225 average time/residue: 0.3021 time to fit residues: 104.0859 Evaluate side-chains 229 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 203 time to evaluate : 1.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 chunk 119 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 127 optimal weight: 0.6980 chunk 136 optimal weight: 0.5980 chunk 99 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 157 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 18139 Z= 0.229 Angle : 0.503 8.464 24867 Z= 0.260 Chirality : 0.045 0.175 2903 Planarity : 0.004 0.065 3006 Dihedral : 11.281 89.990 2979 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.04 % Allowed : 21.56 % Favored : 76.40 % 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: 0.40 (0.19), residues: 2094 helix: 0.61 (0.23), residues: 546 sheet: 0.70 (0.30), residues: 342 loop : 0.08 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 332 HIS 0.004 0.001 HIS B 337 PHE 0.028 0.001 PHE D 221 TYR 0.012 0.001 TYR A 225 ARG 0.005 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 201 time to evaluate : 2.072 Fit side-chains revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8423 (tp-100) cc_final: 0.8142 (tp-100) REVERT: D 296 ASP cc_start: 0.8233 (t0) cc_final: 0.7966 (t0) REVERT: D 344 LYS cc_start: 0.6602 (ptmm) cc_final: 0.6006 (ptmm) REVERT: E 204 LYS cc_start: 0.7829 (OUTLIER) cc_final: 0.7465 (mtpp) REVERT: E 254 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.7555 (mp) REVERT: B 104 MET cc_start: 0.8882 (mmm) cc_final: 0.8571 (tpt) REVERT: B 223 GLU cc_start: 0.8246 (tp30) cc_final: 0.7845 (tt0) REVERT: A 163 ASN cc_start: 0.8590 (t0) cc_final: 0.8372 (t0) REVERT: A 170 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: A 345 LEU cc_start: 0.6968 (OUTLIER) cc_final: 0.6660 (tp) REVERT: C 345 LEU cc_start: 0.3924 (OUTLIER) cc_final: 0.3714 (mt) outliers start: 32 outliers final: 24 residues processed: 218 average time/residue: 0.3134 time to fit residues: 105.9514 Evaluate side-chains 220 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 191 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 1.9990 chunk 192 optimal weight: 0.8980 chunk 175 optimal weight: 0.9990 chunk 186 optimal weight: 0.7980 chunk 112 optimal weight: 0.9980 chunk 81 optimal weight: 0.2980 chunk 146 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 168 optimal weight: 2.9990 chunk 176 optimal weight: 1.9990 chunk 122 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18139 Z= 0.193 Angle : 0.495 8.445 24867 Z= 0.256 Chirality : 0.044 0.175 2903 Planarity : 0.004 0.064 3006 Dihedral : 11.261 89.314 2979 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.04 % Allowed : 21.45 % Favored : 76.51 % 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: 0.40 (0.19), residues: 2094 helix: 0.61 (0.23), residues: 546 sheet: 0.70 (0.30), residues: 342 loop : 0.08 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 PHE 0.028 0.001 PHE D 221 TYR 0.010 0.001 TYR A 225 ARG 0.005 0.000 ARG A 138 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 193 time to evaluate : 1.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8426 (tp-100) cc_final: 0.8143 (tp-100) REVERT: D 109 LYS cc_start: 0.8580 (mmtm) cc_final: 0.8353 (mmtt) REVERT: D 296 ASP cc_start: 0.8228 (t0) cc_final: 0.7957 (t0) REVERT: E 204 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7460 (mtpp) REVERT: E 254 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7526 (mp) REVERT: B 104 MET cc_start: 0.8875 (mmm) cc_final: 0.8577 (tpt) REVERT: B 223 GLU cc_start: 0.8250 (tp30) cc_final: 0.7847 (tt0) REVERT: A 163 ASN cc_start: 0.8577 (t0) cc_final: 0.8357 (t0) REVERT: A 170 GLU cc_start: 0.8378 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: A 345 LEU cc_start: 0.6938 (OUTLIER) cc_final: 0.6641 (tp) REVERT: C 345 LEU cc_start: 0.3927 (OUTLIER) cc_final: 0.3719 (mt) outliers start: 32 outliers final: 25 residues processed: 209 average time/residue: 0.2938 time to fit residues: 94.4236 Evaluate side-chains 222 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 192 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 103 SER Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 204 LYS Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 0.5980 chunk 120 optimal weight: 0.1980 chunk 93 optimal weight: 0.7980 chunk 137 optimal weight: 0.5980 chunk 207 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 127 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 131 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN C 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18139 Z= 0.176 Angle : 0.487 8.485 24867 Z= 0.252 Chirality : 0.044 0.176 2903 Planarity : 0.004 0.064 3006 Dihedral : 11.237 88.300 2979 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.94 % Allowed : 21.61 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 2094 helix: 0.62 (0.23), residues: 546 sheet: 0.71 (0.30), residues: 342 loop : 0.07 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 PHE 0.028 0.001 PHE D 221 TYR 0.010 0.001 TYR A 225 ARG 0.005 0.000 ARG A 138 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4188 Ramachandran restraints generated. 2094 Oldfield, 0 Emsley, 2094 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 198 time to evaluate : 1.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 208 GLN cc_start: 0.8409 (tp-100) cc_final: 0.8139 (tp-100) REVERT: D 109 LYS cc_start: 0.8549 (mmtm) cc_final: 0.8319 (mmtt) REVERT: D 296 ASP cc_start: 0.8225 (t0) cc_final: 0.7970 (t0) REVERT: D 344 LYS cc_start: 0.6682 (ptmm) cc_final: 0.6093 (ptmm) REVERT: E 204 LYS cc_start: 0.7787 (OUTLIER) cc_final: 0.7442 (mtpp) REVERT: E 254 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7523 (mp) REVERT: B 104 MET cc_start: 0.8872 (mmm) cc_final: 0.8576 (tpt) REVERT: B 223 GLU cc_start: 0.8246 (tp30) cc_final: 0.7841 (tt0) REVERT: A 163 ASN cc_start: 0.8566 (t0) cc_final: 0.8344 (t0) REVERT: A 170 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.7848 (mt-10) REVERT: A 288 SER cc_start: 0.8891 (p) cc_final: 0.8633 (t) REVERT: A 345 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6619 (tp) REVERT: C 345 LEU cc_start: 0.3929 (OUTLIER) cc_final: 0.3726 (mt) outliers start: 30 outliers final: 23 residues processed: 213 average time/residue: 0.2878 time to fit residues: 93.8104 Evaluate side-chains 223 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 195 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 56 GLU Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 232 PHE Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 155 VAL Chi-restraints excluded: chain D residue 218 MET Chi-restraints excluded: chain D residue 232 PHE Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 114 THR Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 96 ILE Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 250 LEU Chi-restraints excluded: chain C residue 345 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 175 optimal weight: 1.9990 chunk 50 optimal weight: 0.0670 chunk 152 optimal weight: 0.3980 chunk 24 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 136 ASN C 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.167239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.123595 restraints weight = 117317.328| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 5.20 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3187 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3187 r_free = 0.3187 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3187 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 18139 Z= 0.197 Angle : 0.496 8.446 24867 Z= 0.257 Chirality : 0.044 0.177 2903 Planarity : 0.004 0.064 3006 Dihedral : 11.238 87.622 2979 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.15 % Allowed : 21.40 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.39 (0.19), residues: 2094 helix: 0.58 (0.23), residues: 546 sheet: 0.72 (0.30), residues: 342 loop : 0.07 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 PHE 0.030 0.001 PHE D 221 TYR 0.011 0.001 TYR A 225 ARG 0.005 0.000 ARG A 138 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3527.91 seconds wall clock time: 64 minutes 44.62 seconds (3884.62 seconds total)