Starting phenix.real_space_refine on Mon Jul 22 08:34:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud5_42147/07_2024/8ud5_42147.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud5_42147/07_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_42147/07_2024/8ud5_42147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud5_42147/07_2024/8ud5_42147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud5_42147/07_2024/8ud5_42147.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ud5_42147/07_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-5388/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: 16.86, per 1000 atoms: 0.95 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: 6.82 Conformation dependent library (CDL) restraints added in 5.6 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: 7.38 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: 6.61 Time building geometry restraints manager: 7.48 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 2.440 nonbonded pdb=" O HIS E 242 " pdb=" OG SER E 287 " model vdw 2.240 2.440 nonbonded pdb=" OG1 THR B 195 " pdb=" OD2 ASP B 323 " model vdw 2.271 2.440 nonbonded pdb=" OH TYR A 193 " pdb=" OE2 GLU A 304 " model vdw 2.281 2.440 nonbonded pdb=" O HIS D 242 " pdb=" OG SER D 287 " model vdw 2.293 2.440 ... (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 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: 3.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 63.830 Find NCS groups from input model: 1.130 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.170 ------------------------------------------------------------------------------- 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 : 1.866 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: 0.2860 time to fit residues: 95.8712 Evaluate side-chains 207 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 204 time to evaluate : 1.855 ------------------------------------------------------------------------------- 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: 3.9990 chunk 87 optimal weight: 0.0270 chunk 53 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 84 optimal weight: 0.5980 chunk 163 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 99 optimal weight: 0.0670 chunk 121 optimal weight: 0.8980 chunk 188 optimal weight: 0.5980 overall best weight: 0.4376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 18 GLN B 187 GLN A 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.0976 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= 0.162 Angle : 0.485 10.041 24867 Z= 0.259 Chirality : 0.044 0.171 2903 Planarity : 0.004 0.081 3006 Dihedral : 12.033 89.440 2985 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.77 % Allowed : 21.29 % Favored : 76.94 % 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: 0.72 (0.19), residues: 2094 helix: 0.81 (0.23), residues: 546 sheet: 0.84 (0.30), residues: 342 loop : 0.33 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 86 HIS 0.003 0.001 HIS B 337 PHE 0.010 0.001 PHE B 7 TYR 0.012 0.001 TYR A 225 ARG 0.005 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 256 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 224 time to evaluate : 1.973 Fit side-chains revert: symmetry clash REVERT: F 264 GLU cc_start: 0.7600 (mp0) cc_final: 0.7310 (mt-10) REVERT: B 223 GLU cc_start: 0.8216 (tp30) cc_final: 0.7826 (tt0) REVERT: B 341 PHE cc_start: 0.8525 (t80) cc_final: 0.8236 (t80) REVERT: A 163 ASN cc_start: 0.8463 (t0) cc_final: 0.8213 (t0) REVERT: A 243 SER cc_start: 0.8900 (m) cc_final: 0.8681 (p) REVERT: C 321 THR cc_start: 0.8402 (OUTLIER) cc_final: 0.8135 (m) outliers start: 32 outliers final: 17 residues processed: 237 average time/residue: 0.2953 time to fit residues: 105.8110 Evaluate side-chains 226 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 208 time to evaluate : 1.846 ------------------------------------------------------------------------------- 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 A residue 300 ASP 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 104 optimal weight: 0.9990 chunk 58 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 128 optimal weight: 0.5980 chunk 52 optimal weight: 0.9980 chunk 189 optimal weight: 0.9990 chunk 204 optimal weight: 10.0000 chunk 168 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 151 optimal weight: 0.0370 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN B 175 GLN C 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.1253 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= 0.217 Angle : 0.496 8.999 24867 Z= 0.260 Chirality : 0.045 0.163 2903 Planarity : 0.004 0.075 3006 Dihedral : 11.798 92.899 2982 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.77 % Allowed : 21.61 % Favored : 76.61 % 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: 0.64 (0.19), residues: 2094 helix: 0.76 (0.23), residues: 546 sheet: 0.83 (0.30), residues: 342 loop : 0.27 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 86 HIS 0.003 0.001 HIS B 337 PHE 0.011 0.001 PHE D 329 TYR 0.014 0.001 TYR A 225 ARG 0.006 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: 29 poor density : 210 time to evaluate : 1.788 Fit side-chains revert: symmetry clash REVERT: B 223 GLU cc_start: 0.8140 (tp30) cc_final: 0.7717 (tt0) REVERT: A 149 LYS cc_start: 0.7825 (OUTLIER) cc_final: 0.7597 (mmmm) REVERT: A 163 ASN cc_start: 0.8516 (t0) cc_final: 0.8262 (t0) REVERT: A 345 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6614 (tp) REVERT: C 321 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8169 (m) outliers start: 29 outliers final: 18 residues processed: 222 average time/residue: 0.3079 time to fit residues: 103.0919 Evaluate side-chains 223 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 202 time to evaluate : 1.847 ------------------------------------------------------------------------------- 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 232 PHE Chi-restraints excluded: chain F residue 285 THR Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 138 ARG 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 B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 300 ASP 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 321 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 186 optimal weight: 2.9990 chunk 142 optimal weight: 0.9980 chunk 98 optimal weight: 0.0980 chunk 20 optimal weight: 5.9990 chunk 90 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 201 optimal weight: 5.9990 chunk 99 optimal weight: 0.9990 chunk 179 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 B 74 ASN A 62 ASN C 62 ASN C 163 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 18139 Z= 0.371 Angle : 0.555 8.620 24867 Z= 0.289 Chirality : 0.047 0.168 2903 Planarity : 0.004 0.069 3006 Dihedral : 11.805 93.100 2982 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.58 % Allowed : 20.97 % 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: 0.32 (0.19), residues: 2094 helix: 0.42 (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 0.008 0.001 TRP A 332 HIS 0.004 0.001 HIS B 337 PHE 0.025 0.002 PHE D 221 TYR 0.017 0.002 TYR A 225 ARG 0.006 0.001 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 252 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 210 time to evaluate : 1.977 Fit side-chains revert: symmetry clash REVERT: F 110 LYS cc_start: 0.8666 (mttp) cc_final: 0.8356 (mtpp) REVERT: E 254 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7531 (mp) REVERT: B 223 GLU cc_start: 0.8186 (tp30) cc_final: 0.7788 (tt0) REVERT: B 258 PHE cc_start: 0.8349 (t80) cc_final: 0.8127 (t80) REVERT: A 149 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7653 (mmmm) REVERT: A 163 ASN cc_start: 0.8658 (t0) cc_final: 0.8339 (t0) REVERT: A 345 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6710 (tp) REVERT: C 321 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8296 (m) outliers start: 42 outliers final: 22 residues processed: 233 average time/residue: 0.2936 time to fit residues: 104.5527 Evaluate side-chains 226 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 200 time to evaluate : 1.970 ------------------------------------------------------------------------------- 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 144 THR Chi-restraints excluded: chain F residue 192 THR 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 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 E residue 300 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 222 ILE Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 345 LEU 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: 0.0870 chunk 114 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 149 optimal weight: 1.9990 chunk 82 optimal weight: 0.1980 chunk 171 optimal weight: 0.0870 chunk 138 optimal weight: 0.0270 chunk 0 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 180 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 overall best weight: 0.2194 ------------------------------------------------------------------------------- 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** B 74 ASN B 199 ASN A 62 ASN A 187 GLN A 244 GLN C 163 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18139 Z= 0.118 Angle : 0.465 8.511 24867 Z= 0.243 Chirality : 0.043 0.168 2903 Planarity : 0.004 0.064 3006 Dihedral : 11.465 92.048 2982 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.94 % Allowed : 21.29 % 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: 0.61 (0.19), residues: 2094 helix: 0.76 (0.23), residues: 546 sheet: 0.79 (0.29), residues: 342 loop : 0.23 (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 0.024 0.001 PHE D 221 TYR 0.009 0.001 TYR A 342 ARG 0.007 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 248 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 218 time to evaluate : 1.955 Fit side-chains REVERT: F 106 ASP cc_start: 0.8831 (m-30) cc_final: 0.8576 (m-30) REVERT: D 152 GLN cc_start: 0.7757 (pm20) cc_final: 0.7424 (tp40) REVERT: B 223 GLU cc_start: 0.8182 (tp30) cc_final: 0.7744 (tt0) REVERT: A 149 LYS cc_start: 0.7821 (OUTLIER) cc_final: 0.7605 (mmmm) REVERT: A 296 ASP cc_start: 0.8162 (t0) cc_final: 0.7747 (t70) REVERT: C 345 LEU cc_start: 0.3891 (OUTLIER) cc_final: 0.3679 (mt) outliers start: 30 outliers final: 21 residues processed: 233 average time/residue: 0.2928 time to fit residues: 104.5225 Evaluate side-chains 229 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 206 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 47 THR Chi-restraints excluded: chain F residue 91 ASP Chi-restraints excluded: chain F residue 192 THR 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 232 PHE Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain A residue 149 LYS Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 300 ASP 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: 0.1980 chunk 181 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 201 optimal weight: 6.9990 chunk 167 optimal weight: 0.3980 chunk 93 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 66 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 163 ASN A 136 ASN A 244 GLN C 163 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 18139 Z= 0.140 Angle : 0.462 8.440 24867 Z= 0.241 Chirality : 0.043 0.168 2903 Planarity : 0.003 0.061 3006 Dihedral : 11.264 91.065 2979 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.94 % Allowed : 20.86 % Favored : 77.20 % 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: 0.66 (0.19), residues: 2094 helix: 0.88 (0.24), residues: 546 sheet: 0.79 (0.29), residues: 342 loop : 0.24 (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 0.031 0.001 PHE D 221 TYR 0.010 0.001 TYR A 225 ARG 0.007 0.000 ARG A 138 *********************** 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 240 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 210 time to evaluate : 1.817 Fit side-chains revert: symmetry clash REVERT: F 106 ASP cc_start: 0.8846 (m-30) cc_final: 0.8447 (m-30) REVERT: D 87 ASP cc_start: 0.8516 (t0) cc_final: 0.8207 (t0) REVERT: D 152 GLN cc_start: 0.7741 (pm20) cc_final: 0.7413 (tp40) REVERT: E 204 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7385 (mtpp) REVERT: E 254 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.7590 (mp) REVERT: B 223 GLU cc_start: 0.8215 (tp30) cc_final: 0.7812 (tt0) REVERT: A 163 ASN cc_start: 0.8529 (t0) cc_final: 0.8227 (t0) REVERT: A 296 ASP cc_start: 0.8268 (t0) cc_final: 0.7957 (t0) REVERT: A 345 LEU cc_start: 0.6832 (OUTLIER) cc_final: 0.6545 (tp) outliers start: 30 outliers final: 21 residues processed: 226 average time/residue: 0.2967 time to fit residues: 101.8949 Evaluate side-chains 226 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 202 time to evaluate : 1.863 ------------------------------------------------------------------------------- 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 232 PHE 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 E residue 300 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 300 ASP Chi-restraints excluded: chain A residue 345 LEU Chi-restraints excluded: chain C residue 232 PHE Chi-restraints excluded: chain C residue 250 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 194 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 146 optimal weight: 0.0470 chunk 113 optimal weight: 0.8980 chunk 169 optimal weight: 4.9990 chunk 112 optimal weight: 1.9990 chunk 200 optimal weight: 3.9990 chunk 125 optimal weight: 0.5980 chunk 122 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- 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: 0.7799 moved from start: 0.1748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18139 Z= 0.203 Angle : 0.481 6.937 24867 Z= 0.251 Chirality : 0.044 0.164 2903 Planarity : 0.004 0.059 3006 Dihedral : 11.230 90.062 2979 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.31 % Allowed : 20.81 % Favored : 76.88 % 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: 0.62 (0.19), residues: 2094 helix: 0.81 (0.24), residues: 546 sheet: 0.83 (0.30), residues: 342 loop : 0.21 (0.18), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 86 HIS 0.004 0.001 HIS B 337 PHE 0.027 0.001 PHE D 221 TYR 0.013 0.001 TYR A 225 ARG 0.007 0.000 ARG A 138 *********************** 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: 37 poor density : 203 time to evaluate : 2.020 Fit side-chains revert: symmetry clash REVERT: D 152 GLN cc_start: 0.7781 (pm20) cc_final: 0.7579 (pm20) REVERT: E 204 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7425 (mtpp) REVERT: E 254 LEU cc_start: 0.8368 (OUTLIER) cc_final: 0.7557 (mp) REVERT: B 223 GLU cc_start: 0.8244 (tp30) cc_final: 0.7857 (tt0) REVERT: A 163 ASN cc_start: 0.8552 (t0) cc_final: 0.8254 (t0) REVERT: A 233 GLU cc_start: 0.8087 (mp0) cc_final: 0.7835 (mp0) REVERT: A 296 ASP cc_start: 0.8401 (t0) cc_final: 0.8141 (t0) REVERT: A 345 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6607 (tp) outliers start: 37 outliers final: 27 residues processed: 221 average time/residue: 0.2850 time to fit residues: 96.0448 Evaluate side-chains 227 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 197 time to evaluate : 1.794 ------------------------------------------------------------------------------- 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 285 THR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 96 ILE 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 128 ASP Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 300 ASP 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 124 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 127 optimal weight: 0.4980 chunk 136 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 157 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.7815 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18139 Z= 0.237 Angle : 0.490 6.649 24867 Z= 0.256 Chirality : 0.045 0.160 2903 Planarity : 0.004 0.059 3006 Dihedral : 11.228 88.877 2979 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.42 % Allowed : 21.02 % Favored : 76.56 % 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: 0.51 (0.19), residues: 2094 helix: 0.69 (0.23), residues: 546 sheet: 0.79 (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 332 HIS 0.004 0.001 HIS B 337 PHE 0.030 0.001 PHE D 221 TYR 0.013 0.001 TYR A 225 ARG 0.006 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 238 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 199 time to evaluate : 1.855 Fit side-chains revert: symmetry clash REVERT: F 264 GLU cc_start: 0.7611 (mt-10) cc_final: 0.6762 (mp0) REVERT: E 204 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7443 (mtpp) REVERT: E 254 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7566 (mp) REVERT: B 223 GLU cc_start: 0.8257 (tp30) cc_final: 0.7865 (tt0) REVERT: A 163 ASN cc_start: 0.8605 (t0) cc_final: 0.8314 (t0) REVERT: A 259 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7250 (mttp) REVERT: A 296 ASP cc_start: 0.8428 (t0) cc_final: 0.8180 (t0) REVERT: A 345 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6723 (tp) outliers start: 39 outliers final: 31 residues processed: 217 average time/residue: 0.2879 time to fit residues: 95.7781 Evaluate side-chains 231 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 196 time to evaluate : 1.808 ------------------------------------------------------------------------------- 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 285 THR Chi-restraints excluded: chain F residue 320 VAL Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain D residue 36 ASP Chi-restraints excluded: chain D residue 51 VAL Chi-restraints excluded: chain D residue 96 ILE 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 128 ASP Chi-restraints excluded: chain E residue 204 LYS Chi-restraints excluded: chain E residue 254 LEU Chi-restraints excluded: chain E residue 300 ASP Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 114 THR Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 209 MET Chi-restraints excluded: chain A residue 259 LYS Chi-restraints excluded: chain A residue 300 ASP 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 182 optimal weight: 0.9990 chunk 192 optimal weight: 0.1980 chunk 175 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 146 optimal weight: 0.0010 chunk 57 optimal weight: 0.4980 chunk 168 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 chunk 122 optimal weight: 0.0070 overall best weight: 0.2804 ------------------------------------------------------------------------------- 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 244 GLN C 163 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18139 Z= 0.131 Angle : 0.448 6.693 24867 Z= 0.235 Chirality : 0.043 0.160 2903 Planarity : 0.003 0.058 3006 Dihedral : 11.085 86.320 2979 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.15 % Allowed : 21.18 % 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: 0.65 (0.19), residues: 2094 helix: 0.79 (0.24), residues: 552 sheet: 0.79 (0.29), residues: 342 loop : 0.27 (0.19), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 332 HIS 0.003 0.000 HIS B 337 PHE 0.028 0.001 PHE D 221 TYR 0.008 0.001 TYR B 225 ARG 0.006 0.000 ARG B 224 *********************** 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 242 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 208 time to evaluate : 2.010 Fit side-chains revert: symmetry clash REVERT: D 152 GLN cc_start: 0.7633 (pm20) cc_final: 0.7310 (tp40) REVERT: D 296 ASP cc_start: 0.8003 (t0) cc_final: 0.7763 (t0) REVERT: E 204 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7406 (mtpp) REVERT: B 223 GLU cc_start: 0.8229 (tp30) cc_final: 0.7803 (tt0) REVERT: B 228 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7745 (mt-10) REVERT: A 87 ASP cc_start: 0.8761 (t0) cc_final: 0.8511 (t0) REVERT: A 163 ASN cc_start: 0.8551 (t0) cc_final: 0.8264 (t0) REVERT: A 296 ASP cc_start: 0.8155 (t0) cc_final: 0.7742 (t70) REVERT: A 345 LEU cc_start: 0.6741 (OUTLIER) cc_final: 0.6461 (tp) outliers start: 34 outliers final: 26 residues processed: 227 average time/residue: 0.3013 time to fit residues: 105.8812 Evaluate side-chains 227 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 1.908 ------------------------------------------------------------------------------- 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 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 106 ASP Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 244 GLN Chi-restraints excluded: chain A residue 300 ASP 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 250 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 197 optimal weight: 0.4980 chunk 120 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 137 optimal weight: 0.0770 chunk 207 optimal weight: 10.0000 chunk 190 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 127 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 131 optimal weight: 0.5980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 244 GLN ** C 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 187 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 18139 Z= 0.188 Angle : 0.655 59.198 24867 Z= 0.388 Chirality : 0.045 0.699 2903 Planarity : 0.004 0.079 3006 Dihedral : 11.088 86.316 2979 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.83 % Allowed : 21.61 % Favored : 76.56 % Cbeta Deviations : 0.05 % 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: 0.64 (0.19), residues: 2094 helix: 0.79 (0.24), residues: 552 sheet: 0.79 (0.29), residues: 342 loop : 0.25 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 86 HIS 0.003 0.001 HIS B 337 PHE 0.028 0.001 PHE D 221 TYR 0.008 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 227 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 1.978 Fit side-chains revert: symmetry clash REVERT: D 87 ASP cc_start: 0.8466 (t0) cc_final: 0.8132 (t0) REVERT: D 152 GLN cc_start: 0.7636 (pm20) cc_final: 0.7314 (tp40) REVERT: D 296 ASP cc_start: 0.8003 (t0) cc_final: 0.7767 (t0) REVERT: E 204 LYS cc_start: 0.7755 (OUTLIER) cc_final: 0.7408 (mtpp) REVERT: B 223 GLU cc_start: 0.8230 (tp30) cc_final: 0.7804 (tt0) REVERT: B 228 GLU cc_start: 0.8009 (mt-10) cc_final: 0.7747 (mt-10) REVERT: A 87 ASP cc_start: 0.8765 (t0) cc_final: 0.8556 (t0) REVERT: A 163 ASN cc_start: 0.8553 (t0) cc_final: 0.8269 (t0) REVERT: A 296 ASP cc_start: 0.8151 (t0) cc_final: 0.7729 (t70) REVERT: A 345 LEU cc_start: 0.6740 (OUTLIER) cc_final: 0.6460 (tp) outliers start: 28 outliers final: 25 residues processed: 215 average time/residue: 0.2904 time to fit residues: 95.5157 Evaluate side-chains 225 residues out of total 1824 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 198 time to evaluate : 1.716 ------------------------------------------------------------------------------- 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 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 106 ASP Chi-restraints excluded: chain B residue 202 GLU Chi-restraints excluded: chain B residue 232 PHE Chi-restraints excluded: chain B residue 252 ILE Chi-restraints excluded: chain B residue 290 CYS Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 197 SER Chi-restraints excluded: chain A residue 300 ASP 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 250 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: 1.9990 chunk 152 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 165 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 169 optimal weight: 4.9990 chunk 20 optimal weight: 0.0170 chunk 30 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.186073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.139380 restraints weight = 116491.965| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 5.33 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3424 r_free = 0.3424 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 18139 Z= 0.188 Angle : 0.655 59.198 24867 Z= 0.388 Chirality : 0.045 0.699 2903 Planarity : 0.004 0.079 3006 Dihedral : 11.088 86.316 2979 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.77 % Allowed : 21.61 % Favored : 76.61 % Cbeta Deviations : 0.05 % 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: 0.64 (0.19), residues: 2094 helix: 0.79 (0.24), residues: 552 sheet: 0.79 (0.29), residues: 342 loop : 0.25 (0.18), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 86 HIS 0.003 0.001 HIS B 337 PHE 0.028 0.001 PHE D 221 TYR 0.008 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: 3544.31 seconds wall clock time: 64 minutes 34.74 seconds (3874.74 seconds total)