Starting phenix.real_space_refine on Sun Nov 17 19:26:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbg_27283/11_2024/8dbg_27283.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbg_27283/11_2024/8dbg_27283.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbg_27283/11_2024/8dbg_27283.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbg_27283/11_2024/8dbg_27283.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbg_27283/11_2024/8dbg_27283.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dbg_27283/11_2024/8dbg_27283.cif" } resolution = 2.2 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= 0.300 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: 6 Type Number sf(0) Gaussians P 30 5.49 5 Mg 12 5.21 5 S 102 5.16 5 C 8952 2.51 5 N 2520 2.21 5 O 2826 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 102 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 14442 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "E" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "F" Number of atoms: 2362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2362 Classifications: {'peptide': 309} Link IDs: {'PTRANS': 9, 'TRANS': 299} Chain breaks: 1 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "E" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 43 Unusual residues: {' MG': 2, 'ATP': 1, 'PO4': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 318 residue: pdb=" N HIS A 12 " occ=0.58 ... (8 atoms not shown) pdb=" NE2 HIS A 12 " occ=0.58 residue: pdb=" N ARG A 22 " occ=0.80 ... (9 atoms not shown) pdb=" NH2 ARG A 22 " occ=0.80 residue: pdb=" N GLU A 26 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 26 " occ=0.40 residue: pdb=" N LYS A 29 " occ=0.40 ... (7 atoms not shown) pdb=" NZ LYS A 29 " occ=0.40 residue: pdb=" N LYS A 33 " occ=0.01 ... (7 atoms not shown) pdb=" NZ LYS A 33 " occ=0.01 residue: pdb=" N SER A 36 " occ=0.01 ... (4 atoms not shown) pdb=" OG SER A 36 " occ=0.01 residue: pdb=" N ASN A 37 " occ=0.50 ... (6 atoms not shown) pdb=" ND2 ASN A 37 " occ=0.50 residue: pdb=" N CYS A 41 " occ=0.89 ... (4 atoms not shown) pdb=" SG CYS A 41 " occ=0.89 residue: pdb=" N GLU A 43 " occ=0.40 ... (7 atoms not shown) pdb=" OE2 GLU A 43 " occ=0.40 residue: pdb=" N GLU A 46 " occ=0.88 ... (7 atoms not shown) pdb=" OE2 GLU A 46 " occ=0.88 residue: pdb=" N SER A 58 " occ=0.10 ... (4 atoms not shown) pdb=" OG SER A 58 " occ=0.10 residue: pdb=" N GLY A 59 " occ=0.01 ... (2 atoms not shown) pdb=" O GLY A 59 " occ=0.01 ... (remaining 306 not shown) Time building chain proxies: 8.80, per 1000 atoms: 0.61 Number of scatterers: 14442 At special positions: 0 Unit cell: (122.396, 129.839, 76.911, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 102 16.00 P 30 15.00 Mg 12 11.99 O 2826 8.00 N 2520 7.00 C 8952 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 - 3.00 Amino acid : True - 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: 3.53 Conformation dependent library (CDL) restraints added in 1.8 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3504 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 18 sheets defined 44.0% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 12 through 24 Processing helix chain 'A' and resid 62 through 80 Processing helix chain 'A' and resid 107 through 120 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 147 through 159 Processing helix chain 'A' and resid 161 through 164 Processing helix chain 'A' and resid 174 through 186 Processing helix chain 'A' and resid 226 through 239 Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS A 283 " --> pdb=" O ASP A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 306 Processing helix chain 'A' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER A 314 " --> pdb=" O TYR A 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 24 Processing helix chain 'B' and resid 62 through 80 Processing helix chain 'B' and resid 107 through 120 Processing helix chain 'B' and resid 131 through 138 Processing helix chain 'B' and resid 147 through 159 Processing helix chain 'B' and resid 161 through 164 Processing helix chain 'B' and resid 174 through 186 Processing helix chain 'B' and resid 226 through 239 Processing helix chain 'B' and resid 256 through 264 Processing helix chain 'B' and resid 277 through 284 removed outlier: 3.667A pdb=" N HIS B 283 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 306 Processing helix chain 'B' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER B 314 " --> pdb=" O TYR B 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 24 Processing helix chain 'C' and resid 62 through 80 Processing helix chain 'C' and resid 107 through 120 Processing helix chain 'C' and resid 131 through 138 Processing helix chain 'C' and resid 147 through 159 Processing helix chain 'C' and resid 161 through 164 Processing helix chain 'C' and resid 174 through 186 Processing helix chain 'C' and resid 226 through 239 Processing helix chain 'C' and resid 256 through 264 Processing helix chain 'C' and resid 277 through 284 removed outlier: 3.668A pdb=" N HIS C 283 " --> pdb=" O ASP C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 292 through 306 Processing helix chain 'C' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER C 314 " --> pdb=" O TYR C 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 24 Processing helix chain 'D' and resid 62 through 80 Processing helix chain 'D' and resid 107 through 120 Processing helix chain 'D' and resid 131 through 138 Processing helix chain 'D' and resid 147 through 159 Processing helix chain 'D' and resid 161 through 164 Processing helix chain 'D' and resid 174 through 186 Processing helix chain 'D' and resid 226 through 239 Processing helix chain 'D' and resid 256 through 264 Processing helix chain 'D' and resid 277 through 284 removed outlier: 3.668A pdb=" N HIS D 283 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 292 through 306 Processing helix chain 'D' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER D 314 " --> pdb=" O TYR D 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 24 Processing helix chain 'E' and resid 62 through 80 Processing helix chain 'E' and resid 107 through 120 Processing helix chain 'E' and resid 131 through 138 Processing helix chain 'E' and resid 147 through 159 Processing helix chain 'E' and resid 161 through 164 Processing helix chain 'E' and resid 174 through 186 Processing helix chain 'E' and resid 226 through 239 Processing helix chain 'E' and resid 256 through 264 Processing helix chain 'E' and resid 277 through 284 removed outlier: 3.668A pdb=" N HIS E 283 " --> pdb=" O ASP E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 292 through 306 Processing helix chain 'E' and resid 309 through 314 removed outlier: 3.632A pdb=" N SER E 314 " --> pdb=" O TYR E 311 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 24 Processing helix chain 'F' and resid 62 through 80 Processing helix chain 'F' and resid 107 through 120 Processing helix chain 'F' and resid 131 through 138 Processing helix chain 'F' and resid 147 through 159 Processing helix chain 'F' and resid 161 through 164 Processing helix chain 'F' and resid 174 through 186 Processing helix chain 'F' and resid 226 through 239 Processing helix chain 'F' and resid 256 through 264 Processing helix chain 'F' and resid 277 through 284 removed outlier: 3.668A pdb=" N HIS F 283 " --> pdb=" O ASP F 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 292 through 306 Processing helix chain 'F' and resid 309 through 314 removed outlier: 3.631A pdb=" N SER F 314 " --> pdb=" O TYR F 311 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS A 5 " --> pdb=" O TYR A 54 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL A 56 " --> pdb=" O LYS A 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE A 7 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL A 53 " --> pdb=" O THR A 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL A 88 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE A 55 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS A 123 " --> pdb=" O VAL A 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET A 127 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 124 " --> pdb=" O ASP A 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU A 145 " --> pdb=" O ILE A 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR A 126 " --> pdb=" O LEU A 145 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET A 222 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY A 251 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA A 268 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS A 250 " --> pdb=" O THR A 272 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS B 5 " --> pdb=" O TYR B 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL B 56 " --> pdb=" O LYS B 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE B 7 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL B 53 " --> pdb=" O THR B 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL B 88 " --> pdb=" O VAL B 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE B 55 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS B 123 " --> pdb=" O VAL B 85 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET B 127 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE B 124 " --> pdb=" O ASP B 143 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU B 145 " --> pdb=" O ILE B 124 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR B 126 " --> pdb=" O LEU B 145 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 30 through 34 Processing sheet with id=AA6, first strand: chain 'B' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET B 222 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY B 251 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA B 268 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS B 250 " --> pdb=" O THR B 272 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS C 5 " --> pdb=" O TYR C 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL C 56 " --> pdb=" O LYS C 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE C 7 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL C 53 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL C 88 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE C 55 " --> pdb=" O VAL C 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS C 123 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET C 127 " --> pdb=" O ILE C 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE C 124 " --> pdb=" O ASP C 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU C 145 " --> pdb=" O ILE C 124 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N THR C 126 " --> pdb=" O LEU C 145 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 30 through 34 Processing sheet with id=AA9, first strand: chain 'C' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET C 222 " --> pdb=" O THR C 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY C 251 " --> pdb=" O MET C 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA C 268 " --> pdb=" O VAL C 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS C 250 " --> pdb=" O THR C 272 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS D 5 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL D 56 " --> pdb=" O LYS D 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE D 7 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL D 53 " --> pdb=" O THR D 86 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL D 88 " --> pdb=" O VAL D 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE D 55 " --> pdb=" O VAL D 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS D 123 " --> pdb=" O VAL D 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET D 127 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE D 124 " --> pdb=" O ASP D 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU D 145 " --> pdb=" O ILE D 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR D 126 " --> pdb=" O LEU D 145 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 30 through 34 Processing sheet with id=AB3, first strand: chain 'D' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET D 222 " --> pdb=" O THR D 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY D 251 " --> pdb=" O MET D 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA D 268 " --> pdb=" O VAL D 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS D 250 " --> pdb=" O THR D 272 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.224A pdb=" N LYS E 5 " --> pdb=" O TYR E 54 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N VAL E 56 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE E 7 " --> pdb=" O VAL E 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL E 53 " --> pdb=" O THR E 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL E 88 " --> pdb=" O VAL E 53 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE E 55 " --> pdb=" O VAL E 88 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS E 123 " --> pdb=" O VAL E 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET E 127 " --> pdb=" O ILE E 89 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE E 124 " --> pdb=" O ASP E 143 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU E 145 " --> pdb=" O ILE E 124 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N THR E 126 " --> pdb=" O LEU E 145 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 30 through 34 Processing sheet with id=AB6, first strand: chain 'E' and resid 205 through 208 removed outlier: 6.696A pdb=" N MET E 222 " --> pdb=" O THR E 249 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY E 251 " --> pdb=" O MET E 222 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N ALA E 268 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N HIS E 250 " --> pdb=" O THR E 272 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 4 through 8 removed outlier: 6.225A pdb=" N LYS F 5 " --> pdb=" O TYR F 54 " (cutoff:3.500A) removed outlier: 7.412A pdb=" N VAL F 56 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N PHE F 7 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N VAL F 53 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N VAL F 88 " --> pdb=" O VAL F 53 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE F 55 " --> pdb=" O VAL F 88 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N HIS F 123 " --> pdb=" O VAL F 85 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N MET F 127 " --> pdb=" O ILE F 89 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE F 124 " --> pdb=" O ASP F 143 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N LEU F 145 " --> pdb=" O ILE F 124 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N THR F 126 " --> pdb=" O LEU F 145 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 30 through 34 Processing sheet with id=AB9, first strand: chain 'F' and resid 205 through 208 removed outlier: 6.697A pdb=" N MET F 222 " --> pdb=" O THR F 249 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N GLY F 251 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ALA F 268 " --> pdb=" O VAL F 244 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N HIS F 250 " --> pdb=" O THR F 272 " (cutoff:3.500A) 714 hydrogen bonds defined for protein. 1998 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.05 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 4701 1.33 - 1.45: 1661 1.45 - 1.57: 8086 1.57 - 1.69: 30 1.69 - 1.81: 150 Bond restraints: 14628 Sorted by residual: bond pdb=" O4 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O4 PO4 A 403 " pdb=" P PO4 A 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" O4 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.568 1.498 0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" O2 PO4 E 403 " pdb=" P PO4 E 403 " ideal model delta sigma weight residual 1.567 1.498 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" O2 PO4 C 403 " pdb=" P PO4 C 403 " ideal model delta sigma weight residual 1.567 1.498 0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 14623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.50: 19039 1.50 - 3.01: 644 3.01 - 4.51: 123 4.51 - 6.01: 24 6.01 - 7.51: 6 Bond angle restraints: 19836 Sorted by residual: angle pdb=" PB ATP F 401 " pdb=" O3B ATP F 401 " pdb=" PG ATP F 401 " ideal model delta sigma weight residual 139.87 132.36 7.51 1.00e+00 1.00e+00 5.65e+01 angle pdb=" PB ATP A 401 " pdb=" O3B ATP A 401 " pdb=" PG ATP A 401 " ideal model delta sigma weight residual 139.87 132.39 7.48 1.00e+00 1.00e+00 5.60e+01 angle pdb=" PB ATP C 401 " pdb=" O3B ATP C 401 " pdb=" PG ATP C 401 " ideal model delta sigma weight residual 139.87 132.39 7.48 1.00e+00 1.00e+00 5.59e+01 angle pdb=" PB ATP E 401 " pdb=" O3B ATP E 401 " pdb=" PG ATP E 401 " ideal model delta sigma weight residual 139.87 132.40 7.47 1.00e+00 1.00e+00 5.58e+01 angle pdb=" PB ATP B 401 " pdb=" O3B ATP B 401 " pdb=" PG ATP B 401 " ideal model delta sigma weight residual 139.87 132.40 7.47 1.00e+00 1.00e+00 5.58e+01 ... (remaining 19831 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8016 17.95 - 35.90: 678 35.90 - 53.84: 216 53.84 - 71.79: 67 71.79 - 89.74: 47 Dihedral angle restraints: 9024 sinusoidal: 3648 harmonic: 5376 Sorted by residual: dihedral pdb=" CA SER E 8 " pdb=" C SER E 8 " pdb=" N GLY E 9 " pdb=" CA GLY E 9 " ideal model delta harmonic sigma weight residual 180.00 160.63 19.37 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER D 8 " pdb=" C SER D 8 " pdb=" N GLY D 9 " pdb=" CA GLY D 9 " ideal model delta harmonic sigma weight residual 180.00 160.64 19.36 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA SER F 8 " pdb=" C SER F 8 " pdb=" N GLY F 9 " pdb=" CA GLY F 9 " ideal model delta harmonic sigma weight residual 180.00 160.65 19.35 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 9021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1304 0.040 - 0.079: 716 0.079 - 0.119: 247 0.119 - 0.158: 43 0.158 - 0.198: 24 Chirality restraints: 2334 Sorted by residual: chirality pdb=" CG LEU D 248 " pdb=" CB LEU D 248 " pdb=" CD1 LEU D 248 " pdb=" CD2 LEU D 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.20 2.00e-01 2.50e+01 9.77e-01 chirality pdb=" CG LEU E 248 " pdb=" CB LEU E 248 " pdb=" CD1 LEU E 248 " pdb=" CD2 LEU E 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.19 2.00e-01 2.50e+01 9.50e-01 chirality pdb=" CG LEU B 248 " pdb=" CB LEU B 248 " pdb=" CD1 LEU B 248 " pdb=" CD2 LEU B 248 " both_signs ideal model delta sigma weight residual False -2.59 -2.39 -0.19 2.00e-01 2.50e+01 9.50e-01 ... (remaining 2331 not shown) Planarity restraints: 2502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER F 180 " -0.009 2.00e-02 2.50e+03 1.70e-02 2.89e+00 pdb=" C SER F 180 " 0.029 2.00e-02 2.50e+03 pdb=" O SER F 180 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE F 181 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 180 " 0.008 2.00e-02 2.50e+03 1.69e-02 2.84e+00 pdb=" C SER A 180 " -0.029 2.00e-02 2.50e+03 pdb=" O SER A 180 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE A 181 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 180 " 0.008 2.00e-02 2.50e+03 1.68e-02 2.84e+00 pdb=" C SER C 180 " -0.029 2.00e-02 2.50e+03 pdb=" O SER C 180 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE C 181 " 0.010 2.00e-02 2.50e+03 ... (remaining 2499 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 114 2.55 - 3.13: 11505 3.13 - 3.72: 23613 3.72 - 4.31: 33275 4.31 - 4.90: 55499 Nonbonded interactions: 124006 Sorted by model distance: nonbonded pdb="MG MG D 404 " pdb=" O HOH D 501 " model vdw 1.958 2.170 nonbonded pdb="MG MG B 404 " pdb=" O HOH B 501 " model vdw 1.959 2.170 nonbonded pdb="MG MG F 404 " pdb=" O HOH F 501 " model vdw 1.959 2.170 nonbonded pdb="MG MG A 404 " pdb=" O HOH A 501 " model vdw 1.959 2.170 nonbonded pdb="MG MG E 404 " pdb=" O HOH E 501 " model vdw 1.959 2.170 ... (remaining 124001 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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=0.01 max=1.00 mean=0.91 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.360 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: 0.540 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 34.210 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.070 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:13.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 14628 Z= 0.464 Angle : 0.693 7.513 19836 Z= 0.437 Chirality : 0.054 0.198 2334 Planarity : 0.003 0.019 2502 Dihedral : 17.531 89.739 5520 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.97 % Allowed : 12.53 % Favored : 85.50 % 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 (0.20), residues: 1830 helix: 1.27 (0.20), residues: 744 sheet: 0.06 (0.25), residues: 474 loop : -0.38 (0.22), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 162 HIS 0.005 0.001 HIS E 130 PHE 0.011 0.002 PHE D 189 TYR 0.022 0.004 TYR D 146 ARG 0.004 0.001 ARG F 177 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 339 time to evaluate : 1.690 Fit side-chains REVERT: A 6 ILE cc_start: 0.9058 (mm) cc_final: 0.8813 (mm) REVERT: A 294 MET cc_start: 0.8704 (pmm) cc_final: 0.8435 (pmm) REVERT: C 127 MET cc_start: 0.8754 (ttm) cc_final: 0.8254 (ttm) REVERT: D 127 MET cc_start: 0.8752 (ttm) cc_final: 0.8256 (ttm) REVERT: F 6 ILE cc_start: 0.9058 (mm) cc_final: 0.8811 (mm) REVERT: F 294 MET cc_start: 0.8718 (pmm) cc_final: 0.8453 (pmm) outliers start: 31 outliers final: 24 residues processed: 362 average time/residue: 1.3467 time to fit residues: 533.6393 Evaluate side-chains 306 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 282 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 314 SER Chi-restraints excluded: chain C residue 160 SER Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 314 SER Chi-restraints excluded: chain D residue 160 SER Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 314 SER Chi-restraints excluded: chain E residue 160 SER Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 160 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 314 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 0.9990 chunk 136 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 46 optimal weight: 0.0870 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 163 optimal weight: 0.8980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN C 135 GLN C 305 ASN D 38 GLN D 135 GLN D 305 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14628 Z= 0.180 Angle : 0.524 6.153 19836 Z= 0.297 Chirality : 0.048 0.164 2334 Planarity : 0.003 0.022 2502 Dihedral : 13.061 86.411 2196 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.99 % Allowed : 11.51 % Favored : 85.50 % 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: 0.76 (0.20), residues: 1830 helix: 1.54 (0.20), residues: 756 sheet: 0.11 (0.24), residues: 474 loop : -0.38 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 162 HIS 0.004 0.001 HIS D 130 PHE 0.009 0.001 PHE C 138 TYR 0.012 0.001 TYR C 146 ARG 0.002 0.000 ARG C 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 321 time to evaluate : 1.612 Fit side-chains REVERT: A 6 ILE cc_start: 0.9051 (mm) cc_final: 0.8806 (mm) REVERT: A 115 MET cc_start: 0.8785 (mtm) cc_final: 0.8550 (mtp) REVERT: A 294 MET cc_start: 0.8657 (pmm) cc_final: 0.8400 (pmm) REVERT: B 6 ILE cc_start: 0.9074 (mm) cc_final: 0.8853 (mm) REVERT: B 220 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7370 (m-30) REVERT: C 127 MET cc_start: 0.8747 (ttm) cc_final: 0.8302 (ttm) REVERT: C 263 ASN cc_start: 0.8183 (m-40) cc_final: 0.7978 (m110) REVERT: D 127 MET cc_start: 0.8746 (ttm) cc_final: 0.8304 (ttm) REVERT: D 263 ASN cc_start: 0.8184 (m-40) cc_final: 0.7970 (m110) REVERT: E 6 ILE cc_start: 0.9073 (mm) cc_final: 0.8851 (mm) REVERT: E 220 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7374 (m-30) REVERT: F 6 ILE cc_start: 0.9053 (mm) cc_final: 0.8807 (mm) REVERT: F 294 MET cc_start: 0.8655 (pmm) cc_final: 0.8398 (pmm) outliers start: 47 outliers final: 28 residues processed: 353 average time/residue: 1.4596 time to fit residues: 561.0153 Evaluate side-chains 331 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 301 time to evaluate : 1.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 HIS Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 220 ASP Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain E residue 270 VAL Chi-restraints excluded: chain F residue 12 HIS Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.5980 chunk 136 optimal weight: 0.4980 chunk 111 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 163 optimal weight: 0.9980 chunk 176 optimal weight: 3.9990 chunk 145 optimal weight: 0.9980 chunk 162 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14628 Z= 0.183 Angle : 0.509 5.544 19836 Z= 0.288 Chirality : 0.048 0.165 2334 Planarity : 0.003 0.021 2502 Dihedral : 11.548 79.020 2184 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 2.80 % Allowed : 11.45 % Favored : 85.75 % 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: 0.91 (0.20), residues: 1830 helix: 1.84 (0.20), residues: 756 sheet: -0.02 (0.24), residues: 474 loop : -0.37 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 162 HIS 0.003 0.001 HIS C 130 PHE 0.008 0.001 PHE F 138 TYR 0.012 0.002 TYR C 146 ARG 0.002 0.000 ARG A 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 298 time to evaluate : 1.683 Fit side-chains REVERT: A 6 ILE cc_start: 0.9065 (mm) cc_final: 0.8812 (mm) REVERT: A 115 MET cc_start: 0.8808 (mtm) cc_final: 0.8584 (mtp) REVERT: A 294 MET cc_start: 0.8656 (pmm) cc_final: 0.8366 (pmm) REVERT: B 6 ILE cc_start: 0.9063 (mm) cc_final: 0.8858 (mm) REVERT: E 6 ILE cc_start: 0.9062 (mm) cc_final: 0.8853 (mm) REVERT: F 6 ILE cc_start: 0.9066 (mm) cc_final: 0.8813 (mm) REVERT: F 294 MET cc_start: 0.8661 (pmm) cc_final: 0.8368 (pmm) outliers start: 44 outliers final: 30 residues processed: 329 average time/residue: 1.5216 time to fit residues: 541.7352 Evaluate side-chains 318 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 288 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 chunk 164 optimal weight: 4.9990 chunk 173 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN D 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14628 Z= 0.394 Angle : 0.634 6.869 19836 Z= 0.357 Chirality : 0.054 0.212 2334 Planarity : 0.004 0.026 2502 Dihedral : 13.272 89.856 2184 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.35 % Allowed : 11.70 % Favored : 85.94 % 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: 0.77 (0.20), residues: 1830 helix: 1.69 (0.20), residues: 756 sheet: -0.07 (0.24), residues: 474 loop : -0.40 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP B 162 HIS 0.006 0.002 HIS B 130 PHE 0.009 0.002 PHE B 189 TYR 0.018 0.003 TYR D 146 ARG 0.005 0.000 ARG F 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 300 time to evaluate : 1.717 Fit side-chains REVERT: A 6 ILE cc_start: 0.9095 (mm) cc_final: 0.8886 (mm) REVERT: B 220 ASP cc_start: 0.7875 (OUTLIER) cc_final: 0.7386 (m-30) REVERT: C 220 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7377 (m-30) REVERT: C 260 ARG cc_start: 0.8578 (mtt180) cc_final: 0.8314 (mtt180) REVERT: E 39 GLU cc_start: 0.8916 (mt-10) cc_final: 0.8681 (mt-10) REVERT: F 6 ILE cc_start: 0.9095 (mm) cc_final: 0.8888 (mm) outliers start: 37 outliers final: 29 residues processed: 326 average time/residue: 1.5802 time to fit residues: 557.4949 Evaluate side-chains 327 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 296 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 220 ASP Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 237 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 129 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14628 Z= 0.246 Angle : 0.552 6.214 19836 Z= 0.312 Chirality : 0.050 0.182 2334 Planarity : 0.003 0.025 2502 Dihedral : 12.468 89.160 2184 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.86 % Allowed : 11.32 % Favored : 85.81 % 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: 0.82 (0.20), residues: 1830 helix: 1.78 (0.20), residues: 756 sheet: -0.07 (0.24), residues: 474 loop : -0.43 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 162 HIS 0.004 0.001 HIS E 130 PHE 0.008 0.001 PHE B 189 TYR 0.016 0.002 TYR D 146 ARG 0.002 0.000 ARG F 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 304 time to evaluate : 1.675 Fit side-chains REVERT: A 6 ILE cc_start: 0.9086 (mm) cc_final: 0.8866 (mm) REVERT: A 237 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7825 (tp) REVERT: C 220 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7380 (m-30) REVERT: D 220 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7364 (m-30) REVERT: E 153 LYS cc_start: 0.8372 (OUTLIER) cc_final: 0.8155 (tttp) REVERT: E 177 ARG cc_start: 0.8319 (ttm110) cc_final: 0.8050 (ttm110) REVERT: F 6 ILE cc_start: 0.9087 (mm) cc_final: 0.8869 (mm) REVERT: F 39 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8602 (mt-10) REVERT: F 237 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7838 (tp) outliers start: 45 outliers final: 29 residues processed: 336 average time/residue: 1.5304 time to fit residues: 555.8908 Evaluate side-chains 339 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 305 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 237 LEU Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 220 ASP Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 153 LYS Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain E residue 237 LEU Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 220 ASP Chi-restraints excluded: chain F residue 237 LEU Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 174 optimal weight: 0.0270 chunk 144 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 91 optimal weight: 0.5980 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14628 Z= 0.190 Angle : 0.515 5.635 19836 Z= 0.291 Chirality : 0.048 0.187 2334 Planarity : 0.003 0.023 2502 Dihedral : 11.721 83.102 2184 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.29 % Allowed : 12.47 % Favored : 85.24 % 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: 0.93 (0.20), residues: 1830 helix: 1.92 (0.20), residues: 756 sheet: -0.09 (0.24), residues: 456 loop : -0.36 (0.22), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 162 HIS 0.003 0.001 HIS C 304 PHE 0.008 0.001 PHE F 189 TYR 0.014 0.002 TYR C 146 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 303 time to evaluate : 1.838 Fit side-chains REVERT: A 6 ILE cc_start: 0.9085 (mm) cc_final: 0.8843 (mm) REVERT: A 237 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7844 (tp) REVERT: C 237 LEU cc_start: 0.8101 (OUTLIER) cc_final: 0.7760 (tp) REVERT: D 237 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7811 (tp) REVERT: D 260 ARG cc_start: 0.8529 (mtt180) cc_final: 0.8219 (mtt180) REVERT: E 177 ARG cc_start: 0.8328 (ttm110) cc_final: 0.8102 (ttm110) REVERT: F 6 ILE cc_start: 0.9086 (mm) cc_final: 0.8846 (mm) outliers start: 36 outliers final: 26 residues processed: 333 average time/residue: 1.5012 time to fit residues: 541.8778 Evaluate side-chains 323 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 294 time to evaluate : 1.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 99 optimal weight: 0.5980 chunk 127 optimal weight: 0.8980 chunk 98 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 173 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14628 Z= 0.186 Angle : 0.509 5.057 19836 Z= 0.287 Chirality : 0.048 0.169 2334 Planarity : 0.003 0.022 2502 Dihedral : 11.290 81.689 2178 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.23 % Allowed : 12.72 % Favored : 85.05 % 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: 0.90 (0.20), residues: 1830 helix: 1.98 (0.20), residues: 756 sheet: -0.30 (0.23), residues: 486 loop : -0.33 (0.23), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 162 HIS 0.003 0.001 HIS C 304 PHE 0.007 0.001 PHE F 189 TYR 0.015 0.002 TYR D 146 ARG 0.002 0.000 ARG F 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 297 time to evaluate : 1.712 Fit side-chains REVERT: A 6 ILE cc_start: 0.9084 (mm) cc_final: 0.8847 (mm) REVERT: A 237 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7820 (tp) REVERT: B 220 ASP cc_start: 0.7802 (t0) cc_final: 0.7469 (t70) REVERT: B 222 MET cc_start: 0.7617 (ptp) cc_final: 0.7309 (ttm) REVERT: C 237 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7754 (tp) REVERT: D 220 ASP cc_start: 0.7887 (OUTLIER) cc_final: 0.7342 (m-30) REVERT: D 237 LEU cc_start: 0.8110 (OUTLIER) cc_final: 0.7776 (tp) REVERT: E 39 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8640 (mt-10) REVERT: E 177 ARG cc_start: 0.8336 (ttm110) cc_final: 0.8101 (ttm110) REVERT: E 222 MET cc_start: 0.7664 (ptp) cc_final: 0.7370 (ttm) REVERT: F 6 ILE cc_start: 0.9086 (mm) cc_final: 0.8849 (mm) outliers start: 35 outliers final: 27 residues processed: 325 average time/residue: 1.5692 time to fit residues: 552.3551 Evaluate side-chains 318 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 287 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 237 LEU Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 220 ASP Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 103 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 16 optimal weight: 0.3980 chunk 136 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14628 Z= 0.163 Angle : 0.489 4.640 19836 Z= 0.276 Chirality : 0.047 0.171 2334 Planarity : 0.003 0.022 2502 Dihedral : 10.830 77.289 2178 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.84 % Allowed : 14.31 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.20), residues: 1830 helix: 2.06 (0.20), residues: 756 sheet: -0.23 (0.23), residues: 480 loop : -0.40 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 162 HIS 0.002 0.001 HIS A 193 PHE 0.006 0.001 PHE A 189 TYR 0.013 0.001 TYR C 146 ARG 0.001 0.000 ARG D 301 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 286 time to evaluate : 1.728 Fit side-chains REVERT: A 6 ILE cc_start: 0.9081 (mm) cc_final: 0.8827 (mm) REVERT: C 237 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7751 (tp) REVERT: C 260 ARG cc_start: 0.8549 (mtt180) cc_final: 0.8311 (mtt180) REVERT: D 237 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7777 (tp) REVERT: D 260 ARG cc_start: 0.8529 (mtt180) cc_final: 0.8270 (mtt180) REVERT: E 177 ARG cc_start: 0.8296 (ttm110) cc_final: 0.8093 (ttm110) REVERT: E 220 ASP cc_start: 0.7810 (t0) cc_final: 0.7473 (t70) REVERT: F 6 ILE cc_start: 0.9084 (mm) cc_final: 0.8829 (mm) outliers start: 29 outliers final: 24 residues processed: 308 average time/residue: 1.5472 time to fit residues: 515.6509 Evaluate side-chains 299 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 273 time to evaluate : 1.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 GLU Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 2.9990 chunk 166 optimal weight: 0.0770 chunk 151 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 152 optimal weight: 0.0030 chunk 106 optimal weight: 0.4980 overall best weight: 0.6750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 17 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14628 Z= 0.172 Angle : 0.497 4.799 19836 Z= 0.280 Chirality : 0.048 0.169 2334 Planarity : 0.003 0.022 2502 Dihedral : 10.747 76.430 2176 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 1.78 % Allowed : 13.99 % Favored : 84.22 % 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: 0.95 (0.20), residues: 1830 helix: 2.05 (0.20), residues: 756 sheet: -0.22 (0.23), residues: 480 loop : -0.39 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 162 HIS 0.002 0.001 HIS B 250 PHE 0.007 0.001 PHE A 189 TYR 0.014 0.002 TYR D 146 ARG 0.002 0.000 ARG F 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 273 time to evaluate : 1.671 Fit side-chains REVERT: A 6 ILE cc_start: 0.9076 (mm) cc_final: 0.8829 (mm) REVERT: B 39 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8676 (mt-10) REVERT: B 222 MET cc_start: 0.7623 (ptp) cc_final: 0.7345 (ttm) REVERT: C 237 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7763 (tp) REVERT: D 237 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7788 (tp) REVERT: D 260 ARG cc_start: 0.8530 (mtt180) cc_final: 0.8236 (mtt180) REVERT: E 220 ASP cc_start: 0.7844 (t0) cc_final: 0.7518 (t70) REVERT: F 6 ILE cc_start: 0.9083 (mm) cc_final: 0.8833 (mm) outliers start: 28 outliers final: 24 residues processed: 294 average time/residue: 1.6319 time to fit residues: 518.4010 Evaluate side-chains 298 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 272 time to evaluate : 1.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 81 optimal weight: 0.0030 chunk 118 optimal weight: 2.9990 chunk 179 optimal weight: 0.8980 chunk 165 optimal weight: 0.9990 chunk 142 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN C 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14628 Z= 0.179 Angle : 0.503 5.027 19836 Z= 0.283 Chirality : 0.048 0.168 2334 Planarity : 0.003 0.022 2502 Dihedral : 10.744 76.249 2176 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.72 % Allowed : 14.38 % Favored : 83.91 % 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: 0.94 (0.20), residues: 1830 helix: 2.05 (0.20), residues: 756 sheet: -0.22 (0.23), residues: 480 loop : -0.40 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 162 HIS 0.003 0.001 HIS B 250 PHE 0.007 0.001 PHE A 189 TYR 0.015 0.002 TYR D 146 ARG 0.002 0.000 ARG F 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 276 time to evaluate : 1.712 Fit side-chains REVERT: A 6 ILE cc_start: 0.9077 (mm) cc_final: 0.8830 (mm) REVERT: B 6 ILE cc_start: 0.9034 (mm) cc_final: 0.8832 (mm) REVERT: B 39 GLU cc_start: 0.8906 (mt-10) cc_final: 0.8679 (mt-10) REVERT: B 220 ASP cc_start: 0.7815 (OUTLIER) cc_final: 0.7515 (t70) REVERT: B 222 MET cc_start: 0.7645 (ptp) cc_final: 0.7341 (ttm) REVERT: C 237 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7791 (tp) REVERT: D 237 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7787 (tp) REVERT: D 260 ARG cc_start: 0.8528 (mtt180) cc_final: 0.8225 (mtt180) REVERT: E 220 ASP cc_start: 0.7840 (t0) cc_final: 0.7516 (t70) REVERT: F 6 ILE cc_start: 0.9082 (mm) cc_final: 0.8834 (mm) outliers start: 27 outliers final: 23 residues processed: 296 average time/residue: 1.5476 time to fit residues: 497.1387 Evaluate side-chains 302 residues out of total 1572 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 1.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain B residue 178 VAL Chi-restraints excluded: chain B residue 208 VAL Chi-restraints excluded: chain B residue 220 ASP Chi-restraints excluded: chain C residue 62 GLU Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 208 VAL Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain C residue 270 VAL Chi-restraints excluded: chain D residue 62 GLU Chi-restraints excluded: chain D residue 208 VAL Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 249 THR Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain E residue 62 GLU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 208 VAL Chi-restraints excluded: chain F residue 62 GLU Chi-restraints excluded: chain F residue 178 VAL Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 270 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 0.0980 chunk 43 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 143 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 38 GLN C 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.145539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.118630 restraints weight = 12236.851| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 1.03 r_work: 0.3156 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 2.32 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3076 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3076 r_free = 0.3076 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 324 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2877 r_free = 0.2877 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2877 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14628 Z= 0.242 Angle : 0.549 5.754 19836 Z= 0.309 Chirality : 0.050 0.190 2334 Planarity : 0.003 0.021 2502 Dihedral : 11.380 82.733 2176 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.84 % Allowed : 14.25 % Favored : 83.91 % 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: 0.89 (0.20), residues: 1830 helix: 1.98 (0.20), residues: 756 sheet: -0.28 (0.23), residues: 480 loop : -0.35 (0.24), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP E 154 HIS 0.004 0.001 HIS E 130 PHE 0.008 0.001 PHE A 189 TYR 0.018 0.002 TYR D 146 ARG 0.003 0.000 ARG F 49 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: