Starting phenix.real_space_refine on Fri Mar 15 04:18:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcb_22807/03_2024/7kcb_22807_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcb_22807/03_2024/7kcb_22807.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcb_22807/03_2024/7kcb_22807.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcb_22807/03_2024/7kcb_22807.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcb_22807/03_2024/7kcb_22807_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kcb_22807/03_2024/7kcb_22807_updated.pdb" } resolution = 2.77 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= 0.004 sd= 0.378 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: 7 Type Number sf(0) Gaussians Zn 8 6.06 5 P 8 5.49 5 S 56 5.16 5 C 6648 2.51 5 N 1788 2.21 5 O 2016 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Residue "A GLU 108": "OE1" <-> "OE2" Residue "A TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 204": "OE1" <-> "OE2" Residue "A ASP 220": "OD1" <-> "OD2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A ASP 236": "OD1" <-> "OD2" Residue "A GLU 253": "OE1" <-> "OE2" Residue "A PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 300": "OD1" <-> "OD2" Residue "A PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "B GLU 4": "OE1" <-> "OE2" Residue "B GLU 108": "OE1" <-> "OE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 204": "OE1" <-> "OE2" Residue "B ASP 220": "OD1" <-> "OD2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B ASP 236": "OD1" <-> "OD2" Residue "B GLU 253": "OE1" <-> "OE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 300": "OD1" <-> "OD2" Residue "B PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 330": "OE1" <-> "OE2" Residue "C GLU 4": "OE1" <-> "OE2" Residue "C GLU 108": "OE1" <-> "OE2" Residue "C TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 204": "OE1" <-> "OE2" Residue "C ASP 220": "OD1" <-> "OD2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C ASP 236": "OD1" <-> "OD2" Residue "C GLU 253": "OE1" <-> "OE2" Residue "C PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 300": "OD1" <-> "OD2" Residue "C PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 330": "OE1" <-> "OE2" Residue "D GLU 4": "OE1" <-> "OE2" Residue "D GLU 108": "OE1" <-> "OE2" Residue "D TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 204": "OE1" <-> "OE2" Residue "D ASP 220": "OD1" <-> "OD2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D ASP 236": "OD1" <-> "OD2" Residue "D GLU 253": "OE1" <-> "OE2" Residue "D PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 300": "OD1" <-> "OD2" Residue "D PHE 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 330": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 10536 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2582 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "B" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2582 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "C" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2582 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "D" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2582 Classifications: {'peptide': 347} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 333} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {' ZN': 2, 'ETF': 1, 'NAD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {' ZN': 2, 'ETF': 1, 'NAD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {' ZN': 2, 'ETF': 1, 'NAD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {' ZN': 2, 'ETF': 1, 'NAD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 340 SG CYS A 43 24.343 24.842 37.230 1.00 44.63 S ATOM 1159 SG CYS A 153 27.829 26.711 36.626 1.00 39.07 S ATOM 747 SG CYS A 97 34.965 44.773 29.715 1.00 47.83 S ATOM 766 SG CYS A 100 34.515 45.294 33.347 1.00 42.66 S ATOM 793 SG CYS A 103 35.835 42.103 32.542 1.00 40.41 S ATOM 851 SG CYS A 111 32.308 42.848 31.855 1.00 44.33 S ATOM 2922 SG CYS B 43 61.757 54.958 37.230 1.00 44.89 S ATOM 3741 SG CYS B 153 58.271 53.089 36.626 1.00 39.12 S ATOM 3329 SG CYS B 97 51.135 35.027 29.715 1.00 47.89 S ATOM 3348 SG CYS B 100 51.585 34.506 33.347 1.00 42.78 S ATOM 3375 SG CYS B 103 50.265 37.697 32.542 1.00 40.33 S ATOM 3433 SG CYS B 111 53.792 36.952 31.855 1.00 44.41 S ATOM 5504 SG CYS C 43 61.757 24.842 69.870 1.00 45.07 S ATOM 6323 SG CYS C 153 58.271 26.711 70.474 1.00 39.36 S ATOM 5911 SG CYS C 97 51.135 44.773 77.385 1.00 48.04 S ATOM 5930 SG CYS C 100 51.585 45.294 73.753 1.00 42.86 S ATOM 5957 SG CYS C 103 50.265 42.103 74.558 1.00 40.33 S ATOM 6015 SG CYS C 111 53.792 42.848 75.245 1.00 44.16 S ATOM 8086 SG CYS D 43 24.343 54.958 69.870 1.00 44.58 S ATOM 8905 SG CYS D 153 27.829 53.089 70.474 1.00 38.71 S ATOM 8493 SG CYS D 97 34.965 35.027 77.385 1.00 47.73 S ATOM 8512 SG CYS D 100 34.515 34.506 73.753 1.00 42.83 S ATOM 8539 SG CYS D 103 35.835 37.697 74.558 1.00 40.35 S ATOM 8597 SG CYS D 111 32.308 36.952 75.245 1.00 44.12 S Time building chain proxies: 5.88, per 1000 atoms: 0.56 Number of scatterers: 10536 At special positions: 0 Unit cell: (87.15, 80.85, 108.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 8 29.99 S 56 16.00 P 8 15.00 F 12 9.00 O 2016 8.00 N 1788 7.00 C 6648 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 277 " - pdb=" SG CYS D 277 " distance=2.09 Simple disulfide: pdb=" SG CYS B 277 " - pdb=" SG CYS C 277 " distance=2.09 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: 3.86 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 401 " pdb="ZN ZN A 401 " - pdb=" NE2 HIS A 66 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 43 " pdb="ZN ZN A 401 " - pdb=" SG CYS A 153 " pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 111 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 97 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 100 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 103 " pdb=" ZN B 401 " pdb="ZN ZN B 401 " - pdb=" NE2 HIS B 66 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 43 " pdb="ZN ZN B 401 " - pdb=" SG CYS B 153 " pdb=" ZN B 402 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 111 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 97 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 100 " pdb="ZN ZN B 402 " - pdb=" SG CYS B 103 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" NE2 HIS C 66 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 43 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 153 " pdb=" ZN C 402 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 111 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 97 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 100 " pdb="ZN ZN C 402 " - pdb=" SG CYS C 103 " pdb=" ZN D 401 " pdb="ZN ZN D 401 " - pdb=" NE2 HIS D 66 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 43 " pdb="ZN ZN D 401 " - pdb=" SG CYS D 153 " pdb=" ZN D 402 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 111 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 97 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 100 " pdb="ZN ZN D 402 " - pdb=" SG CYS D 103 " Number of angles added : 24 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2424 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 44 helices and 16 sheets defined 26.8% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 44 through 51 Processing helix chain 'A' and resid 101 through 105 Processing helix chain 'A' and resid 145 through 151 Proline residue: A 150 - end of helix Processing helix chain 'A' and resid 154 through 164 Processing helix chain 'A' and resid 183 through 193 removed outlier: 3.992A pdb=" N GLN A 188 " --> pdb=" O SER A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 212 Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 249 through 256 removed outlier: 3.824A pdb=" N THR A 256 " --> pdb=" O ILE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 322 through 332 Proline residue: A 326 - end of helix removed outlier: 3.943A pdb=" N GLU A 330 " --> pdb=" O GLU A 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 51 Processing helix chain 'B' and resid 101 through 105 Processing helix chain 'B' and resid 145 through 151 Proline residue: B 150 - end of helix Processing helix chain 'B' and resid 154 through 164 Processing helix chain 'B' and resid 183 through 193 removed outlier: 3.992A pdb=" N GLN B 188 " --> pdb=" O SER B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 212 Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 249 through 256 removed outlier: 3.824A pdb=" N THR B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 285 Processing helix chain 'B' and resid 298 through 309 Processing helix chain 'B' and resid 322 through 332 Proline residue: B 326 - end of helix removed outlier: 3.943A pdb=" N GLU B 330 " --> pdb=" O GLU B 327 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 51 Processing helix chain 'C' and resid 101 through 105 Processing helix chain 'C' and resid 145 through 151 Proline residue: C 150 - end of helix Processing helix chain 'C' and resid 154 through 164 Processing helix chain 'C' and resid 183 through 193 removed outlier: 3.992A pdb=" N GLN C 188 " --> pdb=" O SER C 184 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 249 through 256 removed outlier: 3.824A pdb=" N THR C 256 " --> pdb=" O ILE C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 Processing helix chain 'C' and resid 298 through 309 Processing helix chain 'C' and resid 322 through 332 Proline residue: C 326 - end of helix removed outlier: 3.943A pdb=" N GLU C 330 " --> pdb=" O GLU C 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 51 Processing helix chain 'D' and resid 101 through 105 Processing helix chain 'D' and resid 145 through 151 Proline residue: D 150 - end of helix Processing helix chain 'D' and resid 154 through 164 Processing helix chain 'D' and resid 183 through 193 removed outlier: 3.992A pdb=" N GLN D 188 " --> pdb=" O SER D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 212 Processing helix chain 'D' and resid 227 through 233 Processing helix chain 'D' and resid 249 through 256 removed outlier: 3.824A pdb=" N THR D 256 " --> pdb=" O ILE D 252 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 Processing helix chain 'D' and resid 298 through 309 Processing helix chain 'D' and resid 322 through 332 Proline residue: D 326 - end of helix removed outlier: 3.943A pdb=" N GLU D 330 " --> pdb=" O GLU D 327 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 5 through 10 Processing sheet with id= B, first strand: chain 'A' and resid 128 through 132 removed outlier: 6.223A pdb=" N ASN A 36 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL A 72 " --> pdb=" O ASN A 36 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR A 87 " --> pdb=" O ILE A 139 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 39 through 42 removed outlier: 4.703A pdb=" N TYR A 341 " --> pdb=" O VAL A 42 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 289 through 292 removed outlier: 6.028A pdb=" N ARG A 196 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE A 175 " --> pdb=" O ARG A 196 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU A 198 " --> pdb=" O ILE A 175 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL A 217 " --> pdb=" O GLY A 199 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP A 201 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE A 219 " --> pdb=" O ASP A 201 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 5 through 10 Processing sheet with id= F, first strand: chain 'B' and resid 128 through 132 removed outlier: 6.223A pdb=" N ASN B 36 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL B 72 " --> pdb=" O ASN B 36 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR B 87 " --> pdb=" O ILE B 139 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 39 through 42 removed outlier: 4.703A pdb=" N TYR B 341 " --> pdb=" O VAL B 42 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 289 through 292 removed outlier: 6.028A pdb=" N ARG B 196 " --> pdb=" O VAL B 173 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE B 175 " --> pdb=" O ARG B 196 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU B 198 " --> pdb=" O ILE B 175 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL B 217 " --> pdb=" O GLY B 199 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP B 201 " --> pdb=" O VAL B 217 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE B 219 " --> pdb=" O ASP B 201 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 5 through 10 Processing sheet with id= J, first strand: chain 'C' and resid 128 through 132 removed outlier: 6.223A pdb=" N ASN C 36 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL C 72 " --> pdb=" O ASN C 36 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR C 87 " --> pdb=" O ILE C 139 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 39 through 42 removed outlier: 4.703A pdb=" N TYR C 341 " --> pdb=" O VAL C 42 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 289 through 292 removed outlier: 6.028A pdb=" N ARG C 196 " --> pdb=" O VAL C 173 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE C 175 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU C 198 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL C 217 " --> pdb=" O GLY C 199 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP C 201 " --> pdb=" O VAL C 217 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE C 219 " --> pdb=" O ASP C 201 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 5 through 10 Processing sheet with id= N, first strand: chain 'D' and resid 128 through 132 removed outlier: 6.223A pdb=" N ASN D 36 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL D 72 " --> pdb=" O ASN D 36 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N TYR D 87 " --> pdb=" O ILE D 139 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 39 through 42 removed outlier: 4.703A pdb=" N TYR D 341 " --> pdb=" O VAL D 42 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 289 through 292 removed outlier: 6.028A pdb=" N ARG D 196 " --> pdb=" O VAL D 173 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE D 175 " --> pdb=" O ARG D 196 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU D 198 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL D 217 " --> pdb=" O GLY D 199 " (cutoff:3.500A) removed outlier: 7.634A pdb=" N ASP D 201 " --> pdb=" O VAL D 217 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N ILE D 219 " --> pdb=" O ASP D 201 " (cutoff:3.500A) 312 hydrogen bonds defined for protein. 840 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: 3.39 Time building geometry restraints manager: 4.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3416 1.34 - 1.46: 2540 1.46 - 1.59: 4704 1.59 - 1.71: 16 1.71 - 1.84: 80 Bond restraints: 10756 Sorted by residual: bond pdb=" CB VAL C 58 " pdb=" CG1 VAL C 58 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.22e+00 bond pdb=" CB VAL D 58 " pdb=" CG1 VAL D 58 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.22e+00 bond pdb=" CB VAL A 58 " pdb=" CG1 VAL A 58 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.22e+00 bond pdb=" CB VAL B 58 " pdb=" CG1 VAL B 58 " ideal model delta sigma weight residual 1.521 1.432 0.089 3.30e-02 9.18e+02 7.22e+00 bond pdb=" O3 NAD D 403 " pdb=" PA NAD D 403 " ideal model delta sigma weight residual 1.653 1.600 0.053 2.00e-02 2.50e+03 7.06e+00 ... (remaining 10751 not shown) Histogram of bond angle deviations from ideal: 98.80 - 105.99: 256 105.99 - 113.18: 5916 113.18 - 120.37: 4108 120.37 - 127.55: 4192 127.55 - 134.74: 140 Bond angle restraints: 14612 Sorted by residual: angle pdb=" C ALA B 234 " pdb=" N THR B 235 " pdb=" CA THR B 235 " ideal model delta sigma weight residual 122.11 128.85 -6.74 1.64e+00 3.72e-01 1.69e+01 angle pdb=" C ALA D 234 " pdb=" N THR D 235 " pdb=" CA THR D 235 " ideal model delta sigma weight residual 122.11 128.85 -6.74 1.64e+00 3.72e-01 1.69e+01 angle pdb=" C ALA C 234 " pdb=" N THR C 235 " pdb=" CA THR C 235 " ideal model delta sigma weight residual 122.11 128.85 -6.74 1.64e+00 3.72e-01 1.69e+01 angle pdb=" C ALA A 234 " pdb=" N THR A 235 " pdb=" CA THR A 235 " ideal model delta sigma weight residual 122.11 128.85 -6.74 1.64e+00 3.72e-01 1.69e+01 angle pdb=" N THR A 235 " pdb=" CA THR A 235 " pdb=" CB THR A 235 " ideal model delta sigma weight residual 110.67 105.61 5.06 1.39e+00 5.18e-01 1.33e+01 ... (remaining 14607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 5470 16.66 - 33.33: 644 33.33 - 49.99: 216 49.99 - 66.65: 64 66.65 - 83.31: 12 Dihedral angle restraints: 6406 sinusoidal: 2542 harmonic: 3864 Sorted by residual: dihedral pdb=" CA SER B 1 " pdb=" C SER B 1 " pdb=" N ILE B 2 " pdb=" CA ILE B 2 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA SER D 1 " pdb=" C SER D 1 " pdb=" N ILE D 2 " pdb=" CA ILE D 2 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 dihedral pdb=" CA SER C 1 " pdb=" C SER C 1 " pdb=" N ILE C 2 " pdb=" CA ILE C 2 " ideal model delta harmonic sigma weight residual 180.00 159.90 20.10 0 5.00e+00 4.00e-02 1.62e+01 ... (remaining 6403 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.066: 1148 0.066 - 0.130: 408 0.130 - 0.195: 56 0.195 - 0.260: 8 0.260 - 0.325: 4 Chirality restraints: 1624 Sorted by residual: chirality pdb=" CB VAL D 58 " pdb=" CA VAL D 58 " pdb=" CG1 VAL D 58 " pdb=" CG2 VAL D 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB VAL B 58 " pdb=" CA VAL B 58 " pdb=" CG1 VAL B 58 " pdb=" CG2 VAL B 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 chirality pdb=" CB VAL A 58 " pdb=" CA VAL A 58 " pdb=" CG1 VAL A 58 " pdb=" CG2 VAL A 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1621 not shown) Planarity restraints: 1856 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 118 " 0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLY B 118 " -0.057 2.00e-02 2.50e+03 pdb=" O GLY B 118 " 0.021 2.00e-02 2.50e+03 pdb=" N TYR B 119 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY C 118 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLY C 118 " 0.057 2.00e-02 2.50e+03 pdb=" O GLY C 118 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR C 119 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 118 " -0.017 2.00e-02 2.50e+03 3.32e-02 1.10e+01 pdb=" C GLY D 118 " 0.057 2.00e-02 2.50e+03 pdb=" O GLY D 118 " -0.021 2.00e-02 2.50e+03 pdb=" N TYR D 119 " -0.020 2.00e-02 2.50e+03 ... (remaining 1853 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2622 2.79 - 3.31: 9682 3.31 - 3.84: 19414 3.84 - 4.37: 24796 4.37 - 4.90: 40634 Nonbonded interactions: 97148 Sorted by model distance: nonbonded pdb="ZN ZN A 401 " pdb=" O ETF A 404 " model vdw 2.258 2.230 nonbonded pdb="ZN ZN C 401 " pdb=" O ETF C 404 " model vdw 2.258 2.230 nonbonded pdb="ZN ZN D 401 " pdb=" O ETF D 404 " model vdw 2.258 2.230 nonbonded pdb="ZN ZN B 401 " pdb=" O ETF B 404 " model vdw 2.258 2.230 nonbonded pdb=" O CYS C 153 " pdb=" OG1 THR C 157 " model vdw 2.324 2.440 ... (remaining 97143 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 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: 0.010 Extract box with map and model: 1.930 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 32.270 Find NCS groups from input model: 0.830 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:13.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 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 : 0.011 0.089 10756 Z= 0.755 Angle : 0.910 8.241 14612 Z= 0.510 Chirality : 0.064 0.325 1624 Planarity : 0.006 0.063 1856 Dihedral : 17.035 83.309 3976 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.99 % Allowed : 21.64 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % 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: -3.27 (0.19), residues: 1380 helix: -2.26 (0.19), residues: 452 sheet: -1.92 (0.27), residues: 280 loop : -2.10 (0.21), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 172 HIS 0.009 0.002 HIS B 240 PHE 0.017 0.003 PHE B 221 TYR 0.017 0.003 TYR C 258 ARG 0.003 0.001 ARG A 260 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 148 time to evaluate : 1.208 Fit side-chains REVERT: A 5 THR cc_start: 0.8573 (m) cc_final: 0.8279 (t) REVERT: A 17 LYS cc_start: 0.6700 (tttm) cc_final: 0.6265 (ttpt) REVERT: A 196 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8353 (mtp180) REVERT: A 275 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7762 (mttp) REVERT: B 5 THR cc_start: 0.8578 (m) cc_final: 0.8285 (t) REVERT: B 17 LYS cc_start: 0.6711 (tttm) cc_final: 0.6271 (ttpt) REVERT: B 196 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.8366 (mtp180) REVERT: B 275 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7759 (mttp) REVERT: C 5 THR cc_start: 0.8574 (m) cc_final: 0.8282 (t) REVERT: C 17 LYS cc_start: 0.6696 (tttm) cc_final: 0.6262 (ttpt) REVERT: C 196 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8361 (mtp180) REVERT: C 275 LYS cc_start: 0.7968 (mtmm) cc_final: 0.7762 (mttp) REVERT: D 5 THR cc_start: 0.8574 (m) cc_final: 0.8282 (t) REVERT: D 17 LYS cc_start: 0.6711 (tttm) cc_final: 0.6276 (ttpt) REVERT: D 196 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8360 (mtp180) REVERT: D 275 LYS cc_start: 0.7967 (mtmm) cc_final: 0.7760 (mttp) outliers start: 32 outliers final: 16 residues processed: 176 average time/residue: 1.1716 time to fit residues: 222.8236 Evaluate side-chains 143 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 123 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain A residue 196 ARG Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 196 ARG Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 323 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 196 ARG Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 196 ARG Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 323 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 106 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 64 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 135 GLN A 147 GLN B 36 ASN B 135 GLN B 147 GLN C 36 ASN C 135 GLN C 147 GLN D 36 ASN D 135 GLN D 147 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.1450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 10756 Z= 0.148 Angle : 0.456 4.564 14612 Z= 0.236 Chirality : 0.044 0.136 1624 Planarity : 0.004 0.045 1856 Dihedral : 9.071 56.426 1736 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.61 % Allowed : 20.99 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.20), residues: 1380 helix: -0.76 (0.23), residues: 448 sheet: -1.48 (0.29), residues: 240 loop : -1.50 (0.21), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 50 HIS 0.003 0.001 HIS B 15 PHE 0.008 0.001 PHE B 221 TYR 0.014 0.001 TYR B 258 ARG 0.002 0.000 ARG D 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8526 (OUTLIER) cc_final: 0.8228 (t) REVERT: A 17 LYS cc_start: 0.6751 (tttm) cc_final: 0.6214 (ttpt) REVERT: B 5 THR cc_start: 0.8530 (OUTLIER) cc_final: 0.8234 (t) REVERT: B 17 LYS cc_start: 0.6733 (tttm) cc_final: 0.6231 (ttpt) REVERT: C 5 THR cc_start: 0.8529 (OUTLIER) cc_final: 0.8233 (t) REVERT: C 17 LYS cc_start: 0.6752 (tttm) cc_final: 0.6207 (ttpt) REVERT: D 5 THR cc_start: 0.8528 (OUTLIER) cc_final: 0.8231 (t) REVERT: D 17 LYS cc_start: 0.6742 (tttm) cc_final: 0.6225 (ttpt) outliers start: 28 outliers final: 4 residues processed: 154 average time/residue: 1.2523 time to fit residues: 207.5793 Evaluate side-chains 116 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 294 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 34 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 110 optimal weight: 8.9990 chunk 122 optimal weight: 0.9980 chunk 42 optimal weight: 7.9990 chunk 99 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS A 147 GLN B 138 HIS B 147 GLN C 138 HIS C 147 GLN D 138 HIS D 147 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 10756 Z= 0.442 Angle : 0.579 6.611 14612 Z= 0.292 Chirality : 0.048 0.145 1624 Planarity : 0.004 0.039 1856 Dihedral : 9.569 57.675 1708 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.22 % Allowed : 21.83 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.98 (0.20), residues: 1380 helix: -1.03 (0.22), residues: 452 sheet: -1.47 (0.29), residues: 264 loop : -1.34 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 92 HIS 0.003 0.001 HIS B 48 PHE 0.014 0.002 PHE A 221 TYR 0.018 0.002 TYR D 258 ARG 0.003 0.000 ARG D 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 128 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8257 (t) REVERT: A 17 LYS cc_start: 0.7384 (tttm) cc_final: 0.6811 (ttpt) REVERT: A 182 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8563 (mp) REVERT: B 5 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8264 (t) REVERT: B 17 LYS cc_start: 0.7387 (tttm) cc_final: 0.6818 (ttpt) REVERT: B 182 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8566 (mp) REVERT: C 5 THR cc_start: 0.8482 (OUTLIER) cc_final: 0.8260 (t) REVERT: C 17 LYS cc_start: 0.7382 (tttm) cc_final: 0.6810 (ttpt) REVERT: C 182 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8560 (mp) REVERT: D 5 THR cc_start: 0.8485 (OUTLIER) cc_final: 0.8263 (t) REVERT: D 17 LYS cc_start: 0.7391 (tttm) cc_final: 0.6829 (ttpt) REVERT: D 182 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8568 (mp) outliers start: 56 outliers final: 32 residues processed: 172 average time/residue: 1.0514 time to fit residues: 198.2268 Evaluate side-chains 154 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 114 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 13 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 131 optimal weight: 0.9990 chunk 117 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 109 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 147 GLN C 147 GLN D 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10756 Z= 0.186 Angle : 0.460 5.580 14612 Z= 0.233 Chirality : 0.044 0.137 1624 Planarity : 0.003 0.031 1856 Dihedral : 9.175 58.941 1708 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.92 % Allowed : 23.69 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.21), residues: 1380 helix: -0.48 (0.24), residues: 452 sheet: -1.54 (0.29), residues: 264 loop : -1.07 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 92 HIS 0.001 0.000 HIS C 138 PHE 0.011 0.001 PHE B 221 TYR 0.015 0.001 TYR B 258 ARG 0.002 0.000 ARG D 310 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 112 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8366 (t) REVERT: A 17 LYS cc_start: 0.7419 (tttm) cc_final: 0.6895 (ttpt) REVERT: A 33 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7792 (mt) REVERT: A 347 LYS cc_start: 0.7262 (mttm) cc_final: 0.6595 (mtmt) REVERT: B 5 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8374 (t) REVERT: B 17 LYS cc_start: 0.7428 (tttm) cc_final: 0.6896 (ttpt) REVERT: B 33 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7791 (mt) REVERT: B 347 LYS cc_start: 0.7329 (mttm) cc_final: 0.6565 (mtmt) REVERT: C 17 LYS cc_start: 0.7224 (tttm) cc_final: 0.6695 (ttpt) REVERT: C 33 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7790 (mt) REVERT: C 347 LYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6586 (mtmt) REVERT: D 17 LYS cc_start: 0.7433 (tttm) cc_final: 0.6908 (ttpt) REVERT: D 33 LEU cc_start: 0.8206 (OUTLIER) cc_final: 0.7795 (mt) REVERT: D 347 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6619 (mtmt) outliers start: 42 outliers final: 16 residues processed: 147 average time/residue: 1.0514 time to fit residues: 168.5541 Evaluate side-chains 136 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 347 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 112 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 67 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 33 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 147 GLN C 147 GLN D 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 10756 Z= 0.439 Angle : 0.568 5.853 14612 Z= 0.284 Chirality : 0.048 0.141 1624 Planarity : 0.004 0.029 1856 Dihedral : 9.604 59.219 1708 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.41 % Allowed : 21.36 % Favored : 73.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.21), residues: 1380 helix: -0.88 (0.23), residues: 452 sheet: -1.49 (0.30), residues: 264 loop : -1.07 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 92 HIS 0.002 0.001 HIS B 48 PHE 0.014 0.002 PHE B 221 TYR 0.017 0.002 TYR B 258 ARG 0.002 0.000 ARG D 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 119 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7533 (tttm) cc_final: 0.6972 (ttpt) REVERT: A 182 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8539 (mp) REVERT: A 253 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6964 (tt0) REVERT: A 318 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7506 (mttp) REVERT: A 347 LYS cc_start: 0.7323 (mttm) cc_final: 0.6604 (mtmt) REVERT: B 17 LYS cc_start: 0.7535 (tttm) cc_final: 0.6975 (ttpt) REVERT: B 182 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8542 (mp) REVERT: B 253 GLU cc_start: 0.7351 (tm-30) cc_final: 0.6955 (tt0) REVERT: B 318 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7500 (mttp) REVERT: B 347 LYS cc_start: 0.7421 (mttm) cc_final: 0.6710 (mtmt) REVERT: C 17 LYS cc_start: 0.7530 (tttm) cc_final: 0.6971 (ttpt) REVERT: C 182 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8535 (mp) REVERT: C 318 LYS cc_start: 0.7795 (OUTLIER) cc_final: 0.7500 (mttp) REVERT: C 347 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6596 (mtmt) REVERT: D 17 LYS cc_start: 0.7534 (tttm) cc_final: 0.6985 (ttpt) REVERT: D 182 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8544 (mp) REVERT: D 253 GLU cc_start: 0.7359 (tm-30) cc_final: 0.6962 (tt0) REVERT: D 318 LYS cc_start: 0.7798 (OUTLIER) cc_final: 0.7501 (mttp) outliers start: 58 outliers final: 39 residues processed: 167 average time/residue: 1.0203 time to fit residues: 186.0241 Evaluate side-chains 166 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 118 time to evaluate : 1.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 56 LEU Chi-restraints excluded: chain B residue 58 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 56 LEU Chi-restraints excluded: chain C residue 58 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 247 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 56 LEU Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 318 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 147 GLN C 147 GLN D 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10756 Z= 0.182 Angle : 0.460 5.383 14612 Z= 0.231 Chirality : 0.044 0.137 1624 Planarity : 0.003 0.028 1856 Dihedral : 9.131 59.924 1708 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 4.57 % Allowed : 22.76 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.21), residues: 1380 helix: -0.42 (0.24), residues: 452 sheet: -1.53 (0.30), residues: 264 loop : -0.84 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 92 HIS 0.001 0.000 HIS A 138 PHE 0.010 0.001 PHE C 221 TYR 0.015 0.001 TYR A 258 ARG 0.003 0.000 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 129 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7352 (tttm) cc_final: 0.6791 (ttpt) REVERT: A 33 LEU cc_start: 0.8200 (OUTLIER) cc_final: 0.7798 (mt) REVERT: A 253 GLU cc_start: 0.7371 (tm-30) cc_final: 0.6810 (mt-10) REVERT: A 318 LYS cc_start: 0.7891 (OUTLIER) cc_final: 0.7598 (mttp) REVERT: A 347 LYS cc_start: 0.7191 (mttm) cc_final: 0.6491 (mtmt) REVERT: B 17 LYS cc_start: 0.7366 (tttm) cc_final: 0.6802 (ttpt) REVERT: B 33 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7800 (mt) REVERT: B 253 GLU cc_start: 0.7362 (tm-30) cc_final: 0.6800 (mt-10) REVERT: B 318 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7582 (mttp) REVERT: B 347 LYS cc_start: 0.7345 (mttm) cc_final: 0.6551 (mtmt) REVERT: C 17 LYS cc_start: 0.7356 (tttm) cc_final: 0.6788 (ttpt) REVERT: C 33 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7794 (mt) REVERT: C 253 GLU cc_start: 0.7357 (tm-30) cc_final: 0.6794 (mt-10) REVERT: C 318 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7581 (mttp) REVERT: C 347 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6432 (mtmt) REVERT: D 17 LYS cc_start: 0.7365 (tttm) cc_final: 0.6802 (ttpt) REVERT: D 33 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7803 (mt) REVERT: D 253 GLU cc_start: 0.7369 (tm-30) cc_final: 0.6810 (mt-10) REVERT: D 318 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7587 (mttp) REVERT: D 347 LYS cc_start: 0.7381 (mttm) cc_final: 0.6588 (mtmt) outliers start: 49 outliers final: 17 residues processed: 173 average time/residue: 1.0857 time to fit residues: 204.0960 Evaluate side-chains 144 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 118 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 318 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 147 GLN C 147 GLN D 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10756 Z= 0.262 Angle : 0.487 5.164 14612 Z= 0.244 Chirality : 0.045 0.136 1624 Planarity : 0.003 0.030 1856 Dihedral : 9.245 59.903 1708 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.17 % Allowed : 23.69 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.21), residues: 1380 helix: -0.44 (0.24), residues: 452 sheet: -1.46 (0.30), residues: 264 loop : -0.80 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 92 HIS 0.001 0.000 HIS C 48 PHE 0.011 0.002 PHE C 221 TYR 0.016 0.001 TYR D 258 ARG 0.003 0.000 ARG B 310 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 124 time to evaluate : 1.096 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7349 (tttm) cc_final: 0.6800 (ttpt) REVERT: A 182 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8575 (mp) REVERT: A 253 GLU cc_start: 0.7383 (tm-30) cc_final: 0.6801 (mt-10) REVERT: A 318 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7539 (mttp) REVERT: A 347 LYS cc_start: 0.7216 (mttm) cc_final: 0.6493 (mtmt) REVERT: B 17 LYS cc_start: 0.7351 (tttm) cc_final: 0.6798 (ttpt) REVERT: B 182 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8579 (mp) REVERT: B 253 GLU cc_start: 0.7366 (tm-30) cc_final: 0.6808 (mt-10) REVERT: B 318 LYS cc_start: 0.7838 (OUTLIER) cc_final: 0.7529 (mttp) REVERT: B 347 LYS cc_start: 0.7374 (mttm) cc_final: 0.6572 (mtmt) REVERT: C 17 LYS cc_start: 0.7349 (tttm) cc_final: 0.6794 (ttpt) REVERT: C 182 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8573 (mp) REVERT: C 253 GLU cc_start: 0.7372 (tm-30) cc_final: 0.6811 (mt-10) REVERT: C 318 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7527 (mttp) REVERT: C 347 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6482 (mtmt) REVERT: D 17 LYS cc_start: 0.7357 (tttm) cc_final: 0.6807 (ttpt) REVERT: D 182 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8584 (mp) REVERT: D 253 GLU cc_start: 0.7370 (tm-30) cc_final: 0.6815 (mt-10) REVERT: D 318 LYS cc_start: 0.7842 (OUTLIER) cc_final: 0.7530 (mttp) REVERT: D 347 LYS cc_start: 0.7302 (mttm) cc_final: 0.6579 (mtmt) outliers start: 34 outliers final: 21 residues processed: 153 average time/residue: 1.0122 time to fit residues: 169.0535 Evaluate side-chains 151 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 121 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 318 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 83 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 147 GLN C 147 GLN D 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10756 Z= 0.190 Angle : 0.461 6.124 14612 Z= 0.230 Chirality : 0.044 0.135 1624 Planarity : 0.003 0.030 1856 Dihedral : 8.986 59.129 1708 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.45 % Allowed : 23.69 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.21), residues: 1380 helix: -0.24 (0.24), residues: 452 sheet: -1.45 (0.31), residues: 264 loop : -0.69 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 92 HIS 0.001 0.000 HIS D 138 PHE 0.011 0.001 PHE C 221 TYR 0.015 0.001 TYR A 258 ARG 0.003 0.000 ARG D 310 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 124 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7334 (tttm) cc_final: 0.6788 (ttpt) REVERT: A 33 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7823 (mt) REVERT: A 253 GLU cc_start: 0.7387 (tm-30) cc_final: 0.6822 (mt-10) REVERT: A 318 LYS cc_start: 0.7895 (OUTLIER) cc_final: 0.7568 (mttp) REVERT: A 347 LYS cc_start: 0.7162 (mttm) cc_final: 0.6451 (mtmt) REVERT: B 17 LYS cc_start: 0.7337 (tttm) cc_final: 0.6786 (ttpt) REVERT: B 33 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7813 (mt) REVERT: B 253 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6816 (mt-10) REVERT: B 318 LYS cc_start: 0.7884 (OUTLIER) cc_final: 0.7561 (mttp) REVERT: B 347 LYS cc_start: 0.7309 (mttm) cc_final: 0.6519 (mtmt) REVERT: C 17 LYS cc_start: 0.7331 (tttm) cc_final: 0.6780 (ttpt) REVERT: C 253 GLU cc_start: 0.7384 (tm-30) cc_final: 0.6819 (mt-10) REVERT: C 318 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7557 (mttp) REVERT: C 347 LYS cc_start: 0.7155 (OUTLIER) cc_final: 0.6454 (mtmt) REVERT: D 17 LYS cc_start: 0.7340 (tttm) cc_final: 0.6794 (ttpt) REVERT: D 33 LEU cc_start: 0.8207 (OUTLIER) cc_final: 0.7833 (mt) REVERT: D 253 GLU cc_start: 0.7381 (tm-30) cc_final: 0.6821 (mt-10) REVERT: D 318 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7562 (mttp) REVERT: D 347 LYS cc_start: 0.7239 (mttm) cc_final: 0.6498 (mtmt) outliers start: 37 outliers final: 18 residues processed: 156 average time/residue: 1.1539 time to fit residues: 195.1962 Evaluate side-chains 146 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 120 time to evaluate : 1.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 318 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 121 optimal weight: 0.5980 chunk 80 optimal weight: 8.9990 chunk 129 optimal weight: 6.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 147 GLN C 147 GLN D 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.051 10756 Z= 0.565 Angle : 0.635 7.073 14612 Z= 0.315 Chirality : 0.052 0.146 1624 Planarity : 0.004 0.031 1856 Dihedral : 9.781 59.957 1708 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 3.64 % Allowed : 23.23 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.20), residues: 1380 helix: -0.91 (0.22), residues: 452 sheet: -1.37 (0.31), residues: 260 loop : -1.03 (0.21), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 92 HIS 0.002 0.001 HIS B 48 PHE 0.016 0.003 PHE A 221 TYR 0.018 0.002 TYR C 258 ARG 0.003 0.000 ARG C 340 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 123 time to evaluate : 1.170 Fit side-chains REVERT: A 17 LYS cc_start: 0.7380 (tttm) cc_final: 0.6825 (ttpt) REVERT: A 182 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8459 (mp) REVERT: A 253 GLU cc_start: 0.7423 (tm-30) cc_final: 0.6955 (tt0) REVERT: A 318 LYS cc_start: 0.7816 (OUTLIER) cc_final: 0.7513 (mttp) REVERT: A 347 LYS cc_start: 0.7349 (OUTLIER) cc_final: 0.6544 (mtmt) REVERT: B 17 LYS cc_start: 0.7380 (tttm) cc_final: 0.6827 (ttpt) REVERT: B 182 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8457 (mp) REVERT: B 253 GLU cc_start: 0.7417 (tm-30) cc_final: 0.6959 (tt0) REVERT: B 318 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7509 (mttp) REVERT: B 347 LYS cc_start: 0.7428 (mttm) cc_final: 0.6568 (mtmt) REVERT: C 17 LYS cc_start: 0.7374 (tttm) cc_final: 0.6822 (ttpt) REVERT: C 182 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8455 (mp) REVERT: C 253 GLU cc_start: 0.7420 (tm-30) cc_final: 0.6959 (tt0) REVERT: C 277 CYS cc_start: 0.7251 (m) cc_final: 0.7020 (m) REVERT: C 318 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7506 (mttp) REVERT: C 347 LYS cc_start: 0.7336 (OUTLIER) cc_final: 0.6533 (mtmt) REVERT: D 17 LYS cc_start: 0.7384 (tttm) cc_final: 0.6835 (ttpt) REVERT: D 182 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8465 (mp) REVERT: D 253 GLU cc_start: 0.7416 (tm-30) cc_final: 0.6956 (tt0) REVERT: D 277 CYS cc_start: 0.7252 (m) cc_final: 0.7021 (m) REVERT: D 318 LYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7507 (mttp) REVERT: D 347 LYS cc_start: 0.7377 (mttm) cc_final: 0.6568 (mtmt) outliers start: 39 outliers final: 23 residues processed: 156 average time/residue: 1.2092 time to fit residues: 203.5424 Evaluate side-chains 158 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 125 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 182 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain A residue 347 LYS Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 182 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 182 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 347 LYS Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 318 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 89 optimal weight: 0.1980 chunk 135 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 85 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 147 GLN C 147 GLN D 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10756 Z= 0.152 Angle : 0.465 8.315 14612 Z= 0.230 Chirality : 0.043 0.135 1624 Planarity : 0.003 0.030 1856 Dihedral : 9.028 59.989 1708 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.17 % Allowed : 23.79 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.21), residues: 1380 helix: -0.26 (0.24), residues: 448 sheet: -1.44 (0.31), residues: 264 loop : -0.59 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 54 HIS 0.002 0.000 HIS A 138 PHE 0.010 0.001 PHE A 221 TYR 0.014 0.001 TYR B 258 ARG 0.003 0.000 ARG D 310 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7317 (tttm) cc_final: 0.6732 (ttpt) REVERT: A 33 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7779 (mt) REVERT: A 208 GLU cc_start: 0.7444 (mp0) cc_final: 0.6495 (mm-30) REVERT: A 253 GLU cc_start: 0.7400 (tm-30) cc_final: 0.6819 (mt-10) REVERT: A 318 LYS cc_start: 0.7850 (OUTLIER) cc_final: 0.7609 (mttp) REVERT: A 347 LYS cc_start: 0.7066 (mttm) cc_final: 0.6359 (mtmt) REVERT: B 17 LYS cc_start: 0.7317 (tttm) cc_final: 0.6733 (ttpt) REVERT: B 33 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7782 (mt) REVERT: B 208 GLU cc_start: 0.7450 (mp0) cc_final: 0.6504 (mm-30) REVERT: B 253 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6820 (mt-10) REVERT: B 318 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7592 (mttp) REVERT: B 347 LYS cc_start: 0.7269 (mttm) cc_final: 0.6447 (mtmt) REVERT: C 17 LYS cc_start: 0.7316 (tttm) cc_final: 0.6728 (ttpt) REVERT: C 33 LEU cc_start: 0.8152 (OUTLIER) cc_final: 0.7775 (mt) REVERT: C 208 GLU cc_start: 0.7448 (mp0) cc_final: 0.6502 (mm-30) REVERT: C 253 GLU cc_start: 0.7398 (tm-30) cc_final: 0.6822 (mt-10) REVERT: C 318 LYS cc_start: 0.7880 (OUTLIER) cc_final: 0.7593 (mttp) REVERT: C 347 LYS cc_start: 0.7108 (mttm) cc_final: 0.6365 (mtmt) REVERT: D 17 LYS cc_start: 0.7343 (tttm) cc_final: 0.6747 (ttpt) REVERT: D 33 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7776 (mt) REVERT: D 208 GLU cc_start: 0.7456 (mp0) cc_final: 0.6505 (mm-30) REVERT: D 253 GLU cc_start: 0.7399 (tm-30) cc_final: 0.6824 (mt-10) REVERT: D 318 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7592 (mttp) REVERT: D 347 LYS cc_start: 0.7188 (mttm) cc_final: 0.6528 (mtmt) outliers start: 34 outliers final: 21 residues processed: 160 average time/residue: 1.1613 time to fit residues: 201.0948 Evaluate side-chains 156 residues out of total 1072 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 GLU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 289 SER Chi-restraints excluded: chain A residue 294 TYR Chi-restraints excluded: chain A residue 313 VAL Chi-restraints excluded: chain A residue 318 LYS Chi-restraints excluded: chain B residue 13 GLU Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 289 SER Chi-restraints excluded: chain B residue 294 TYR Chi-restraints excluded: chain B residue 313 VAL Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 289 SER Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain C residue 313 VAL Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain D residue 13 GLU Chi-restraints excluded: chain D residue 33 LEU Chi-restraints excluded: chain D residue 245 VAL Chi-restraints excluded: chain D residue 289 SER Chi-restraints excluded: chain D residue 294 TYR Chi-restraints excluded: chain D residue 313 VAL Chi-restraints excluded: chain D residue 318 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 108 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 110 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 147 GLN C 147 GLN D 147 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.128389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.103495 restraints weight = 9686.802| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.33 r_work: 0.2960 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10756 Z= 0.232 Angle : 0.488 8.455 14612 Z= 0.241 Chirality : 0.045 0.135 1624 Planarity : 0.003 0.030 1856 Dihedral : 9.061 59.166 1708 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.26 % Allowed : 23.88 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.21), residues: 1380 helix: -0.17 (0.24), residues: 448 sheet: -1.44 (0.31), residues: 264 loop : -0.57 (0.22), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 92 HIS 0.001 0.000 HIS A 113 PHE 0.011 0.002 PHE D 221 TYR 0.016 0.001 TYR C 258 ARG 0.002 0.000 ARG D 310 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3626.18 seconds wall clock time: 65 minutes 5.35 seconds (3905.35 seconds total)