Starting phenix.real_space_refine on Wed Feb 14 07:52:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f03_31395/02_2024/7f03_31395_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f03_31395/02_2024/7f03_31395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f03_31395/02_2024/7f03_31395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f03_31395/02_2024/7f03_31395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f03_31395/02_2024/7f03_31395_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f03_31395/02_2024/7f03_31395_updated.pdb" } resolution = 3.29 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= 0.003 sd= 0.051 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 7 5.49 5 Mg 2 5.21 5 S 46 5.16 5 C 5798 2.51 5 N 1517 2.21 5 O 1521 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A ASP 101": "OD1" <-> "OD2" Residue "A ASP 121": "OD1" <-> "OD2" Residue "A ASP 151": "OD1" <-> "OD2" Residue "B PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B GLU 67": "OE1" <-> "OE2" Residue "B PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 181": "OD1" <-> "OD2" Residue "C TYR 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 47": "OD1" <-> "OD2" Residue "C TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 229": "OE1" <-> "OE2" Residue "D TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "E GLU 10": "OE1" <-> "OE2" Residue "E ASP 70": "OD1" <-> "OD2" Residue "E GLU 191": "OE1" <-> "OE2" Residue "F GLU 20": "OE1" <-> "OE2" Residue "F TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8891 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "B" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1848 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 11, 'TRANS': 219} Chain: "D" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "E" Number of atoms: 1586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1586 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 6, 'TRANS': 195} Chain: "F" Number of atoms: 1663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1663 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 16, 'TRANS': 203} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 5.14, per 1000 atoms: 0.58 Number of scatterers: 8891 At special positions: 0 Unit cell: (100.672, 94.848, 117.312, 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 46 16.00 P 7 15.00 Mg 2 11.99 O 1521 8.00 N 1517 7.00 C 5798 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.73 Conformation dependent library (CDL) restraints added in 1.8 seconds 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 6 sheets defined 59.5% alpha, 4.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.77 Creating SS restraints... Processing helix chain 'A' and resid 40 through 48 Processing helix chain 'A' and resid 91 through 97 removed outlier: 3.555A pdb=" N LEU A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 113 Processing helix chain 'A' and resid 124 through 126 No H-bonds generated for 'chain 'A' and resid 124 through 126' Processing helix chain 'A' and resid 131 through 142 removed outlier: 4.417A pdb=" N ARG A 139 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N LEU A 140 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N TRP A 141 " --> pdb=" O LEU A 137 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 175 removed outlier: 3.884A pdb=" N GLN A 175 " --> pdb=" O GLN A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'B' and resid 3 through 14 Processing helix chain 'B' and resid 18 through 39 removed outlier: 3.948A pdb=" N ALA B 22 " --> pdb=" O ALA B 19 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ASN B 23 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Proline residue: B 24 - end of helix Proline residue: B 36 - end of helix removed outlier: 4.011A pdb=" N ILE B 39 " --> pdb=" O PRO B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 76 removed outlier: 3.778A pdb=" N ARG B 48 " --> pdb=" O GLN B 44 " (cutoff:3.500A) Proline residue: B 51 - end of helix removed outlier: 3.631A pdb=" N GLU B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG B 68 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE B 70 " --> pdb=" O LEU B 66 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASP B 73 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN B 75 " --> pdb=" O ARG B 71 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP B 76 " --> pdb=" O ASP B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 118 removed outlier: 4.052A pdb=" N LEU B 106 " --> pdb=" O MET B 102 " (cutoff:3.500A) Proline residue: B 107 - end of helix Proline residue: B 113 - end of helix removed outlier: 3.857A pdb=" N MET B 117 " --> pdb=" O PRO B 113 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 135 Processing helix chain 'B' and resid 137 through 143 removed outlier: 3.785A pdb=" N GLY B 141 " --> pdb=" O THR B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 151 Processing helix chain 'B' and resid 159 through 164 removed outlier: 3.726A pdb=" N LEU B 164 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 184 Processing helix chain 'B' and resid 190 through 204 removed outlier: 3.932A pdb=" N ILE B 195 " --> pdb=" O GLY B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 219 Processing helix chain 'C' and resid 12 through 39 removed outlier: 3.955A pdb=" N ILE C 22 " --> pdb=" O GLY C 19 " (cutoff:3.500A) Proline residue: C 23 - end of helix removed outlier: 3.887A pdb=" N TRP C 39 " --> pdb=" O GLY C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 83 removed outlier: 3.538A pdb=" N ILE C 56 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR C 58 " --> pdb=" O ARG C 55 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N VAL C 61 " --> pdb=" O TYR C 58 " (cutoff:3.500A) Proline residue: C 62 - end of helix removed outlier: 3.985A pdb=" N ILE C 70 " --> pdb=" O SER C 67 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL C 83 " --> pdb=" O ILE C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 87 through 119 removed outlier: 4.291A pdb=" N VAL C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA C 94 " --> pdb=" O ASN C 90 " (cutoff:3.500A) Proline residue: C 98 - end of helix Proline residue: C 117 - end of helix Processing helix chain 'C' and resid 127 through 146 removed outlier: 3.728A pdb=" N LEU C 133 " --> pdb=" O LEU C 129 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU C 135 " --> pdb=" O SER C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 184 Proline residue: C 171 - end of helix removed outlier: 3.887A pdb=" N THR C 182 " --> pdb=" O GLU C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 196 through 198 No H-bonds generated for 'chain 'C' and resid 196 through 198' Processing helix chain 'C' and resid 200 through 228 Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'D' and resid 18 through 52 Proline residue: D 31 - end of helix removed outlier: 3.696A pdb=" N ALA D 51 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 48 Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 107 through 114 Processing helix chain 'E' and resid 124 through 126 No H-bonds generated for 'chain 'E' and resid 124 through 126' Processing helix chain 'E' and resid 131 through 141 removed outlier: 3.728A pdb=" N ALA E 136 " --> pdb=" O GLN E 132 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG E 139 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU E 140 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N TRP E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 176 removed outlier: 3.607A pdb=" N ALA E 170 " --> pdb=" O THR E 166 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN E 171 " --> pdb=" O GLN E 167 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N THR E 173 " --> pdb=" O MET E 169 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N GLU E 174 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLN E 175 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N GLY E 176 " --> pdb=" O HIS E 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 16 Processing helix chain 'F' and resid 22 through 38 removed outlier: 3.856A pdb=" N PHE F 35 " --> pdb=" O VAL F 31 " (cutoff:3.500A) Proline residue: F 36 - end of helix Processing helix chain 'F' and resid 43 through 68 removed outlier: 3.632A pdb=" N ARG F 48 " --> pdb=" O GLN F 44 " (cutoff:3.500A) Proline residue: F 51 - end of helix removed outlier: 4.059A pdb=" N GLU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N ARG F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 74 No H-bonds generated for 'chain 'F' and resid 71 through 74' Processing helix chain 'F' and resid 89 through 110 removed outlier: 3.527A pdb=" N VAL F 103 " --> pdb=" O ALA F 99 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU F 106 " --> pdb=" O MET F 102 " (cutoff:3.500A) Proline residue: F 107 - end of helix Processing helix chain 'F' and resid 112 through 118 removed outlier: 3.698A pdb=" N MET F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 123 through 151 Proline residue: F 138 - end of helix Proline residue: F 146 - end of helix Processing helix chain 'F' and resid 159 through 163 Processing helix chain 'F' and resid 167 through 184 Proline residue: F 171 - end of helix removed outlier: 3.539A pdb=" N PHE F 175 " --> pdb=" O LEU F 172 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR F 177 " --> pdb=" O ILE F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 190 through 219 removed outlier: 3.880A pdb=" N ILE F 195 " --> pdb=" O GLY F 191 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR F 205 " --> pdb=" O ALA F 201 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU F 206 " --> pdb=" O GLY F 202 " (cutoff:3.500A) Proline residue: F 208 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 3 through 5 removed outlier: 3.585A pdb=" N GLU A 57 " --> pdb=" O ARG A 5 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 194 through 198 removed outlier: 6.255A pdb=" N TRP A 29 " --> pdb=" O ARG A 195 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ILE A 197 " --> pdb=" O TRP A 29 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N GLN A 31 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL A 179 " --> pdb=" O GLU A 28 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TRP A 148 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 7.894A pdb=" N THR A 182 " --> pdb=" O TRP A 148 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N LEU A 150 " --> pdb=" O THR A 182 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N LEU A 77 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASP A 151 " --> pdb=" O LEU A 77 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE A 79 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 7 through 9 removed outlier: 3.703A pdb=" N LEU A 20 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N CYS A 9 " --> pdb=" O SER A 18 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N SER A 18 " --> pdb=" O CYS A 9 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'E' and resid 2 through 5 Processing sheet with id= E, first strand: chain 'E' and resid 195 through 198 removed outlier: 6.096A pdb=" N VAL E 179 " --> pdb=" O VAL E 30 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE E 32 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LEU E 181 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LEU E 77 " --> pdb=" O ILE E 149 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ASP E 151 " --> pdb=" O LEU E 77 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE E 79 " --> pdb=" O ASP E 151 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 9 through 11 removed outlier: 3.770A pdb=" N CYS E 9 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE E 17 " --> pdb=" O CYS E 9 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ARG E 11 " --> pdb=" O THR E 15 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N THR E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 416 hydrogen bonds defined for protein. 1044 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: 2.28 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1353 1.31 - 1.43: 2352 1.43 - 1.56: 5297 1.56 - 1.68: 13 1.68 - 1.81: 87 Bond restraints: 9102 Sorted by residual: bond pdb=" N3B ANP A 302 " pdb=" PG ANP A 302 " ideal model delta sigma weight residual 1.795 1.629 0.166 2.00e-02 2.50e+03 6.89e+01 bond pdb=" N3B ANP E 302 " pdb=" PG ANP E 302 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.75e+01 bond pdb=" O3A ANP E 302 " pdb=" PB ANP E 302 " ideal model delta sigma weight residual 1.700 1.603 0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" O3A ANP A 302 " pdb=" PB ANP A 302 " ideal model delta sigma weight residual 1.700 1.603 0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" C11 3PE D 101 " pdb=" O13 3PE D 101 " ideal model delta sigma weight residual 1.408 1.485 -0.077 2.00e-02 2.50e+03 1.49e+01 ... (remaining 9097 not shown) Histogram of bond angle deviations from ideal: 99.97 - 106.80: 341 106.80 - 113.62: 5173 113.62 - 120.45: 3512 120.45 - 127.27: 3237 127.27 - 134.10: 161 Bond angle restraints: 12424 Sorted by residual: angle pdb=" N ALA E 105 " pdb=" CA ALA E 105 " pdb=" C ALA E 105 " ideal model delta sigma weight residual 114.75 108.13 6.62 1.26e+00 6.30e-01 2.76e+01 angle pdb=" C12 3PE D 101 " pdb=" C11 3PE D 101 " pdb=" O13 3PE D 101 " ideal model delta sigma weight residual 108.28 119.31 -11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" N3B ANP E 302 " pdb=" PG ANP E 302 " pdb=" O2G ANP E 302 " ideal model delta sigma weight residual 101.05 110.71 -9.66 3.00e+00 1.11e-01 1.04e+01 angle pdb=" N3B ANP A 302 " pdb=" PG ANP A 302 " pdb=" O2G ANP A 302 " ideal model delta sigma weight residual 101.05 110.56 -9.51 3.00e+00 1.11e-01 1.00e+01 angle pdb=" N GLU F 80 " pdb=" CA GLU F 80 " pdb=" C GLU F 80 " ideal model delta sigma weight residual 113.72 109.16 4.56 1.52e+00 4.33e-01 8.99e+00 ... (remaining 12419 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 4805 17.99 - 35.99: 444 35.99 - 53.98: 88 53.98 - 71.97: 20 71.97 - 89.96: 18 Dihedral angle restraints: 5375 sinusoidal: 2151 harmonic: 3224 Sorted by residual: dihedral pdb=" CA PRO C 12 " pdb=" C PRO C 12 " pdb=" N ARG C 13 " pdb=" CA ARG C 13 " ideal model delta harmonic sigma weight residual 180.00 155.09 24.91 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA LEU A 127 " pdb=" C LEU A 127 " pdb=" N SER A 128 " pdb=" CA SER A 128 " ideal model delta harmonic sigma weight residual -180.00 -156.05 -23.95 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA ILE C 10 " pdb=" C ILE C 10 " pdb=" N PRO C 11 " pdb=" CA PRO C 11 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 5372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1347 0.078 - 0.156: 112 0.156 - 0.233: 1 0.233 - 0.311: 1 0.311 - 0.389: 2 Chirality restraints: 1463 Sorted by residual: chirality pdb=" C3' ANP A 302 " pdb=" C2' ANP A 302 " pdb=" C4' ANP A 302 " pdb=" O3' ANP A 302 " both_signs ideal model delta sigma weight residual False -2.36 -2.75 0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C3' ANP E 302 " pdb=" C2' ANP E 302 " pdb=" C4' ANP E 302 " pdb=" O3' ANP E 302 " both_signs ideal model delta sigma weight residual False -2.36 -2.68 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" C2' ANP E 302 " pdb=" C1' ANP E 302 " pdb=" C3' ANP E 302 " pdb=" O2' ANP E 302 " both_signs ideal model delta sigma weight residual False -2.72 -2.47 -0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1460 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN F 23 " -0.029 5.00e-02 4.00e+02 4.48e-02 3.21e+00 pdb=" N PRO F 24 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 24 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 24 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 195 " 0.029 5.00e-02 4.00e+02 4.47e-02 3.20e+00 pdb=" N PRO C 196 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 196 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 196 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 44 " -0.029 5.00e-02 4.00e+02 4.44e-02 3.16e+00 pdb=" N PRO C 45 " 0.077 5.00e-02 4.00e+02 pdb=" CA PRO C 45 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 45 " -0.025 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.49: 46 2.49 - 3.09: 6389 3.09 - 3.69: 13321 3.69 - 4.30: 19551 4.30 - 4.90: 32904 Nonbonded interactions: 72211 Sorted by model distance: nonbonded pdb="MG MG A 301 " pdb=" O3G ANP A 302 " model vdw 1.885 2.170 nonbonded pdb=" OG1 THR A 41 " pdb="MG MG A 301 " model vdw 1.939 2.170 nonbonded pdb=" OG1 THR E 41 " pdb="MG MG E 301 " model vdw 1.988 2.170 nonbonded pdb="MG MG A 301 " pdb=" O HOH A 402 " model vdw 2.000 2.170 nonbonded pdb="MG MG E 301 " pdb=" O HOH E 401 " model vdw 2.005 2.170 ... (remaining 72206 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 'E' } ncs_group { reference = chain 'B' 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=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: 1.660 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: 7.260 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.410 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 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 : 0.005 0.166 9102 Z= 0.341 Angle : 0.749 11.028 12424 Z= 0.375 Chirality : 0.045 0.389 1463 Planarity : 0.005 0.045 1523 Dihedral : 15.391 89.964 3291 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.11 % Allowed : 0.33 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.26), residues: 1118 helix: 0.60 (0.22), residues: 666 sheet: -0.39 (1.16), residues: 22 loop : -1.51 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 55 HIS 0.006 0.001 HIS E 73 PHE 0.018 0.001 PHE B 3 TYR 0.014 0.001 TYR F 124 ARG 0.008 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 204 time to evaluate : 1.065 Fit side-chains REVERT: B 68 ARG cc_start: 0.8505 (ttm170) cc_final: 0.8158 (mtm-85) REVERT: B 71 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7838 (ttp80) REVERT: C 181 ASN cc_start: 0.8600 (t160) cc_final: 0.8238 (t0) REVERT: C 233 PRO cc_start: 0.8412 (Cg_endo) cc_final: 0.8166 (Cg_exo) REVERT: F 10 GLU cc_start: 0.8049 (tp30) cc_final: 0.7804 (tp30) outliers start: 1 outliers final: 0 residues processed: 205 average time/residue: 0.2370 time to fit residues: 64.8627 Evaluate side-chains 166 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 0.3980 chunk 57 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN C 49 GLN F 17 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9102 Z= 0.213 Angle : 0.625 6.116 12424 Z= 0.311 Chirality : 0.042 0.149 1463 Planarity : 0.006 0.057 1523 Dihedral : 9.696 80.643 1311 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.29 % Allowed : 9.60 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.26), residues: 1118 helix: 0.53 (0.21), residues: 688 sheet: -0.53 (1.07), residues: 22 loop : -1.63 (0.29), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 55 HIS 0.007 0.001 HIS E 73 PHE 0.021 0.001 PHE A 97 TYR 0.009 0.001 TYR C 48 ARG 0.007 0.000 ARG E 100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 176 time to evaluate : 1.033 Fit side-chains REVERT: B 71 ARG cc_start: 0.7996 (ttp80) cc_final: 0.7696 (ttp80) REVERT: C 49 GLN cc_start: 0.7323 (mt0) cc_final: 0.7036 (mt0) REVERT: C 181 ASN cc_start: 0.8735 (t0) cc_final: 0.8535 (t0) REVERT: F 10 GLU cc_start: 0.8084 (tp30) cc_final: 0.7813 (tp30) outliers start: 21 outliers final: 15 residues processed: 187 average time/residue: 0.2403 time to fit residues: 60.0959 Evaluate side-chains 177 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 162 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 GLU Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 0.0870 chunk 31 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 28 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 0.0570 chunk 81 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 overall best weight: 0.7278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 94 ASN ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN C 7 GLN E 172 HIS F 17 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9102 Z= 0.181 Angle : 0.589 7.005 12424 Z= 0.288 Chirality : 0.041 0.207 1463 Planarity : 0.005 0.045 1523 Dihedral : 8.312 77.362 1311 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.51 % Allowed : 14.39 % Favored : 83.10 % 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: -0.29 (0.26), residues: 1118 helix: 0.68 (0.21), residues: 683 sheet: -0.48 (1.09), residues: 22 loop : -1.63 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 55 HIS 0.005 0.001 HIS E 73 PHE 0.024 0.001 PHE A 97 TYR 0.005 0.001 TYR C 139 ARG 0.005 0.000 ARG E 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 167 time to evaluate : 1.108 Fit side-chains REVERT: F 10 GLU cc_start: 0.8103 (tp30) cc_final: 0.7860 (tp30) outliers start: 23 outliers final: 14 residues processed: 180 average time/residue: 0.2375 time to fit residues: 57.5635 Evaluate side-chains 178 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 164 time to evaluate : 1.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 0.0070 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 96 optimal weight: 0.4980 chunk 29 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9102 Z= 0.158 Angle : 0.575 6.858 12424 Z= 0.280 Chirality : 0.041 0.198 1463 Planarity : 0.005 0.042 1523 Dihedral : 7.872 77.701 1311 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.05 % Allowed : 15.81 % Favored : 81.13 % 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: -0.14 (0.26), residues: 1118 helix: 0.78 (0.21), residues: 682 sheet: -0.35 (1.09), residues: 22 loop : -1.52 (0.29), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 55 HIS 0.005 0.001 HIS E 73 PHE 0.019 0.001 PHE A 97 TYR 0.007 0.001 TYR C 139 ARG 0.007 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 170 time to evaluate : 0.993 Fit side-chains REVERT: F 10 GLU cc_start: 0.8090 (tp30) cc_final: 0.7873 (tp30) REVERT: F 76 ASP cc_start: 0.7375 (p0) cc_final: 0.7170 (p0) outliers start: 28 outliers final: 19 residues processed: 188 average time/residue: 0.2350 time to fit residues: 59.2745 Evaluate side-chains 177 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 80 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 17 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9102 Z= 0.250 Angle : 0.620 8.300 12424 Z= 0.302 Chirality : 0.043 0.170 1463 Planarity : 0.005 0.042 1523 Dihedral : 7.926 79.753 1311 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.40 % Allowed : 17.45 % Favored : 80.15 % 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: -0.19 (0.26), residues: 1118 helix: 0.75 (0.21), residues: 680 sheet: -0.18 (1.13), residues: 22 loop : -1.57 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 55 HIS 0.006 0.001 HIS A 73 PHE 0.015 0.001 PHE B 3 TYR 0.005 0.001 TYR C 139 ARG 0.007 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 1.094 Fit side-chains outliers start: 22 outliers final: 19 residues processed: 169 average time/residue: 0.2577 time to fit residues: 58.2287 Evaluate side-chains 168 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 149 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 94 ASN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 89 optimal weight: 0.0670 chunk 50 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 56 optimal weight: 0.5980 chunk 104 optimal weight: 5.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN F 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9102 Z= 0.187 Angle : 0.588 7.629 12424 Z= 0.287 Chirality : 0.041 0.142 1463 Planarity : 0.005 0.041 1523 Dihedral : 7.740 80.018 1311 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 3.16 % Allowed : 17.34 % Favored : 79.50 % 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: -0.06 (0.26), residues: 1118 helix: 0.85 (0.21), residues: 679 sheet: -0.57 (0.83), residues: 34 loop : -1.50 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 55 HIS 0.005 0.001 HIS E 73 PHE 0.011 0.001 PHE C 41 TYR 0.005 0.001 TYR C 139 ARG 0.007 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 156 time to evaluate : 1.042 Fit side-chains outliers start: 29 outliers final: 21 residues processed: 174 average time/residue: 0.2469 time to fit residues: 57.1622 Evaluate side-chains 168 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 79 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN F 17 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9102 Z= 0.248 Angle : 0.612 6.740 12424 Z= 0.300 Chirality : 0.042 0.147 1463 Planarity : 0.005 0.040 1523 Dihedral : 7.787 79.592 1311 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.38 % Allowed : 17.99 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.26), residues: 1118 helix: 0.79 (0.21), residues: 679 sheet: -0.44 (0.88), residues: 34 loop : -1.54 (0.30), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 55 HIS 0.005 0.001 HIS E 73 PHE 0.011 0.001 PHE D 20 TYR 0.009 0.001 TYR C 139 ARG 0.007 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 155 time to evaluate : 0.965 Fit side-chains REVERT: C 48 TYR cc_start: 0.6344 (p90) cc_final: 0.5679 (p90) REVERT: D 14 MET cc_start: 0.6628 (pmm) cc_final: 0.6424 (pmm) outliers start: 31 outliers final: 26 residues processed: 173 average time/residue: 0.2443 time to fit residues: 56.1068 Evaluate side-chains 180 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 154 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 96 HIS Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 21 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 0.0370 chunk 73 optimal weight: 0.0870 chunk 53 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.2636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 66 HIS ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN C 7 GLN E 66 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9102 Z= 0.154 Angle : 0.597 10.130 12424 Z= 0.288 Chirality : 0.041 0.282 1463 Planarity : 0.005 0.040 1523 Dihedral : 7.438 74.247 1311 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 2.51 % Allowed : 19.08 % Favored : 78.41 % 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: 0.15 (0.26), residues: 1118 helix: 1.02 (0.21), residues: 682 sheet: -0.28 (0.89), residues: 34 loop : -1.46 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 55 HIS 0.004 0.000 HIS E 73 PHE 0.012 0.001 PHE C 41 TYR 0.008 0.001 TYR C 48 ARG 0.008 0.000 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 161 time to evaluate : 0.993 Fit side-chains REVERT: C 48 TYR cc_start: 0.6259 (p90) cc_final: 0.6051 (p90) REVERT: D 14 MET cc_start: 0.6461 (pmm) cc_final: 0.6221 (pmm) outliers start: 23 outliers final: 15 residues processed: 171 average time/residue: 0.2427 time to fit residues: 55.0946 Evaluate side-chains 169 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 154 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 121 THR Chi-restraints excluded: chain C residue 184 HIS Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain E residue 8 LEU Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 4.9990 chunk 103 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 7 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9102 Z= 0.321 Angle : 0.668 9.488 12424 Z= 0.327 Chirality : 0.044 0.242 1463 Planarity : 0.005 0.040 1523 Dihedral : 7.760 71.798 1311 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.62 % Allowed : 19.96 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.26), residues: 1118 helix: 0.84 (0.21), residues: 680 sheet: -0.20 (0.91), residues: 34 loop : -1.65 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 180 HIS 0.008 0.001 HIS A 73 PHE 0.014 0.002 PHE D 20 TYR 0.018 0.001 TYR C 48 ARG 0.007 0.001 ARG B 71 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 154 time to evaluate : 1.030 Fit side-chains outliers start: 24 outliers final: 22 residues processed: 168 average time/residue: 0.2392 time to fit residues: 53.6523 Evaluate side-chains 174 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 152 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 LEU Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 7 GLN Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain D residue 27 MET Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 96 HIS Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 192 SER Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN C 7 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9102 Z= 0.233 Angle : 0.634 9.589 12424 Z= 0.310 Chirality : 0.042 0.229 1463 Planarity : 0.005 0.040 1523 Dihedral : 7.671 72.013 1311 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.40 % Allowed : 20.17 % Favored : 77.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.26), residues: 1118 helix: 0.91 (0.21), residues: 673 sheet: -0.15 (0.91), residues: 34 loop : -1.60 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP F 55 HIS 0.005 0.001 HIS E 73 PHE 0.012 0.001 PHE D 20 TYR 0.006 0.001 TYR C 48 ARG 0.007 0.000 ARG B 71 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2236 Ramachandran restraints generated. 1118 Oldfield, 0 Emsley, 1118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 157 time to evaluate : 1.015 Fit side-chains outliers start: 22 outliers final: 18 residues processed: 170 average time/residue: 0.2419 time to fit residues: 54.8795 Evaluate side-chains 173 residues out of total 917 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 155 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 93 GLU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain C residue 22 ILE Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 112 SER Chi-restraints excluded: chain C residue 228 MET Chi-restraints excluded: chain D residue 8 TRP Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain E residue 96 HIS Chi-restraints excluded: chain E residue 121 ASP Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.3980 chunk 88 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 78 optimal weight: 3.9990 chunk 5 optimal weight: 0.0270 overall best weight: 0.8440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.112822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.099000 restraints weight = 14801.168| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.98 r_work: 0.3222 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9102 Z= 0.203 Angle : 0.621 9.385 12424 Z= 0.303 Chirality : 0.041 0.214 1463 Planarity : 0.005 0.040 1523 Dihedral : 7.459 71.917 1311 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.73 % Allowed : 19.96 % Favored : 77.32 % 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: 0.03 (0.26), residues: 1118 helix: 0.96 (0.21), residues: 673 sheet: 0.03 (0.92), residues: 34 loop : -1.58 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 55 HIS 0.005 0.001 HIS E 73 PHE 0.010 0.001 PHE C 41 TYR 0.009 0.001 TYR C 48 ARG 0.008 0.000 ARG B 71 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2248.23 seconds wall clock time: 41 minutes 7.99 seconds (2467.99 seconds total)