Starting phenix.real_space_refine on Mon Mar 18 19:48:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hi1_34809/03_2024/8hi1_34809.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hi1_34809/03_2024/8hi1_34809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hi1_34809/03_2024/8hi1_34809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hi1_34809/03_2024/8hi1_34809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hi1_34809/03_2024/8hi1_34809.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hi1_34809/03_2024/8hi1_34809.pdb" } resolution = 3.09 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= 0.001 sd= 0.102 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1054 atoms to isotropic. 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 55 5.49 5 S 31 5.16 5 C 6728 2.51 5 N 1916 2.21 5 O 2125 1.98 5 H 10143 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 43": "OD1" <-> "OD2" Residue "A ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A ARG 90": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ASP 134": "OD1" <-> "OD2" Residue "A ARG 146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 160": "OE1" <-> "OE2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ASP 174": "OD1" <-> "OD2" Residue "A ASP 175": "OD1" <-> "OD2" Residue "A GLU 177": "OE1" <-> "OE2" Residue "A ASP 224": "OD1" <-> "OD2" Residue "A ASP 227": "OD1" <-> "OD2" Residue "A TYR 229": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 261": "OD1" <-> "OD2" Residue "A ASP 283": "OD1" <-> "OD2" Residue "A ASP 285": "OD1" <-> "OD2" Residue "A GLU 286": "OE1" <-> "OE2" Residue "B GLU 14": "OE1" <-> "OE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ARG 34": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 126": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 212": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 218": "OD1" <-> "OD2" Residue "B PHE 221": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 240": "OE1" <-> "OE2" Residue "B ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ASP 281": "OD1" <-> "OD2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 36": "OD1" <-> "OD2" Residue "C ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 156": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ASP 174": "OD1" <-> "OD2" Residue "C PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C GLU 177": "OE1" <-> "OE2" Residue "C ASP 180": "OD1" <-> "OD2" Residue "C ASP 283": "OD1" <-> "OD2" Residue "C ASP 285": "OD1" <-> "OD2" Residue "C GLU 286": "OE1" <-> "OE2" Residue "C ASP 291": "OD1" <-> "OD2" Residue "D GLU 14": "OE1" <-> "OE2" Residue "D ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 116": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 123": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 144": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 146": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 245": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 256": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ASP 275": "OD1" <-> "OD2" Residue "D ASP 281": "OD1" <-> "OD2" Residue "E PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "E PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 38": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "F PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 20998 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 4568 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 6, 'TRANS': 282} Chain: "B" Number of atoms: 3576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3576 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 2 Chain: "C" Number of atoms: 4379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4379 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 6, 'TRANS': 278} Chain: "D" Number of atoms: 3731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 3731 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 6, 'TRANS': 237} Chain breaks: 2 Chain: "E" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1475 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "F" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1483 Classifications: {'peptide': 92} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 86} Chain: "G" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 826 Classifications: {'DNA': 26} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 25} Chain: "H" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 960 Classifications: {'DNA': 31} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 30} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 10 Time building chain proxies: 8.84, per 1000 atoms: 0.42 Number of scatterers: 20998 At special positions: 0 Unit cell: (109.65, 117.3, 148.75, 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 31 16.00 P 55 15.00 O 2125 8.00 N 1916 7.00 C 6728 6.00 H 10143 1.00 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: 14.52 Conformation dependent library (CDL) restraints added in 1.8 seconds 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 17 sheets defined 46.1% alpha, 10.0% beta 23 base pairs and 41 stacking pairs defined. Time for finding SS restraints: 8.00 Creating SS restraints... Processing helix chain 'A' and resid 68 through 77 Processing helix chain 'A' and resid 86 through 89 removed outlier: 3.666A pdb=" N VAL A 89 " --> pdb=" O GLU A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 89' Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.536A pdb=" N SER A 101 " --> pdb=" O LEU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 113 removed outlier: 3.792A pdb=" N LEU A 111 " --> pdb=" O LYS A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 139 through 163 removed outlier: 3.505A pdb=" N ARG A 144 " --> pdb=" O MET A 140 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLY A 145 " --> pdb=" O GLN A 141 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG A 146 " --> pdb=" O GLN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 205 removed outlier: 3.938A pdb=" N SER A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 188 " --> pdb=" O GLN A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 228 removed outlier: 3.799A pdb=" N LEU A 228 " --> pdb=" O ASP A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 removed outlier: 4.200A pdb=" N THR A 234 " --> pdb=" O LYS A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 244 removed outlier: 3.963A pdb=" N ASN A 244 " --> pdb=" O GLU A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 265 removed outlier: 4.099A pdb=" N ARG A 256 " --> pdb=" O GLY A 252 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASP A 265 " --> pdb=" O ASP A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 280 removed outlier: 3.951A pdb=" N ARG A 271 " --> pdb=" O LYS A 267 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N VAL A 273 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR A 278 " --> pdb=" O GLN A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 287 Processing helix chain 'B' and resid 68 through 76 removed outlier: 4.154A pdb=" N LEU B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP B 76 " --> pdb=" O GLU B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 114 removed outlier: 4.313A pdb=" N ASN B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 130 removed outlier: 3.651A pdb=" N VAL B 121 " --> pdb=" O LEU B 117 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR B 126 " --> pdb=" O ALA B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 203 Processing helix chain 'B' and resid 219 through 243 removed outlier: 3.721A pdb=" N LEU B 228 " --> pdb=" O ASP B 224 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N TYR B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N ALA B 231 " --> pdb=" O ASP B 227 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N GLU B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N ILE B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 254 through 267 Processing helix chain 'B' and resid 267 through 281 Processing helix chain 'C' and resid 68 through 75 removed outlier: 4.158A pdb=" N LEU C 73 " --> pdb=" O ARG C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 78 No H-bonds generated for 'chain 'C' and resid 76 through 78' Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.559A pdb=" N SER C 101 " --> pdb=" O LEU C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 114 removed outlier: 3.597A pdb=" N LEU C 111 " --> pdb=" O LYS C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 121 removed outlier: 4.115A pdb=" N ALA C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 removed outlier: 3.735A pdb=" N MET C 128 " --> pdb=" O LYS C 124 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG C 129 " --> pdb=" O MET C 125 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 124 through 129' Processing helix chain 'C' and resid 139 through 162 removed outlier: 4.182A pdb=" N ARG C 144 " --> pdb=" O MET C 140 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY C 145 " --> pdb=" O GLN C 141 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA C 149 " --> pdb=" O GLY C 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 179 removed outlier: 4.033A pdb=" N GLY C 179 " --> pdb=" O PHE C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 205 removed outlier: 4.158A pdb=" N GLN C 184 " --> pdb=" O ASP C 180 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ALA C 185 " --> pdb=" O ILE C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 219 through 234 removed outlier: 3.566A pdb=" N TYR C 223 " --> pdb=" O LEU C 219 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LEU C 228 " --> pdb=" O ASP C 224 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N TYR C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ALA C 231 " --> pdb=" O ASP C 227 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N GLU C 232 " --> pdb=" O LEU C 228 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU C 233 " --> pdb=" O TYR C 229 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 244 removed outlier: 4.188A pdb=" N GLU C 240 " --> pdb=" O PRO C 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 263 removed outlier: 4.148A pdb=" N ARG C 256 " --> pdb=" O GLY C 252 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 278 removed outlier: 3.739A pdb=" N ILE C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL C 273 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN C 274 " --> pdb=" O VAL C 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 75 removed outlier: 3.865A pdb=" N LEU D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 102 through 114 removed outlier: 4.152A pdb=" N ASN D 114 " --> pdb=" O LYS D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 129 Processing helix chain 'D' and resid 141 through 152 removed outlier: 3.928A pdb=" N GLY D 145 " --> pdb=" O GLN D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 182 through 205 Processing helix chain 'D' and resid 219 through 244 removed outlier: 3.894A pdb=" N ASP D 227 " --> pdb=" O TYR D 223 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU D 228 " --> pdb=" O ASP D 224 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N TYR D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N ALA D 231 " --> pdb=" O ASP D 227 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLU D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ILE D 235 " --> pdb=" O ALA D 231 " (cutoff:3.500A) Proline residue: D 236 - end of helix Processing helix chain 'D' and resid 254 through 267 removed outlier: 4.641A pdb=" N LYS D 258 " --> pdb=" O ILE D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 280 removed outlier: 4.363A pdb=" N VAL D 273 " --> pdb=" O ILE D 269 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 50 removed outlier: 4.225A pdb=" N ASN E 45 " --> pdb=" O GLU E 41 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN E 48 " --> pdb=" O TRP E 44 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA E 49 " --> pdb=" O ASN E 45 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASN E 50 " --> pdb=" O ARG E 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 36 through 48 removed outlier: 4.196A pdb=" N ASN F 45 " --> pdb=" O GLU F 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A' and resid 30 through 31 removed outlier: 7.511A pdb=" N ALA A 30 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 35 removed outlier: 3.763A pdb=" N ILE A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.717A pdb=" N TRP A 83 " --> pdb=" O TYR A 92 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 25 through 27 removed outlier: 6.925A pdb=" N ILE B 25 " --> pdb=" O LEU B 59 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 31 through 34 Processing sheet with id=AA7, first strand: chain 'B' and resid 81 through 82 removed outlier: 3.611A pdb=" N MET B 81 " --> pdb=" O ALA B 93 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 31 through 35 Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.676A pdb=" N VAL C 82 " --> pdb=" O LEU C 60 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 65 through 67 removed outlier: 3.593A pdb=" N ILE D 66 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 25 through 27 removed outlier: 6.558A pdb=" N ILE D 25 " --> pdb=" O LEU D 59 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 33 through 35 removed outlier: 3.559A pdb=" N ASN D 33 " --> pdb=" O THR D 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 80 through 83 removed outlier: 4.131A pdb=" N TRP D 83 " --> pdb=" O GLN D 91 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLN D 91 " --> pdb=" O TRP D 83 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 24 through 27 removed outlier: 7.046A pdb=" N VAL E 30 " --> pdb=" O ILE E 26 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N PHE E 3 " --> pdb=" O TYR E 61 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA E 56 " --> pdb=" O ILE E 73 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE E 73 " --> pdb=" O ALA E 56 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 78 through 82 removed outlier: 3.592A pdb=" N SER E 78 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE E 85 " --> pdb=" O PHE E 82 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 24 through 27 removed outlier: 3.849A pdb=" N ILE F 26 " --> pdb=" O VAL F 30 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N VAL F 30 " --> pdb=" O ILE F 26 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N PHE F 3 " --> pdb=" O TYR F 61 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA F 56 " --> pdb=" O ILE F 73 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 79 through 82 removed outlier: 3.605A pdb=" N ILE F 85 " --> pdb=" O PHE F 82 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1167 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 54 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 41 stacking parallelities Total time for adding SS restraints: 6.93 Time building geometry restraints manager: 15.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 10143 1.03 - 1.23: 40 1.23 - 1.42: 4676 1.42 - 1.62: 6383 1.62 - 1.81: 62 Bond restraints: 21304 Sorted by residual: bond pdb=" CB ILE D 74 " pdb=" CG2 ILE D 74 " ideal model delta sigma weight residual 1.521 1.474 0.047 3.30e-02 9.18e+02 2.02e+00 bond pdb=" CB GLN F 24 " pdb=" CG GLN F 24 " ideal model delta sigma weight residual 1.520 1.478 0.042 3.00e-02 1.11e+03 1.95e+00 bond pdb=" CB VAL E 32 " pdb=" CG1 VAL E 32 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.84e+00 bond pdb=" C ASP C 65 " pdb=" N ILE C 66 " ideal model delta sigma weight residual 1.329 1.300 0.029 2.19e-02 2.09e+03 1.74e+00 bond pdb=" CG LEU D 60 " pdb=" CD1 LEU D 60 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.58e+00 ... (remaining 21299 not shown) Histogram of bond angle deviations from ideal: 61.54 - 76.04: 2 76.04 - 90.55: 0 90.55 - 105.05: 324 105.05 - 119.55: 29568 119.55 - 134.06: 8481 Bond angle restraints: 38375 Sorted by residual: angle pdb=" C SER C 294 " pdb=" N LEU C 295 " pdb=" H LEU C 295 " ideal model delta sigma weight residual 124.38 71.32 53.06 3.00e+00 1.11e-01 3.13e+02 angle pdb=" CA LEU C 295 " pdb=" N LEU C 295 " pdb=" H LEU C 295 " ideal model delta sigma weight residual 114.08 61.54 52.54 3.00e+00 1.11e-01 3.07e+02 angle pdb=" C SER C 294 " pdb=" N LEU C 295 " pdb=" CA LEU C 295 " ideal model delta sigma weight residual 121.54 132.86 -11.32 1.91e+00 2.74e-01 3.51e+01 angle pdb=" N VAL C 121 " pdb=" CA VAL C 121 " pdb=" C VAL C 121 " ideal model delta sigma weight residual 112.43 108.68 3.75 9.20e-01 1.18e+00 1.66e+01 angle pdb=" CA MET C 140 " pdb=" C MET C 140 " pdb=" N GLN C 141 " ideal model delta sigma weight residual 118.42 122.66 -4.24 1.31e+00 5.83e-01 1.05e+01 ... (remaining 38370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.74: 9134 31.74 - 63.48: 588 63.48 - 95.23: 11 95.23 - 126.97: 0 126.97 - 158.71: 2 Dihedral angle restraints: 9735 sinusoidal: 5645 harmonic: 4090 Sorted by residual: dihedral pdb=" CA ARG B 90 " pdb=" C ARG B 90 " pdb=" N GLN B 91 " pdb=" CA GLN B 91 " ideal model delta harmonic sigma weight residual 180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA ASN E 36 " pdb=" C ASN E 36 " pdb=" N SER E 37 " pdb=" CA SER E 37 " ideal model delta harmonic sigma weight residual -180.00 -158.75 -21.25 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" C4' DT H 29 " pdb=" C3' DT H 29 " pdb=" O3' DT H 29 " pdb=" P DT H 30 " ideal model delta sinusoidal sigma weight residual 220.00 61.29 158.71 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 9732 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1070 0.033 - 0.066: 457 0.066 - 0.099: 170 0.099 - 0.131: 45 0.131 - 0.164: 9 Chirality restraints: 1751 Sorted by residual: chirality pdb=" CA VAL C 35 " pdb=" N VAL C 35 " pdb=" C VAL C 35 " pdb=" CB VAL C 35 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CA ILE B 25 " pdb=" N ILE B 25 " pdb=" C ILE B 25 " pdb=" CB ILE B 25 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA VAL D 213 " pdb=" N VAL D 213 " pdb=" C VAL D 213 " pdb=" CB VAL D 213 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.17e-01 ... (remaining 1748 not shown) Planarity restraints: 2941 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER C 207 " 0.042 5.00e-02 4.00e+02 6.40e-02 6.55e+00 pdb=" N PRO C 208 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO C 208 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO C 208 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER D 207 " -0.033 5.00e-02 4.00e+02 4.91e-02 3.86e+00 pdb=" N PRO D 208 " 0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 208 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 208 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 207 " 0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO B 208 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 208 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 208 " 0.024 5.00e-02 4.00e+02 ... (remaining 2938 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.17: 1038 2.17 - 2.78: 39824 2.78 - 3.38: 53178 3.38 - 3.99: 70414 3.99 - 4.60: 112154 Nonbonded interactions: 276608 Sorted by model distance: nonbonded pdb="HH22 ARG B 49 " pdb=" OE1 GLU E 25 " model vdw 1.562 1.850 nonbonded pdb=" HH TYR D 229 " pdb=" OD2 ASP D 275 " model vdw 1.601 1.850 nonbonded pdb="HH12 ARG C 169 " pdb=" OP1 DG H 28 " model vdw 1.627 1.850 nonbonded pdb="HH11 ARG C 123 " pdb=" O SER C 136 " model vdw 1.628 1.850 nonbonded pdb="HH22 ARG C 169 " pdb=" OG SER C 187 " model vdw 1.629 1.850 ... (remaining 276603 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 23 through 245 or (resid 246 and (name N or name CA or nam \ e C or name O or name CB or name OG1 or name CG2)) or (resid 247 and (name N or \ name CA or name C or name O or name CB or name CG or name CD or name OE1 or name \ OE2)) or (resid 248 and (name N or name CA or name C or name O or name CB or na \ me CG1 or name CG2 or name CD1)) or (resid 249 through 250 and (name N or name C \ A or name C or name O or name CB or name CG or name OD1 or name OD2)) or (resid \ 251 and (name N or name CA or name C or name O or name CB or name CG1 or name CG \ 2 or name CD1)) or (resid 252 and (name N or name CA or name C or name O or name \ HA2 or name HA3)) or resid 253 through 296 or (resid 297 through 298 and (name \ N or name CA or name C or name O or name CB or name CG or name OD1 or name OD2)) \ or (resid 299 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name CE or name NZ )) or (resid 300 and (name N or name CA or name \ C or name O or name CB or name CG or name OD1 or name OD2)) or (resid 301 and ( \ name N or name CA or name C or name O or name CB or name CG or name SD or name C \ E )) or (resid 302 and (name N or name CA or name C or name O or name CB or name \ CG or name CD1 or name CD2)) or (resid 303 and (name N or name CA or name C or \ name O or name CB or name CG1 or name CG2)) or (resid 304 and (name N or name CA \ or name C or name O or name CB or name CG or name CD or name CE or name NZ )) o \ r (resid 305 and (name N or name CA or name C or name O or name CB or name CG or \ name ND1 or name CD2 or name CE1 or name NE2)) or (resid 306 and (name N or nam \ e CA or name C or name O )))) selection = (chain 'C' and ((resid 23 and (name N or name CA or name C or name O or name CB \ or name OG or name HA or name HB2 or name HB3 or name HG )) or resid 24 through \ 74 or (resid 75 and (name N or name CA or name C or name O or name HA2 or name H \ A3)) or resid 76 through 306)) } ncs_group { reference = (chain 'B' and (resid 4 through 85 or (resid 86 and (name N or name CA or name C \ or name O or name CB or name CG or name CD or name OE1 or name OE2)) or resid 8 \ 7 through 88 or (resid 89 and (name N or name CA or name C or name O or name CB \ or name CG1 or name CG2)) or (resid 90 and (name N or name CA or name C or name \ O or name CB or name CG or name CD or name NE or name CZ or name NH1 or name NH2 \ )) or (resid 91 and (name N or name CA or name C or name O or name CB or name CG \ or name CD or name OE1 or name NE2)) or (resid 92 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name \ CE2 or name CZ or name OH )) or (resid 93 and (name N or name CA or name C or na \ me O or name CB )) or resid 94 through 100 or (resid 101 and (name N or name CA \ or name C or name O or name CB or name OG or name HA or name HB2 or name HB3 or \ name HG )) or resid 102 through 281)) selection = (chain 'D' and (resid 4 through 140 or resid 181 through 281)) } ncs_group { reference = (chain 'E' and resid 2 through 92) selection = (chain 'F' and resid 2 through 92) } 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.280 Extract box with map and model: 4.830 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 66.600 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.060 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:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 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 0.048 11161 Z= 0.326 Angle : 0.694 11.317 15328 Z= 0.413 Chirality : 0.043 0.164 1751 Planarity : 0.004 0.064 1760 Dihedral : 17.864 158.710 4263 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.18 (0.16), residues: 1214 helix: -3.79 (0.14), residues: 511 sheet: -3.40 (0.34), residues: 135 loop : -4.63 (0.18), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 22 HIS 0.010 0.002 HIS C 198 PHE 0.014 0.002 PHE E 82 TYR 0.013 0.001 TYR F 61 ARG 0.006 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 176 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 1.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7279 (t0) cc_final: 0.7019 (t0) REVERT: A 125 MET cc_start: 0.6258 (mtt) cc_final: 0.4586 (ttp) REVERT: C 76 ASP cc_start: 0.7224 (m-30) cc_final: 0.6991 (m-30) REVERT: C 140 MET cc_start: 0.3824 (ttt) cc_final: 0.3268 (tpt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.6605 time to fit residues: 153.9718 Evaluate side-chains 103 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 0.0770 chunk 64 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 73 optimal weight: 0.0170 chunk 114 optimal weight: 1.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN B 5 ASN B 127 GLN ** B 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN D 277 GLN E 48 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11161 Z= 0.190 Angle : 0.610 18.355 15328 Z= 0.343 Chirality : 0.041 0.148 1751 Planarity : 0.004 0.049 1760 Dihedral : 18.143 159.468 1971 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 1.06 % Allowed : 8.45 % Favored : 90.49 % 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: -4.57 (0.19), residues: 1214 helix: -2.27 (0.19), residues: 509 sheet: -2.85 (0.32), residues: 170 loop : -3.86 (0.21), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 22 HIS 0.006 0.001 HIS C 198 PHE 0.022 0.001 PHE A 176 TYR 0.014 0.001 TYR D 92 ARG 0.006 0.000 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 114 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7400 (t0) cc_final: 0.7146 (t0) REVERT: A 125 MET cc_start: 0.6281 (mtt) cc_final: 0.4558 (ttp) REVERT: A 224 ASP cc_start: 0.6255 (m-30) cc_final: 0.6033 (m-30) REVERT: B 54 MET cc_start: 0.7831 (mmt) cc_final: 0.7148 (mmt) REVERT: C 76 ASP cc_start: 0.7322 (m-30) cc_final: 0.7068 (m-30) outliers start: 11 outliers final: 6 residues processed: 121 average time/residue: 0.5454 time to fit residues: 92.0258 Evaluate side-chains 109 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 87 ARG Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain E residue 6 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 123 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 39 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11161 Z= 0.268 Angle : 0.619 18.353 15328 Z= 0.348 Chirality : 0.042 0.158 1751 Planarity : 0.005 0.067 1760 Dihedral : 18.264 160.630 1971 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.39 % Favored : 90.61 % Rotamer: Outliers : 1.92 % Allowed : 10.76 % Favored : 87.32 % 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: -4.03 (0.20), residues: 1214 helix: -1.75 (0.20), residues: 516 sheet: -2.75 (0.33), residues: 181 loop : -3.59 (0.22), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 166 HIS 0.015 0.002 HIS C 198 PHE 0.015 0.002 PHE A 176 TYR 0.011 0.001 TYR D 92 ARG 0.008 0.000 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.551 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7485 (t0) cc_final: 0.7220 (t0) REVERT: A 125 MET cc_start: 0.6292 (mtt) cc_final: 0.4578 (ttp) outliers start: 20 outliers final: 13 residues processed: 124 average time/residue: 0.5467 time to fit residues: 96.6914 Evaluate side-chains 105 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 92 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.2980 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.0870 chunk 121 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 2.9990 chunk 32 optimal weight: 0.0470 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 244 ASN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11161 Z= 0.157 Angle : 0.553 19.019 15328 Z= 0.313 Chirality : 0.040 0.144 1751 Planarity : 0.003 0.036 1760 Dihedral : 18.105 161.543 1971 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 1.73 % Allowed : 12.20 % Favored : 86.07 % 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: -3.36 (0.21), residues: 1214 helix: -1.08 (0.21), residues: 514 sheet: -2.25 (0.35), residues: 176 loop : -3.42 (0.22), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 166 HIS 0.006 0.001 HIS C 198 PHE 0.012 0.001 PHE A 176 TYR 0.007 0.001 TYR D 92 ARG 0.002 0.000 ARG B 87 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 1.683 Fit side-chains revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7466 (t0) cc_final: 0.7163 (t0) REVERT: A 125 MET cc_start: 0.6177 (mtt) cc_final: 0.4498 (ttp) REVERT: C 140 MET cc_start: 0.3419 (ttt) cc_final: 0.2635 (tpt) REVERT: D 58 LEU cc_start: 0.6859 (OUTLIER) cc_final: 0.6530 (mt) outliers start: 18 outliers final: 8 residues processed: 124 average time/residue: 0.4842 time to fit residues: 86.4289 Evaluate side-chains 113 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 104 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain F residue 5 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 109 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 11161 Z= 0.291 Angle : 0.609 18.711 15328 Z= 0.342 Chirality : 0.042 0.149 1751 Planarity : 0.004 0.047 1760 Dihedral : 18.229 161.434 1971 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.81 % Favored : 91.19 % Rotamer: Outliers : 2.31 % Allowed : 13.83 % Favored : 83.86 % 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: -3.41 (0.21), residues: 1214 helix: -1.13 (0.21), residues: 523 sheet: -2.10 (0.35), residues: 177 loop : -3.54 (0.22), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 166 HIS 0.014 0.002 HIS C 198 PHE 0.013 0.002 PHE E 3 TYR 0.011 0.001 TYR D 92 ARG 0.008 0.000 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 106 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7493 (t0) cc_final: 0.7244 (t0) REVERT: A 125 MET cc_start: 0.6218 (mtt) cc_final: 0.4490 (ttp) REVERT: C 140 MET cc_start: 0.3733 (ttt) cc_final: 0.2849 (tpt) REVERT: D 58 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6550 (mt) outliers start: 24 outliers final: 19 residues processed: 125 average time/residue: 0.4397 time to fit residues: 80.9602 Evaluate side-chains 120 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 100 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.1980 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 10 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.3374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11161 Z= 0.220 Angle : 0.568 19.013 15328 Z= 0.321 Chirality : 0.041 0.146 1751 Planarity : 0.004 0.036 1760 Dihedral : 18.154 162.233 1971 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.31 % Allowed : 14.60 % Favored : 83.09 % 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: -3.10 (0.21), residues: 1214 helix: -0.90 (0.21), residues: 524 sheet: -1.87 (0.36), residues: 177 loop : -3.40 (0.22), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 166 HIS 0.008 0.001 HIS C 198 PHE 0.009 0.001 PHE D 24 TYR 0.008 0.001 TYR D 92 ARG 0.002 0.000 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 124 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 100 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7540 (t0) cc_final: 0.7231 (t0) REVERT: A 125 MET cc_start: 0.6208 (mtt) cc_final: 0.4499 (ttp) REVERT: C 140 MET cc_start: 0.3821 (ttt) cc_final: 0.2933 (tpt) REVERT: D 58 LEU cc_start: 0.6840 (OUTLIER) cc_final: 0.6507 (mt) REVERT: D 129 ARG cc_start: 0.6943 (ttm170) cc_final: 0.6638 (ttp-170) outliers start: 24 outliers final: 23 residues processed: 117 average time/residue: 0.4692 time to fit residues: 79.8378 Evaluate side-chains 120 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 96 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 14 GLU Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 83 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 20.0000 chunk 69 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 48 optimal weight: 4.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11161 Z= 0.215 Angle : 0.560 19.095 15328 Z= 0.317 Chirality : 0.041 0.145 1751 Planarity : 0.004 0.035 1760 Dihedral : 18.136 162.337 1971 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 1.83 % Allowed : 15.56 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.22), residues: 1214 helix: -0.69 (0.22), residues: 522 sheet: -1.65 (0.37), residues: 177 loop : -3.27 (0.22), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 166 HIS 0.008 0.002 HIS C 29 PHE 0.011 0.001 PHE E 3 TYR 0.008 0.001 TYR D 92 ARG 0.003 0.000 ARG C 156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.638 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7624 (t0) cc_final: 0.7303 (t0) REVERT: A 125 MET cc_start: 0.6096 (mtt) cc_final: 0.4474 (ttp) REVERT: C 140 MET cc_start: 0.3858 (ttt) cc_final: 0.2978 (tpt) REVERT: D 58 LEU cc_start: 0.6903 (OUTLIER) cc_final: 0.6567 (mt) REVERT: D 129 ARG cc_start: 0.7038 (ttm170) cc_final: 0.6794 (ttp-170) outliers start: 19 outliers final: 18 residues processed: 116 average time/residue: 0.4713 time to fit residues: 78.9308 Evaluate side-chains 118 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 99 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 59 SER Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 110 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11161 Z= 0.192 Angle : 0.545 19.203 15328 Z= 0.309 Chirality : 0.040 0.142 1751 Planarity : 0.003 0.035 1760 Dihedral : 18.094 162.562 1971 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 2.02 % Allowed : 16.04 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.60 (0.22), residues: 1214 helix: -0.46 (0.22), residues: 519 sheet: -1.53 (0.38), residues: 167 loop : -3.15 (0.22), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 166 HIS 0.006 0.001 HIS C 198 PHE 0.010 0.001 PHE F 3 TYR 0.008 0.001 TYR D 92 ARG 0.002 0.000 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 1.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7625 (t0) cc_final: 0.7278 (t0) REVERT: A 125 MET cc_start: 0.6006 (mtt) cc_final: 0.4366 (ttp) REVERT: D 58 LEU cc_start: 0.6893 (OUTLIER) cc_final: 0.6568 (mt) REVERT: D 129 ARG cc_start: 0.6992 (ttm170) cc_final: 0.6769 (ttp-170) outliers start: 21 outliers final: 19 residues processed: 120 average time/residue: 0.4513 time to fit residues: 79.7574 Evaluate side-chains 119 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 99 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 ASP Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.0050 chunk 116 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 119 optimal weight: 1.9990 overall best weight: 2.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11161 Z= 0.237 Angle : 0.568 19.058 15328 Z= 0.321 Chirality : 0.041 0.144 1751 Planarity : 0.004 0.035 1760 Dihedral : 18.146 162.632 1971 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 1.92 % Allowed : 16.43 % Favored : 81.65 % 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: -2.60 (0.22), residues: 1214 helix: -0.48 (0.22), residues: 518 sheet: -1.39 (0.38), residues: 176 loop : -3.20 (0.22), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 166 HIS 0.009 0.002 HIS C 29 PHE 0.014 0.001 PHE E 3 TYR 0.010 0.001 TYR D 92 ARG 0.002 0.000 ARG B 13 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 108 time to evaluate : 1.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7655 (t0) cc_final: 0.7322 (t0) REVERT: A 125 MET cc_start: 0.6009 (mtt) cc_final: 0.4368 (ttp) REVERT: C 33 ASN cc_start: 0.7247 (OUTLIER) cc_final: 0.6856 (t0) REVERT: C 140 MET cc_start: 0.4001 (ttt) cc_final: 0.3263 (tpp) REVERT: D 58 LEU cc_start: 0.6863 (OUTLIER) cc_final: 0.6531 (mt) REVERT: E 41 GLU cc_start: 0.7213 (tm-30) cc_final: 0.6963 (tm-30) outliers start: 20 outliers final: 18 residues processed: 124 average time/residue: 0.4547 time to fit residues: 83.0161 Evaluate side-chains 123 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 103 time to evaluate : 1.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 91 GLN Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 26 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 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 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 257 GLN E 50 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11161 Z= 0.214 Angle : 0.561 19.084 15328 Z= 0.316 Chirality : 0.041 0.143 1751 Planarity : 0.004 0.063 1760 Dihedral : 18.135 162.848 1971 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 1.92 % Allowed : 16.62 % Favored : 81.46 % 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: -2.49 (0.22), residues: 1214 helix: -0.38 (0.22), residues: 518 sheet: -1.40 (0.40), residues: 161 loop : -3.09 (0.22), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 166 HIS 0.008 0.001 HIS C 198 PHE 0.012 0.001 PHE E 3 TYR 0.008 0.001 TYR D 92 ARG 0.008 0.000 ARG C 156 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2428 Ramachandran restraints generated. 1214 Oldfield, 0 Emsley, 1214 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 92 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 106 time to evaluate : 1.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 33 ASN cc_start: 0.7653 (t0) cc_final: 0.7297 (t0) REVERT: A 125 MET cc_start: 0.6020 (mtt) cc_final: 0.4374 (ttp) REVERT: C 33 ASN cc_start: 0.7237 (OUTLIER) cc_final: 0.6839 (t0) REVERT: D 58 LEU cc_start: 0.6868 (OUTLIER) cc_final: 0.6532 (mt) REVERT: E 41 GLU cc_start: 0.7193 (tm-30) cc_final: 0.6945 (tm-30) outliers start: 20 outliers final: 17 residues processed: 123 average time/residue: 0.4601 time to fit residues: 82.7060 Evaluate side-chains 121 residues out of total 1041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 102 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 291 ASP Chi-restraints excluded: chain B residue 72 GLU Chi-restraints excluded: chain B residue 199 SER Chi-restraints excluded: chain C residue 33 ASN Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 290 VAL Chi-restraints excluded: chain C residue 305 HIS Chi-restraints excluded: chain D residue 20 ASP Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 232 GLU Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 24 GLN Chi-restraints excluded: chain F residue 5 VAL Chi-restraints excluded: chain F residue 26 ILE Chi-restraints excluded: chain F residue 83 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.5980 chunk 92 optimal weight: 7.9990 chunk 14 optimal weight: 0.3980 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 18 optimal weight: 0.3980 chunk 87 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.207032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.160172 restraints weight = 32802.036| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.54 r_work: 0.3485 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3344 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11161 Z= 0.175 Angle : 0.540 19.283 15328 Z= 0.305 Chirality : 0.040 0.140 1751 Planarity : 0.004 0.056 1760 Dihedral : 18.077 162.900 1971 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 1.83 % Allowed : 16.81 % Favored : 81.36 % 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: -2.26 (0.22), residues: 1214 helix: -0.15 (0.22), residues: 518 sheet: -1.24 (0.41), residues: 161 loop : -3.02 (0.22), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 166 HIS 0.006 0.001 HIS C 198 PHE 0.011 0.001 PHE F 3 TYR 0.007 0.001 TYR B 92 ARG 0.010 0.000 ARG B 13 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4737.04 seconds wall clock time: 84 minutes 0.84 seconds (5040.84 seconds total)