Starting phenix.real_space_refine on Wed Feb 12 20:14:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpi_27636/02_2025/8dpi_27636_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpi_27636/02_2025/8dpi_27636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dpi_27636/02_2025/8dpi_27636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpi_27636/02_2025/8dpi_27636.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpi_27636/02_2025/8dpi_27636_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpi_27636/02_2025/8dpi_27636_trim.cif" } resolution = 3.4 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= 0.002 sd= 0.027 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 56 5.16 5 Cl 1 4.86 5 C 5230 2.51 5 N 1364 2.21 5 O 1499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8150 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1935 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 9, 'TRANS': 254} Chain breaks: 4 Unresolved non-hydrogen bonds: 169 Unresolved non-hydrogen angles: 205 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 3, 'GLU:plan': 2, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1677 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 152 Unresolved non-hydrogen dihedrals: 106 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 6, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 93 Chain: "C" Number of atoms: 2479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2479 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 84 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 9, 'ASN:plan1': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 87 Chain: "D" Number of atoms: 284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 284 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 2, 'TRANS': 39} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "E" Number of atoms: 1734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1734 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "A" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 41 Unusual residues: {'CLR': 1, 'T4U': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.40, per 1000 atoms: 0.66 Number of scatterers: 8150 At special positions: 0 Unit cell: (89.18, 119.21, 133.77, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 1 17.00 S 56 16.00 O 1499 8.00 N 1364 7.00 C 5230 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 992.3 milliseconds 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 14 sheets defined 39.1% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 61 through 80 removed outlier: 3.501A pdb=" N ILE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N SER A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 106 removed outlier: 5.007A pdb=" N PHE A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LEU A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N MET A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.626A pdb=" N LEU A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 157 removed outlier: 4.233A pdb=" N SER A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 166 removed outlier: 4.220A pdb=" N HIS A 162 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 185 removed outlier: 3.773A pdb=" N ALA A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N MET A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE A 183 " --> pdb=" O TRP A 179 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N VAL A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 196 removed outlier: 3.936A pdb=" N VAL A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG A 195 " --> pdb=" O VAL A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 200 Processing helix chain 'A' and resid 211 through 223 removed outlier: 4.419A pdb=" N ILE A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N PHE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 245 removed outlier: 3.639A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 337 removed outlier: 4.218A pdb=" N GLU A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N SER A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Proline residue: A 326 - end of helix removed outlier: 3.505A pdb=" N ILE A 329 " --> pdb=" O CYS A 325 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 360 removed outlier: 3.804A pdb=" N VAL A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TRP A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ILE A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 368 Processing helix chain 'A' and resid 372 through 383 Processing helix chain 'B' and resid 6 through 31 removed outlier: 4.015A pdb=" N GLU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA B 30 " --> pdb=" O ASP B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 95 through 101 removed outlier: 3.510A pdb=" N CYS B 99 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 116 No H-bonds generated for 'chain 'B' and resid 114 through 116' Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 3.968A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.643A pdb=" N LEU B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 170 Processing helix chain 'B' and resid 185 through 202 removed outlier: 3.932A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.631A pdb=" N ARG B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE B 227 " --> pdb=" O ASN B 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 24 Processing helix chain 'C' and resid 29 through 34 removed outlier: 3.510A pdb=" N ILE C 33 " --> pdb=" O THR C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 37 No H-bonds generated for 'chain 'C' and resid 35 through 37' Processing helix chain 'D' and resid 17 through 24 removed outlier: 3.620A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 removed outlier: 3.583A pdb=" N HIS D 44 " --> pdb=" O TYR D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.602A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 4.732A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N GLY B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 9.941A pdb=" N ALA B 105 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.315A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 8.160A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.300A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 6.842A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ALA C 328 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU C 318 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY C 330 " --> pdb=" O SER C 316 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.920A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.967A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.814A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.617A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA C 203 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.601A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG C 251 " --> pdb=" O THR C 243 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.041A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 removed outlier: 3.929A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.224A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR E 115 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.224A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR E 115 " --> pdb=" O TYR E 94 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 removed outlier: 3.517A pdb=" N VAL E 143 " --> pdb=" O ILE E 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.856A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.856A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN E 219 " --> pdb=" O THR E 226 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) 396 hydrogen bonds defined for protein. 1098 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: 2.48 Time building geometry restraints manager: 2.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2562 1.34 - 1.46: 1345 1.46 - 1.57: 4327 1.57 - 1.69: 0 1.69 - 1.81: 84 Bond restraints: 8318 Sorted by residual: bond pdb=" N VAL A 156 " pdb=" CA VAL A 156 " ideal model delta sigma weight residual 1.460 1.514 -0.054 1.09e-02 8.42e+03 2.47e+01 bond pdb=" N VAL A 160 " pdb=" CA VAL A 160 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.21e-02 6.83e+03 7.41e+00 bond pdb=" CA SER A 158 " pdb=" CB SER A 158 " ideal model delta sigma weight residual 1.530 1.489 0.041 1.58e-02 4.01e+03 6.78e+00 bond pdb=" N PRO A 159 " pdb=" CA PRO A 159 " ideal model delta sigma weight residual 1.469 1.438 0.031 1.28e-02 6.10e+03 5.75e+00 bond pdb=" N SER A 158 " pdb=" CA SER A 158 " ideal model delta sigma weight residual 1.457 1.485 -0.028 1.41e-02 5.03e+03 4.04e+00 ... (remaining 8313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 11217 1.97 - 3.93: 99 3.93 - 5.90: 19 5.90 - 7.87: 3 7.87 - 9.83: 1 Bond angle restraints: 11339 Sorted by residual: angle pdb=" CA GLU A 161 " pdb=" C GLU A 161 " pdb=" O GLU A 161 " ideal model delta sigma weight residual 120.70 116.56 4.14 1.03e+00 9.43e-01 1.62e+01 angle pdb=" C GLU A 161 " pdb=" CA GLU A 161 " pdb=" CB GLU A 161 " ideal model delta sigma weight residual 110.90 116.67 -5.77 1.58e+00 4.01e-01 1.33e+01 angle pdb=" O ALA A 155 " pdb=" C ALA A 155 " pdb=" N VAL A 156 " ideal model delta sigma weight residual 122.43 117.84 4.59 1.34e+00 5.57e-01 1.17e+01 angle pdb=" N VAL A 160 " pdb=" CA VAL A 160 " pdb=" C VAL A 160 " ideal model delta sigma weight residual 110.72 107.36 3.36 1.01e+00 9.80e-01 1.11e+01 angle pdb=" N VAL A 352 " pdb=" CA VAL A 352 " pdb=" C VAL A 352 " ideal model delta sigma weight residual 113.53 110.36 3.17 9.80e-01 1.04e+00 1.05e+01 ... (remaining 11334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.49: 4860 31.49 - 62.98: 40 62.98 - 94.47: 7 94.47 - 125.96: 3 125.96 - 157.44: 1 Dihedral angle restraints: 4911 sinusoidal: 1747 harmonic: 3164 Sorted by residual: dihedral pdb=" C09 T4U A 501 " pdb=" C04 T4U A 501 " pdb=" C05 T4U A 501 " pdb=" N13 T4U A 501 " ideal model delta sinusoidal sigma weight residual -79.13 78.31 -157.44 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C04 T4U A 501 " pdb=" C05 T4U A 501 " pdb=" N13 T4U A 501 " pdb=" C07 T4U A 501 " ideal model delta sinusoidal sigma weight residual 68.43 -48.79 117.22 1 3.00e+01 1.11e-03 1.55e+01 dihedral pdb=" C2 CLR A 502 " pdb=" C3 CLR A 502 " pdb=" C4 CLR A 502 " pdb=" C5 CLR A 502 " ideal model delta sinusoidal sigma weight residual -55.03 58.78 -113.81 1 3.00e+01 1.11e-03 1.50e+01 ... (remaining 4908 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.279: 1345 0.279 - 0.557: 0 0.557 - 0.836: 0 0.836 - 1.115: 0 1.115 - 1.393: 1 Chirality restraints: 1346 Sorted by residual: chirality pdb=" C08 T4U A 501 " pdb=" C01 T4U A 501 " pdb=" C07 T4U A 501 " pdb=" C11 T4U A 501 " both_signs ideal model delta sigma weight residual False -2.50 -1.10 -1.39 2.00e-01 2.50e+01 4.85e+01 chirality pdb=" CA VAL A 160 " pdb=" N VAL A 160 " pdb=" C VAL A 160 " pdb=" CB VAL A 160 " both_signs ideal model delta sigma weight residual False 2.44 2.70 -0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA GLU A 161 " pdb=" N GLU A 161 " pdb=" C GLU A 161 " pdb=" CB GLU A 161 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1343 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU A 161 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C GLU A 161 " 0.030 2.00e-02 2.50e+03 pdb=" O GLU A 161 " -0.011 2.00e-02 2.50e+03 pdb=" N HIS A 162 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG E 168 " -0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO E 169 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO E 169 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO E 169 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 364 " -0.018 5.00e-02 4.00e+02 2.70e-02 1.17e+00 pdb=" N PRO A 365 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " -0.015 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 741 2.75 - 3.29: 7554 3.29 - 3.82: 12729 3.82 - 4.36: 14541 4.36 - 4.90: 26432 Nonbonded interactions: 61997 Sorted by model distance: nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.211 3.040 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.219 3.040 nonbonded pdb=" NH1 ARG B 93 " pdb=" OD1 ASP B 124 " model vdw 2.261 3.120 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.272 3.040 nonbonded pdb=" O ILE C 58 " pdb=" OG SER C 316 " model vdw 2.290 3.040 ... (remaining 61992 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 1.220 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: 0.370 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 22.380 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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: 27.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6594 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 : 0.003 0.054 8318 Z= 0.173 Angle : 0.522 9.834 11339 Z= 0.293 Chirality : 0.057 1.393 1346 Planarity : 0.003 0.028 1422 Dihedral : 11.004 157.444 2857 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.31 % Favored : 98.59 % Rotamer: Outliers : 0.98 % Allowed : 1.83 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.26), residues: 1065 helix: 2.12 (0.30), residues: 325 sheet: 1.49 (0.30), residues: 286 loop : 0.38 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 130 HIS 0.004 0.001 HIS E 220 PHE 0.009 0.001 PHE C 199 TYR 0.011 0.001 TYR A 153 ARG 0.002 0.000 ARG B 132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 193 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7217 (pt) cc_final: 0.6993 (mt) REVERT: A 143 MET cc_start: 0.6776 (mmt) cc_final: 0.6550 (mmt) REVERT: A 208 VAL cc_start: 0.7824 (p) cc_final: 0.7553 (t) REVERT: A 238 ILE cc_start: 0.6819 (mm) cc_final: 0.6112 (mm) REVERT: A 300 MET cc_start: 0.7616 (ttp) cc_final: 0.6659 (tpp) REVERT: B 119 GLN cc_start: 0.7944 (tp40) cc_final: 0.7655 (mm-40) REVERT: B 122 LEU cc_start: 0.8231 (mt) cc_final: 0.7994 (mp) REVERT: B 186 VAL cc_start: 0.7001 (t) cc_final: 0.6798 (p) REVERT: B 195 LYS cc_start: 0.7361 (tttt) cc_final: 0.6743 (tttt) REVERT: C 52 ARG cc_start: 0.6935 (mtt-85) cc_final: 0.6675 (mtt-85) REVERT: C 188 MET cc_start: 0.6641 (mmm) cc_final: 0.6284 (mmp) REVERT: C 227 SER cc_start: 0.7461 (t) cc_final: 0.7186 (m) REVERT: C 232 ILE cc_start: 0.7591 (mt) cc_final: 0.7313 (tt) REVERT: C 277 SER cc_start: 0.7519 (t) cc_final: 0.6819 (m) REVERT: E 98 ARG cc_start: 0.7053 (ttp-170) cc_final: 0.6516 (ptt180) REVERT: E 128 MET cc_start: 0.7663 (mmm) cc_final: 0.7343 (mmm) outliers start: 8 outliers final: 2 residues processed: 199 average time/residue: 0.2299 time to fit residues: 60.1571 Evaluate side-chains 162 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 160 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 157 ARG Chi-restraints excluded: chain C residue 196 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 364 ASN B 98 GLN B 229 ASN C 88 ASN C 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.144737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.125330 restraints weight = 12348.482| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.21 r_work: 0.3554 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3401 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8318 Z= 0.300 Angle : 0.651 11.424 11339 Z= 0.345 Chirality : 0.047 0.159 1346 Planarity : 0.005 0.045 1422 Dihedral : 8.436 152.112 1240 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.05 % Allowed : 8.91 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.26), residues: 1065 helix: 1.82 (0.29), residues: 341 sheet: 1.19 (0.30), residues: 288 loop : 0.20 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 130 HIS 0.008 0.002 HIS B 209 PHE 0.020 0.002 PHE C 199 TYR 0.032 0.003 TYR E 59 ARG 0.003 0.001 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 176 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 208 VAL cc_start: 0.8042 (p) cc_final: 0.7675 (m) REVERT: A 300 MET cc_start: 0.7342 (ttp) cc_final: 0.6418 (tpp) REVERT: A 332 ILE cc_start: 0.7046 (mm) cc_final: 0.6771 (tt) REVERT: B 23 LEU cc_start: 0.7065 (mp) cc_final: 0.6697 (mt) REVERT: B 99 CYS cc_start: 0.7981 (p) cc_final: 0.7480 (m) REVERT: B 119 GLN cc_start: 0.8273 (tp40) cc_final: 0.7973 (mm-40) REVERT: B 122 LEU cc_start: 0.8407 (mt) cc_final: 0.8205 (mp) REVERT: B 149 LEU cc_start: 0.7052 (tp) cc_final: 0.6703 (tp) REVERT: B 195 LYS cc_start: 0.7860 (tttt) cc_final: 0.7524 (tttt) REVERT: C 52 ARG cc_start: 0.8287 (mtt-85) cc_final: 0.7975 (mtt-85) REVERT: C 61 MET cc_start: 0.7587 (tmm) cc_final: 0.7276 (tmm) REVERT: C 217 MET cc_start: 0.7695 (mtp) cc_final: 0.7409 (mtp) REVERT: C 227 SER cc_start: 0.8135 (t) cc_final: 0.7780 (m) REVERT: C 277 SER cc_start: 0.7812 (t) cc_final: 0.7134 (m) REVERT: E 67 ARG cc_start: 0.6865 (mtp180) cc_final: 0.6568 (mtp180) outliers start: 25 outliers final: 15 residues processed: 190 average time/residue: 0.2350 time to fit residues: 58.4210 Evaluate side-chains 177 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 183 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 46 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 58 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN C 132 ASN E 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.146303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.127385 restraints weight = 12525.330| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.16 r_work: 0.3593 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8318 Z= 0.190 Angle : 0.545 9.810 11339 Z= 0.290 Chirality : 0.043 0.142 1346 Planarity : 0.004 0.043 1422 Dihedral : 7.894 152.239 1236 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.93 % Allowed : 11.23 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.27), residues: 1065 helix: 2.15 (0.29), residues: 344 sheet: 1.17 (0.30), residues: 288 loop : 0.16 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 130 HIS 0.005 0.001 HIS E 220 PHE 0.018 0.002 PHE B 167 TYR 0.017 0.002 TYR E 59 ARG 0.003 0.000 ARG C 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7350 (ttp) cc_final: 0.6542 (tpp) REVERT: A 332 ILE cc_start: 0.7095 (mm) cc_final: 0.6829 (tt) REVERT: A 372 ASN cc_start: 0.6624 (t0) cc_final: 0.6094 (t0) REVERT: B 23 LEU cc_start: 0.7101 (mp) cc_final: 0.6762 (mt) REVERT: B 99 CYS cc_start: 0.7978 (p) cc_final: 0.7502 (m) REVERT: B 119 GLN cc_start: 0.8229 (tp40) cc_final: 0.7987 (mm-40) REVERT: B 195 LYS cc_start: 0.7732 (tttt) cc_final: 0.7347 (tttt) REVERT: C 52 ARG cc_start: 0.8224 (mtt-85) cc_final: 0.7938 (mtt-85) REVERT: C 117 LEU cc_start: 0.8177 (mt) cc_final: 0.7814 (mt) REVERT: C 196 THR cc_start: 0.7641 (p) cc_final: 0.7425 (p) REVERT: C 217 MET cc_start: 0.7629 (mtp) cc_final: 0.7353 (mtp) REVERT: C 227 SER cc_start: 0.8094 (t) cc_final: 0.7772 (m) REVERT: C 277 SER cc_start: 0.7743 (t) cc_final: 0.7042 (m) REVERT: E 67 ARG cc_start: 0.6830 (mtp180) cc_final: 0.6499 (mtp180) outliers start: 24 outliers final: 21 residues processed: 169 average time/residue: 0.2436 time to fit residues: 53.1363 Evaluate side-chains 177 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 183 LEU Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 89 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN D 44 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.143609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.123905 restraints weight = 12432.714| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.26 r_work: 0.3518 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 moved from start: 0.2960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8318 Z= 0.267 Angle : 0.596 11.090 11339 Z= 0.317 Chirality : 0.045 0.143 1346 Planarity : 0.004 0.055 1422 Dihedral : 8.072 152.607 1235 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.15 % Allowed : 12.45 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.26), residues: 1065 helix: 1.78 (0.29), residues: 357 sheet: 1.09 (0.30), residues: 292 loop : -0.07 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 130 HIS 0.006 0.002 HIS B 209 PHE 0.022 0.002 PHE C 234 TYR 0.028 0.002 TYR E 59 ARG 0.002 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.881 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.6953 (mtt) cc_final: 0.6540 (mtt) REVERT: A 300 MET cc_start: 0.7344 (ttp) cc_final: 0.6576 (tpp) REVERT: A 372 ASN cc_start: 0.6920 (t0) cc_final: 0.6213 (t0) REVERT: B 23 LEU cc_start: 0.7114 (mp) cc_final: 0.6685 (mt) REVERT: B 99 CYS cc_start: 0.7984 (p) cc_final: 0.7530 (m) REVERT: B 119 GLN cc_start: 0.8285 (tp40) cc_final: 0.8022 (mm-40) REVERT: B 195 LYS cc_start: 0.7774 (tttt) cc_final: 0.7468 (tttt) REVERT: C 52 ARG cc_start: 0.8282 (mtt-85) cc_final: 0.7998 (mtt-85) REVERT: C 117 LEU cc_start: 0.8109 (mt) cc_final: 0.7742 (mt) REVERT: C 196 THR cc_start: 0.7611 (p) cc_final: 0.7403 (p) REVERT: C 217 MET cc_start: 0.7650 (mtp) cc_final: 0.7368 (mtp) REVERT: C 227 SER cc_start: 0.8193 (t) cc_final: 0.7830 (m) REVERT: C 234 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6506 (m-80) REVERT: C 277 SER cc_start: 0.7760 (t) cc_final: 0.7050 (m) REVERT: E 67 ARG cc_start: 0.6820 (mtp180) cc_final: 0.6457 (mtp180) outliers start: 34 outliers final: 26 residues processed: 178 average time/residue: 0.2380 time to fit residues: 55.2321 Evaluate side-chains 184 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 86 THR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 183 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 38 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN C 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.144750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.125038 restraints weight = 12356.330| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.28 r_work: 0.3543 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8318 Z= 0.206 Angle : 0.555 10.305 11339 Z= 0.292 Chirality : 0.043 0.137 1346 Planarity : 0.004 0.054 1422 Dihedral : 7.941 152.042 1235 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.52 % Allowed : 13.43 % Favored : 82.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.26), residues: 1065 helix: 2.00 (0.29), residues: 352 sheet: 1.08 (0.30), residues: 292 loop : -0.07 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 130 HIS 0.004 0.001 HIS B 209 PHE 0.015 0.002 PHE B 215 TYR 0.017 0.002 TYR E 59 ARG 0.002 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.6944 (mtt) cc_final: 0.6519 (mtt) REVERT: A 300 MET cc_start: 0.7288 (ttp) cc_final: 0.6529 (tpp) REVERT: B 23 LEU cc_start: 0.7093 (mp) cc_final: 0.6799 (mt) REVERT: B 99 CYS cc_start: 0.8000 (p) cc_final: 0.7517 (m) REVERT: B 119 GLN cc_start: 0.8227 (tp40) cc_final: 0.7988 (mm-40) REVERT: B 149 LEU cc_start: 0.7220 (tp) cc_final: 0.6840 (tp) REVERT: C 52 ARG cc_start: 0.8327 (mtt-85) cc_final: 0.8042 (mtt-85) REVERT: C 117 LEU cc_start: 0.8061 (mt) cc_final: 0.7650 (mt) REVERT: C 150 ARG cc_start: 0.8187 (mmt-90) cc_final: 0.7973 (mmt-90) REVERT: C 217 MET cc_start: 0.7700 (mtp) cc_final: 0.7417 (mtp) REVERT: C 227 SER cc_start: 0.8180 (t) cc_final: 0.7832 (m) REVERT: C 258 ASP cc_start: 0.5966 (t0) cc_final: 0.5356 (t0) REVERT: C 277 SER cc_start: 0.7693 (t) cc_final: 0.6989 (m) REVERT: E 67 ARG cc_start: 0.6792 (mtp180) cc_final: 0.6430 (mtp180) REVERT: E 106 SER cc_start: 0.8707 (t) cc_final: 0.8477 (p) outliers start: 37 outliers final: 30 residues processed: 182 average time/residue: 0.2364 time to fit residues: 56.2964 Evaluate side-chains 192 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 162 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 183 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 1.9990 chunk 96 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.142040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.122724 restraints weight = 12521.898| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.22 r_work: 0.3515 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8318 Z= 0.316 Angle : 0.632 10.998 11339 Z= 0.332 Chirality : 0.046 0.147 1346 Planarity : 0.005 0.060 1422 Dihedral : 8.130 152.335 1235 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 5.01 % Allowed : 13.43 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.26), residues: 1065 helix: 1.72 (0.28), residues: 355 sheet: 0.89 (0.30), residues: 292 loop : -0.33 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 130 HIS 0.007 0.002 HIS B 209 PHE 0.026 0.002 PHE C 234 TYR 0.028 0.002 TYR E 59 ARG 0.002 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 159 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.7039 (mtt) cc_final: 0.6630 (mtt) REVERT: A 148 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7575 (tt) REVERT: A 300 MET cc_start: 0.7376 (ttp) cc_final: 0.6620 (tpp) REVERT: B 23 LEU cc_start: 0.7150 (mp) cc_final: 0.6849 (mt) REVERT: B 99 CYS cc_start: 0.7942 (p) cc_final: 0.7509 (m) REVERT: B 119 GLN cc_start: 0.8265 (tp40) cc_final: 0.8030 (mm-40) REVERT: B 149 LEU cc_start: 0.7335 (tp) cc_final: 0.6975 (tp) REVERT: C 52 ARG cc_start: 0.8344 (mtt-85) cc_final: 0.8060 (mtt-85) REVERT: C 68 ARG cc_start: 0.7383 (mtp180) cc_final: 0.6933 (mtp180) REVERT: C 117 LEU cc_start: 0.8040 (mt) cc_final: 0.7613 (mt) REVERT: C 150 ARG cc_start: 0.8204 (mmt-90) cc_final: 0.8000 (mmt-90) REVERT: C 217 MET cc_start: 0.7694 (mtp) cc_final: 0.7407 (mtp) REVERT: C 227 SER cc_start: 0.8181 (t) cc_final: 0.7846 (m) REVERT: C 262 MET cc_start: 0.6631 (mmm) cc_final: 0.6426 (mmm) REVERT: C 277 SER cc_start: 0.7727 (t) cc_final: 0.6976 (m) REVERT: E 67 ARG cc_start: 0.6804 (mtp180) cc_final: 0.6482 (mtp180) REVERT: E 106 SER cc_start: 0.8757 (t) cc_final: 0.8531 (p) outliers start: 41 outliers final: 35 residues processed: 180 average time/residue: 0.2417 time to fit residues: 56.7165 Evaluate side-chains 191 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 155 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 187 VAL Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 325 MET Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 183 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 1 optimal weight: 10.0000 chunk 67 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 18 optimal weight: 0.2980 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.143666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.124329 restraints weight = 12580.367| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.26 r_work: 0.3539 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3387 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.3582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8318 Z= 0.214 Angle : 0.576 10.791 11339 Z= 0.301 Chirality : 0.044 0.161 1346 Planarity : 0.004 0.056 1422 Dihedral : 7.967 151.707 1235 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.15 % Allowed : 14.77 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.26), residues: 1065 helix: 1.98 (0.29), residues: 355 sheet: 0.86 (0.30), residues: 293 loop : -0.27 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 130 HIS 0.004 0.001 HIS B 209 PHE 0.020 0.002 PHE E 227 TYR 0.020 0.002 TYR B 212 ARG 0.002 0.000 ARG C 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.888 Fit side-chains revert: symmetry clash REVERT: A 107 MET cc_start: 0.6963 (mtt) cc_final: 0.6561 (mtt) REVERT: A 300 MET cc_start: 0.7360 (ttp) cc_final: 0.6573 (tpp) REVERT: B 23 LEU cc_start: 0.7131 (mp) cc_final: 0.6804 (mt) REVERT: B 99 CYS cc_start: 0.8002 (p) cc_final: 0.7501 (m) REVERT: B 119 GLN cc_start: 0.8227 (tp40) cc_final: 0.7990 (mm-40) REVERT: B 149 LEU cc_start: 0.7502 (tp) cc_final: 0.7158 (tp) REVERT: B 225 ARG cc_start: 0.8115 (mmm-85) cc_final: 0.7703 (mmm160) REVERT: C 52 ARG cc_start: 0.8336 (mtt-85) cc_final: 0.8055 (mtt-85) REVERT: C 117 LEU cc_start: 0.7991 (mt) cc_final: 0.7550 (mt) REVERT: C 217 MET cc_start: 0.7719 (mtp) cc_final: 0.7442 (mtp) REVERT: C 227 SER cc_start: 0.8078 (t) cc_final: 0.7776 (m) REVERT: C 258 ASP cc_start: 0.6032 (t0) cc_final: 0.5453 (t0) REVERT: C 277 SER cc_start: 0.7704 (t) cc_final: 0.7002 (m) REVERT: E 67 ARG cc_start: 0.6787 (mtp180) cc_final: 0.6485 (mtp180) REVERT: E 98 ARG cc_start: 0.7850 (ttp-170) cc_final: 0.7557 (ttp-170) REVERT: E 106 SER cc_start: 0.8711 (t) cc_final: 0.8465 (p) outliers start: 34 outliers final: 30 residues processed: 178 average time/residue: 0.2432 time to fit residues: 56.2185 Evaluate side-chains 186 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 156 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 191 VAL Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 183 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 0.5980 chunk 73 optimal weight: 0.1980 chunk 79 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 HIS B 98 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.145541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.126100 restraints weight = 12542.674| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.29 r_work: 0.3561 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3407 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.3666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8318 Z= 0.164 Angle : 0.540 10.743 11339 Z= 0.282 Chirality : 0.043 0.132 1346 Planarity : 0.004 0.050 1422 Dihedral : 7.807 150.573 1235 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.27 % Allowed : 14.77 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.27), residues: 1065 helix: 2.19 (0.29), residues: 354 sheet: 0.80 (0.30), residues: 297 loop : -0.23 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 130 HIS 0.003 0.001 HIS B 209 PHE 0.014 0.001 PHE C 199 TYR 0.017 0.001 TYR B 212 ARG 0.002 0.000 ARG B 93 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.6991 (mtt) cc_final: 0.6605 (mtt) REVERT: A 300 MET cc_start: 0.7288 (ttp) cc_final: 0.6579 (tpp) REVERT: B 23 LEU cc_start: 0.7104 (mp) cc_final: 0.6763 (mt) REVERT: B 99 CYS cc_start: 0.8003 (p) cc_final: 0.7504 (m) REVERT: B 119 GLN cc_start: 0.8207 (tp40) cc_final: 0.8000 (mm-40) REVERT: B 149 LEU cc_start: 0.7447 (tp) cc_final: 0.7115 (tp) REVERT: C 52 ARG cc_start: 0.8328 (mtt-85) cc_final: 0.8066 (mtt-85) REVERT: C 117 LEU cc_start: 0.7975 (mt) cc_final: 0.7552 (mt) REVERT: C 227 SER cc_start: 0.8174 (t) cc_final: 0.7889 (m) REVERT: C 230 ASN cc_start: 0.7386 (m-40) cc_final: 0.7151 (m-40) REVERT: C 258 ASP cc_start: 0.6008 (t0) cc_final: 0.5435 (t0) REVERT: C 277 SER cc_start: 0.7678 (t) cc_final: 0.6995 (m) REVERT: E 98 ARG cc_start: 0.7856 (ttp-170) cc_final: 0.7556 (ttp-170) REVERT: E 106 SER cc_start: 0.8683 (t) cc_final: 0.8434 (p) outliers start: 35 outliers final: 26 residues processed: 175 average time/residue: 0.2356 time to fit residues: 54.6334 Evaluate side-chains 176 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain B residue 223 ASN Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 183 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 64 optimal weight: 0.3980 chunk 29 optimal weight: 0.9980 chunk 67 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.145732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.126179 restraints weight = 12693.999| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.31 r_work: 0.3558 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8318 Z= 0.176 Angle : 0.548 9.744 11339 Z= 0.285 Chirality : 0.043 0.138 1346 Planarity : 0.004 0.051 1422 Dihedral : 7.779 149.856 1235 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.66 % Allowed : 15.87 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.27), residues: 1065 helix: 2.25 (0.29), residues: 355 sheet: 0.90 (0.30), residues: 291 loop : -0.25 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 130 HIS 0.003 0.001 HIS B 209 PHE 0.020 0.001 PHE E 227 TYR 0.016 0.001 TYR B 212 ARG 0.002 0.000 ARG B 226 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 152 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.6984 (mtt) cc_final: 0.6606 (mtt) REVERT: A 300 MET cc_start: 0.7263 (ttp) cc_final: 0.6580 (tpp) REVERT: B 23 LEU cc_start: 0.7129 (mp) cc_final: 0.6766 (mt) REVERT: B 99 CYS cc_start: 0.7952 (p) cc_final: 0.7461 (m) REVERT: B 119 GLN cc_start: 0.8208 (tp40) cc_final: 0.7999 (mm-40) REVERT: B 225 ARG cc_start: 0.8120 (mmm-85) cc_final: 0.7688 (mmm160) REVERT: C 52 ARG cc_start: 0.8352 (mtt-85) cc_final: 0.8089 (mtt-85) REVERT: C 117 LEU cc_start: 0.7967 (mt) cc_final: 0.7534 (mt) REVERT: C 217 MET cc_start: 0.7739 (mtp) cc_final: 0.7477 (mtp) REVERT: C 227 SER cc_start: 0.8158 (t) cc_final: 0.7864 (m) REVERT: C 258 ASP cc_start: 0.6032 (t0) cc_final: 0.5472 (t0) REVERT: C 277 SER cc_start: 0.7692 (t) cc_final: 0.7005 (m) REVERT: E 98 ARG cc_start: 0.7874 (ttp-170) cc_final: 0.7510 (mtp180) REVERT: E 106 SER cc_start: 0.8685 (t) cc_final: 0.8433 (p) outliers start: 30 outliers final: 26 residues processed: 168 average time/residue: 0.2289 time to fit residues: 50.3223 Evaluate side-chains 180 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 100 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 13 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 chunk 86 optimal weight: 0.0270 chunk 72 optimal weight: 2.9990 chunk 56 optimal weight: 0.2980 chunk 1 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 364 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.146922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.127591 restraints weight = 12370.140| |-----------------------------------------------------------------------------| r_work (start): 0.3691 rms_B_bonded: 2.27 r_work: 0.3585 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3432 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8318 Z= 0.145 Angle : 0.530 10.067 11339 Z= 0.273 Chirality : 0.042 0.133 1346 Planarity : 0.003 0.043 1422 Dihedral : 7.675 149.009 1235 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.17 % Allowed : 16.73 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.27), residues: 1065 helix: 2.35 (0.29), residues: 355 sheet: 0.92 (0.31), residues: 284 loop : -0.14 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 130 HIS 0.002 0.001 HIS E 220 PHE 0.019 0.001 PHE E 227 TYR 0.015 0.001 TYR B 212 ARG 0.002 0.000 ARG B 226 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2130 Ramachandran restraints generated. 1065 Oldfield, 0 Emsley, 1065 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 0.815 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6666 (mtt) REVERT: B 23 LEU cc_start: 0.7039 (mp) cc_final: 0.6694 (mt) REVERT: B 99 CYS cc_start: 0.7924 (p) cc_final: 0.7403 (m) REVERT: B 119 GLN cc_start: 0.8182 (tp40) cc_final: 0.7981 (mm-40) REVERT: B 225 ARG cc_start: 0.8120 (mmm-85) cc_final: 0.7687 (mmm160) REVERT: C 52 ARG cc_start: 0.8329 (mtt-85) cc_final: 0.8079 (mtt-85) REVERT: C 61 MET cc_start: 0.7661 (tmm) cc_final: 0.7382 (ppp) REVERT: C 117 LEU cc_start: 0.7961 (mt) cc_final: 0.7538 (mt) REVERT: C 258 ASP cc_start: 0.6036 (t0) cc_final: 0.5458 (t0) REVERT: C 277 SER cc_start: 0.7666 (t) cc_final: 0.6974 (m) REVERT: E 34 MET cc_start: 0.6926 (mmm) cc_final: 0.6656 (mmm) REVERT: E 98 ARG cc_start: 0.7853 (ttp-170) cc_final: 0.7484 (mtp180) REVERT: E 106 SER cc_start: 0.8658 (t) cc_final: 0.8397 (p) outliers start: 26 outliers final: 23 residues processed: 164 average time/residue: 0.2338 time to fit residues: 50.3076 Evaluate side-chains 170 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 21 LYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 211 CYS Chi-restraints excluded: chain C residue 59 TYR Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 228 ASP Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 281 SER Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 183 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 62 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 92 optimal weight: 0.3980 chunk 90 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.145350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.126007 restraints weight = 12658.614| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.28 r_work: 0.3560 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8318 Z= 0.199 Angle : 0.557 9.606 11339 Z= 0.291 Chirality : 0.043 0.136 1346 Planarity : 0.004 0.038 1422 Dihedral : 7.751 149.042 1235 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.42 % Allowed : 16.97 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.27), residues: 1065 helix: 2.31 (0.29), residues: 356 sheet: 0.95 (0.31), residues: 283 loop : -0.27 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 130 HIS 0.010 0.002 HIS B 214 PHE 0.022 0.002 PHE E 227 TYR 0.016 0.002 TYR E 59 ARG 0.003 0.000 ARG B 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4906.21 seconds wall clock time: 87 minutes 20.88 seconds (5240.88 seconds total)