Starting phenix.real_space_refine on Fri Aug 22 22:22:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpi_27636/08_2025/8dpi_27636_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpi_27636/08_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_27636/08_2025/8dpi_27636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpi_27636/08_2025/8dpi_27636.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpi_27636/08_2025/8dpi_27636_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpi_27636/08_2025/8dpi_27636_trim.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 3, 'TYR:plan': 2, 'ARG:plan': 5, 'GLN:plan1': 1} 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: {'ARG:plan': 6, 'GLU:plan': 9, 'ASP:plan': 7, 'PHE:plan': 1} 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: {'ASP:plan': 4, 'GLN:plan1': 4, 'ARG:plan': 9, 'GLU:plan': 2, 'ASN:plan1': 2} 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, 'ASP:plan': 2, 'GLU: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, 'ASP:plan': 2, 'ARG:plan': 1} 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: 1.97, per 1000 atoms: 0.24 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: 0.65 Conformation dependent library (CDL) restraints added in 417.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.33 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: 1.37 Time building geometry restraints manager: 0.84 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: 1.030 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.910 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.410 ------------------------------------------------------------------------------- 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 : 0.009 0.821 8321 Z= 0.913 Angle : 0.522 9.834 11343 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 : 4.47 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG B 132 TYR 0.011 0.001 TYR A 153 PHE 0.009 0.001 PHE C 199 TRP 0.014 0.001 TRP A 130 HIS 0.004 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8318) covalent geometry : angle 0.52174 (11339) SS BOND : bond 0.00129 ( 2) SS BOND : angle 0.82409 ( 4) hydrogen bonds : bond 0.22263 ( 389) hydrogen bonds : angle 6.28206 ( 1098) Misc. bond : bond 0.82129 ( 1) *********************** 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 : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ILE cc_start: 0.7217 (pt) cc_final: 0.6991 (mt) REVERT: A 143 MET cc_start: 0.6776 (mmt) cc_final: 0.6551 (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: 0.6111 (mm) REVERT: A 300 MET cc_start: 0.7616 (ttp) cc_final: 0.6660 (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: 0.6283 (mmp) REVERT: C 227 SER cc_start: 0.7461 (t) cc_final: 0.7187 (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: 0.6515 (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: 0.1051 time to fit residues: 27.6083 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 : 0.314 ------------------------------------------------------------------------------- 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 49 optimal weight: 9.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3941 r_free = 0.3941 target = 0.146242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.126838 restraints weight = 12504.518| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.25 r_work: 0.3578 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8321 Z= 0.170 Angle : 0.615 11.520 11343 Z= 0.323 Chirality : 0.045 0.152 1346 Planarity : 0.004 0.039 1422 Dihedral : 8.237 151.602 1240 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.81 % Allowed : 9.04 % Favored : 88.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.26), residues: 1065 helix: 2.02 (0.29), residues: 340 sheet: 1.19 (0.29), residues: 295 loop : 0.36 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 117 TYR 0.023 0.002 TYR E 59 PHE 0.024 0.002 PHE C 241 TRP 0.013 0.002 TRP A 130 HIS 0.006 0.002 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 8318) covalent geometry : angle 0.61450 (11339) SS BOND : bond 0.00503 ( 2) SS BOND : angle 0.92719 ( 4) hydrogen bonds : bond 0.05437 ( 389) hydrogen bonds : angle 4.62650 ( 1098) Misc. bond : bond 0.00058 ( 1) *********************** 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 197 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 208 VAL cc_start: 0.8004 (p) cc_final: 0.7623 (m) REVERT: A 300 MET cc_start: 0.7359 (ttp) cc_final: 0.6302 (tpp) REVERT: A 332 ILE cc_start: 0.7019 (mm) cc_final: 0.6728 (tt) REVERT: B 23 LEU cc_start: 0.7015 (mp) cc_final: 0.6664 (mt) REVERT: B 99 CYS cc_start: 0.8053 (p) cc_final: 0.7491 (m) REVERT: B 119 GLN cc_start: 0.8254 (tp40) cc_final: 0.7966 (mm-40) REVERT: B 122 LEU cc_start: 0.8409 (mt) cc_final: 0.8206 (mp) REVERT: B 149 LEU cc_start: 0.7027 (tp) cc_final: 0.6667 (tp) REVERT: B 195 LYS cc_start: 0.7808 (tttt) cc_final: 0.7456 (tttt) REVERT: C 52 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7923 (mtt-85) REVERT: C 61 MET cc_start: 0.7599 (tmm) cc_final: 0.7317 (tmm) REVERT: C 217 MET cc_start: 0.7728 (mtp) cc_final: 0.7442 (mtp) REVERT: C 227 SER cc_start: 0.8058 (t) cc_final: 0.7716 (m) REVERT: C 277 SER cc_start: 0.7775 (t) cc_final: 0.7170 (m) REVERT: E 67 ARG cc_start: 0.6814 (mtp180) cc_final: 0.6481 (mtp180) REVERT: E 98 ARG cc_start: 0.7826 (ttp-170) cc_final: 0.7155 (ttt180) outliers start: 23 outliers final: 16 residues processed: 186 average time/residue: 0.1058 time to fit residues: 25.9020 Evaluate side-chains 173 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 A residue 364 ASN Chi-restraints excluded: chain B residue 21 LYS 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 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 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.0870 chunk 30 optimal weight: 0.3980 chunk 10 optimal weight: 0.0870 chunk 58 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 95 optimal weight: 0.8980 chunk 41 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 overall best weight: 0.3736 ------------------------------------------------------------------------------- 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 E 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.149003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.130010 restraints weight = 12421.269| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.17 r_work: 0.3606 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3455 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8321 Z= 0.109 Angle : 0.512 11.468 11343 Z= 0.271 Chirality : 0.042 0.144 1346 Planarity : 0.003 0.036 1422 Dihedral : 7.798 151.571 1236 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.93 % Allowed : 10.87 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.27), residues: 1065 helix: 2.37 (0.30), residues: 341 sheet: 1.29 (0.30), residues: 295 loop : 0.27 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 225 TYR 0.014 0.001 TYR E 178 PHE 0.017 0.001 PHE B 167 TRP 0.014 0.001 TRP A 130 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8318) covalent geometry : angle 0.51180 (11339) SS BOND : bond 0.00359 ( 2) SS BOND : angle 0.59791 ( 4) hydrogen bonds : bond 0.04211 ( 389) hydrogen bonds : angle 4.22663 ( 1098) Misc. bond : bond 0.00118 ( 1) *********************** 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 184 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7373 (ttp) cc_final: 0.6406 (tpp) REVERT: A 332 ILE cc_start: 0.7097 (mm) cc_final: 0.6790 (tt) REVERT: A 372 ASN cc_start: 0.6334 (t0) cc_final: 0.6067 (m-40) REVERT: B 23 LEU cc_start: 0.7154 (mp) cc_final: 0.6850 (mt) REVERT: B 95 LYS cc_start: 0.8335 (mmmt) cc_final: 0.8134 (mmtm) REVERT: B 99 CYS cc_start: 0.7965 (p) cc_final: 0.7442 (m) REVERT: B 117 ARG cc_start: 0.8011 (mtp85) cc_final: 0.7649 (mtp180) REVERT: B 119 GLN cc_start: 0.8218 (tp40) cc_final: 0.7967 (mm-40) REVERT: B 122 LEU cc_start: 0.8353 (mt) cc_final: 0.8147 (mp) REVERT: B 195 LYS cc_start: 0.7648 (tttt) cc_final: 0.7284 (tttt) REVERT: C 52 ARG cc_start: 0.8145 (mtt-85) cc_final: 0.7843 (mtt-85) REVERT: C 217 MET cc_start: 0.7661 (mtp) cc_final: 0.7398 (mtp) REVERT: C 227 SER cc_start: 0.8053 (t) cc_final: 0.7768 (m) REVERT: C 277 SER cc_start: 0.7749 (t) cc_final: 0.7091 (m) REVERT: E 67 ARG cc_start: 0.6806 (mtp180) cc_final: 0.6583 (mtp180) REVERT: E 106 SER cc_start: 0.8670 (t) cc_final: 0.8441 (p) outliers start: 24 outliers final: 18 residues processed: 171 average time/residue: 0.1149 time to fit residues: 25.3778 Evaluate side-chains 175 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 A residue 364 ASN Chi-restraints excluded: chain B residue 103 VAL 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 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 223 THR Chi-restraints excluded: chain C residue 281 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 82 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 86 optimal weight: 0.0570 chunk 15 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 92 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 overall best weight: 0.7102 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.146894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.127843 restraints weight = 12564.662| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.19 r_work: 0.3598 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3445 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8321 Z= 0.135 Angle : 0.528 10.105 11343 Z= 0.280 Chirality : 0.043 0.136 1346 Planarity : 0.004 0.043 1422 Dihedral : 7.802 151.358 1236 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.91 % Allowed : 10.62 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.69 (0.27), residues: 1065 helix: 2.22 (0.29), residues: 350 sheet: 1.19 (0.30), residues: 293 loop : 0.20 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 49 TYR 0.019 0.002 TYR E 59 PHE 0.016 0.002 PHE C 199 TRP 0.014 0.001 TRP A 130 HIS 0.004 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 8318) covalent geometry : angle 0.52830 (11339) SS BOND : bond 0.00328 ( 2) SS BOND : angle 0.49237 ( 4) hydrogen bonds : bond 0.04525 ( 389) hydrogen bonds : angle 4.16918 ( 1098) Misc. bond : bond 0.00084 ( 1) *********************** 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 191 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 MET cc_start: 0.7357 (ttp) cc_final: 0.6515 (tpp) REVERT: A 332 ILE cc_start: 0.7053 (mm) cc_final: 0.6774 (tt) REVERT: A 372 ASN cc_start: 0.6480 (t0) cc_final: 0.6118 (m-40) REVERT: B 23 LEU cc_start: 0.7120 (mp) cc_final: 0.6742 (mt) REVERT: B 95 LYS cc_start: 0.8355 (mmmt) cc_final: 0.8073 (mmtp) REVERT: B 99 CYS cc_start: 0.7964 (p) cc_final: 0.7459 (m) REVERT: B 117 ARG cc_start: 0.7992 (mtp85) cc_final: 0.7621 (mtp180) REVERT: B 119 GLN cc_start: 0.8239 (tp40) cc_final: 0.7987 (mm-40) REVERT: B 195 LYS cc_start: 0.7630 (tttt) cc_final: 0.7341 (tttt) REVERT: C 52 ARG cc_start: 0.8146 (mtt-85) cc_final: 0.7863 (mtt-85) REVERT: C 117 LEU cc_start: 0.8185 (mt) cc_final: 0.7794 (mt) REVERT: C 188 MET cc_start: 0.7434 (mmm) cc_final: 0.7082 (mmm) REVERT: C 217 MET cc_start: 0.7667 (mtp) cc_final: 0.7392 (mtp) REVERT: C 227 SER cc_start: 0.8087 (t) cc_final: 0.7741 (m) REVERT: C 234 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6442 (m-80) REVERT: C 277 SER cc_start: 0.7722 (t) cc_final: 0.7068 (m) REVERT: C 340 ASN cc_start: 0.7786 (t0) cc_final: 0.7426 (t0) REVERT: E 67 ARG cc_start: 0.6815 (mtp180) cc_final: 0.6480 (mtp180) outliers start: 32 outliers final: 23 residues processed: 173 average time/residue: 0.1172 time to fit residues: 26.1831 Evaluate side-chains 179 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 155 time to evaluate : 0.293 ------------------------------------------------------------------------------- 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 364 ASN Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 103 VAL 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 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 196 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 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 106 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 100 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 91 optimal weight: 0.8980 chunk 70 optimal weight: 0.0770 chunk 20 optimal weight: 0.0870 chunk 8 optimal weight: 0.5980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 98 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.148289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.129321 restraints weight = 12431.013| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.17 r_work: 0.3616 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8321 Z= 0.101 Angle : 0.486 9.680 11343 Z= 0.259 Chirality : 0.042 0.131 1346 Planarity : 0.003 0.041 1422 Dihedral : 7.696 150.781 1236 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.17 % Allowed : 12.45 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.27), residues: 1065 helix: 2.37 (0.30), residues: 349 sheet: 1.10 (0.29), residues: 300 loop : 0.19 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 93 TYR 0.012 0.001 TYR E 178 PHE 0.017 0.001 PHE B 215 TRP 0.014 0.001 TRP A 130 HIS 0.003 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 8318) covalent geometry : angle 0.48633 (11339) SS BOND : bond 0.00303 ( 2) SS BOND : angle 0.44201 ( 4) hydrogen bonds : bond 0.03864 ( 389) hydrogen bonds : angle 4.04303 ( 1098) Misc. bond : bond 0.00056 ( 1) *********************** 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 180 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.6924 (mtt) cc_final: 0.6502 (mtp) REVERT: A 300 MET cc_start: 0.7298 (ttp) cc_final: 0.6506 (tpp) REVERT: A 329 ILE cc_start: 0.6133 (mm) cc_final: 0.5898 (mm) REVERT: A 332 ILE cc_start: 0.6989 (mm) cc_final: 0.6715 (tt) REVERT: A 371 PHE cc_start: 0.4872 (m-10) cc_final: 0.4649 (m-10) REVERT: B 23 LEU cc_start: 0.7086 (mp) cc_final: 0.6694 (mt) REVERT: B 95 LYS cc_start: 0.8325 (mmmt) cc_final: 0.8028 (mmtp) REVERT: B 99 CYS cc_start: 0.7951 (p) cc_final: 0.7431 (m) REVERT: B 119 GLN cc_start: 0.8255 (tp40) cc_final: 0.8044 (mm-40) REVERT: B 149 LEU cc_start: 0.7123 (tp) cc_final: 0.6863 (tp) REVERT: B 225 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7571 (mmm160) REVERT: C 52 ARG cc_start: 0.8158 (mtt-85) cc_final: 0.7878 (mtt-85) REVERT: C 117 LEU cc_start: 0.8158 (mt) cc_final: 0.7740 (mt) REVERT: C 188 MET cc_start: 0.7383 (mmm) cc_final: 0.7094 (mmm) REVERT: C 227 SER cc_start: 0.8045 (t) cc_final: 0.7697 (m) REVERT: C 234 PHE cc_start: 0.7194 (OUTLIER) cc_final: 0.6466 (m-80) REVERT: C 277 SER cc_start: 0.7699 (t) cc_final: 0.7057 (m) REVERT: C 340 ASN cc_start: 0.7786 (t0) cc_final: 0.7448 (t0) REVERT: E 67 ARG cc_start: 0.6823 (mtp180) cc_final: 0.6504 (mtp180) outliers start: 26 outliers final: 19 residues processed: 166 average time/residue: 0.1105 time to fit residues: 24.1932 Evaluate side-chains 168 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 238 ILE 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 103 VAL 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 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 223 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 104 optimal weight: 5.9990 chunk 23 optimal weight: 0.0970 chunk 83 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 30 optimal weight: 0.0980 chunk 70 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 66 optimal weight: 1.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.147695 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.128775 restraints weight = 12311.321| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.15 r_work: 0.3608 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8321 Z= 0.114 Angle : 0.510 10.137 11343 Z= 0.265 Chirality : 0.042 0.131 1346 Planarity : 0.003 0.043 1422 Dihedral : 7.694 150.456 1236 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.91 % Allowed : 12.09 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.27), residues: 1065 helix: 2.44 (0.29), residues: 349 sheet: 1.05 (0.29), residues: 305 loop : 0.18 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 93 TYR 0.014 0.001 TYR E 59 PHE 0.012 0.001 PHE B 215 TRP 0.014 0.001 TRP A 130 HIS 0.003 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 8318) covalent geometry : angle 0.51010 (11339) SS BOND : bond 0.00287 ( 2) SS BOND : angle 0.41534 ( 4) hydrogen bonds : bond 0.03995 ( 389) hydrogen bonds : angle 3.99367 ( 1098) Misc. bond : bond 0.00052 ( 1) *********************** 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 183 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.6896 (mtt) cc_final: 0.6474 (mtt) REVERT: A 300 MET cc_start: 0.7266 (ttp) cc_final: 0.6539 (tpp) REVERT: A 329 ILE cc_start: 0.6165 (mm) cc_final: 0.5948 (mm) REVERT: A 332 ILE cc_start: 0.7059 (mm) cc_final: 0.6817 (tt) REVERT: A 371 PHE cc_start: 0.5022 (m-10) cc_final: 0.4718 (m-10) REVERT: B 23 LEU cc_start: 0.7101 (mp) cc_final: 0.6800 (mt) REVERT: B 95 LYS cc_start: 0.8324 (mmmt) cc_final: 0.8107 (mmtm) REVERT: B 99 CYS cc_start: 0.7921 (p) cc_final: 0.7452 (m) REVERT: B 119 GLN cc_start: 0.8278 (tp40) cc_final: 0.8063 (mm-40) REVERT: B 149 LEU cc_start: 0.7087 (tp) cc_final: 0.6769 (tp) REVERT: C 52 ARG cc_start: 0.8194 (mtt-85) cc_final: 0.7876 (mtt-85) REVERT: C 117 LEU cc_start: 0.8155 (mt) cc_final: 0.7722 (mt) REVERT: C 188 MET cc_start: 0.7486 (mmm) cc_final: 0.7222 (mmm) REVERT: C 234 PHE cc_start: 0.7282 (OUTLIER) cc_final: 0.6547 (m-80) REVERT: C 277 SER cc_start: 0.7712 (t) cc_final: 0.7053 (m) REVERT: C 298 ASP cc_start: 0.7667 (t0) cc_final: 0.7394 (t0) REVERT: C 340 ASN cc_start: 0.7775 (t0) cc_final: 0.7470 (t0) REVERT: E 67 ARG cc_start: 0.6813 (mtp180) cc_final: 0.6599 (mtp180) outliers start: 32 outliers final: 25 residues processed: 167 average time/residue: 0.1065 time to fit residues: 23.4483 Evaluate side-chains 174 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 148 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 238 ILE 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 103 VAL 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 93 ILE Chi-restraints excluded: chain C residue 98 SER 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 196 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 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 8 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 11 optimal weight: 1.9990 chunk 14 optimal weight: 0.0040 chunk 40 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.148162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.129228 restraints weight = 12495.986| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 2.17 r_work: 0.3618 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8321 Z= 0.105 Angle : 0.506 10.461 11343 Z= 0.262 Chirality : 0.042 0.129 1346 Planarity : 0.003 0.043 1422 Dihedral : 7.656 150.040 1236 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.91 % Allowed : 12.94 % Favored : 83.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.27), residues: 1065 helix: 2.51 (0.29), residues: 349 sheet: 1.10 (0.30), residues: 298 loop : 0.13 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 169 TYR 0.012 0.001 TYR E 59 PHE 0.012 0.001 PHE C 199 TRP 0.014 0.001 TRP A 130 HIS 0.003 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8318) covalent geometry : angle 0.50569 (11339) SS BOND : bond 0.00280 ( 2) SS BOND : angle 0.40786 ( 4) hydrogen bonds : bond 0.03781 ( 389) hydrogen bonds : angle 3.95421 ( 1098) Misc. bond : bond 0.00043 ( 1) *********************** 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 182 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 107 MET cc_start: 0.6947 (mtt) cc_final: 0.6524 (mtt) REVERT: A 238 ILE cc_start: 0.7094 (OUTLIER) cc_final: 0.6471 (mm) REVERT: B 23 LEU cc_start: 0.7098 (mp) cc_final: 0.6785 (mt) REVERT: B 95 LYS cc_start: 0.8326 (mmmt) cc_final: 0.8030 (mmtp) REVERT: B 99 CYS cc_start: 0.7917 (p) cc_final: 0.7444 (m) REVERT: B 119 GLN cc_start: 0.8268 (tp40) cc_final: 0.8065 (mm-40) REVERT: C 52 ARG cc_start: 0.8188 (mtt-85) cc_final: 0.7886 (mtt-85) REVERT: C 117 LEU cc_start: 0.8141 (mt) cc_final: 0.7730 (mt) REVERT: C 188 MET cc_start: 0.7418 (mmm) cc_final: 0.7149 (mmm) REVERT: C 234 PHE cc_start: 0.7273 (OUTLIER) cc_final: 0.6559 (m-80) REVERT: C 258 ASP cc_start: 0.5982 (t0) cc_final: 0.5363 (t0) REVERT: C 277 SER cc_start: 0.7727 (t) cc_final: 0.7068 (m) REVERT: C 298 ASP cc_start: 0.7633 (t0) cc_final: 0.7321 (t0) REVERT: C 340 ASN cc_start: 0.7782 (t0) cc_final: 0.7483 (t0) REVERT: E 34 MET cc_start: 0.6972 (mmm) cc_final: 0.6663 (mmm) outliers start: 32 outliers final: 23 residues processed: 167 average time/residue: 0.1028 time to fit residues: 22.7041 Evaluate side-chains 171 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 VAL Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 359 VAL Chi-restraints excluded: chain B residue 20 ASP Chi-restraints excluded: chain B residue 103 VAL 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 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 196 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.7980 chunk 76 optimal weight: 0.0270 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.146980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.128050 restraints weight = 12395.361| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.16 r_work: 0.3600 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7092 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8321 Z= 0.124 Angle : 0.532 10.425 11343 Z= 0.276 Chirality : 0.042 0.135 1346 Planarity : 0.004 0.045 1422 Dihedral : 7.720 149.990 1236 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.66 % Allowed : 13.92 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.75 (0.27), residues: 1065 helix: 2.43 (0.29), residues: 356 sheet: 1.03 (0.30), residues: 300 loop : 0.19 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 169 TYR 0.017 0.001 TYR E 59 PHE 0.014 0.001 PHE C 234 TRP 0.013 0.001 TRP A 130 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 8318) covalent geometry : angle 0.53226 (11339) SS BOND : bond 0.00269 ( 2) SS BOND : angle 0.47839 ( 4) hydrogen bonds : bond 0.04229 ( 389) hydrogen bonds : angle 4.00332 ( 1098) Misc. bond : bond 0.00043 ( 1) *********************** 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 183 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 153 time to evaluate : 0.334 Fit side-chains revert: symmetry clash REVERT: A 107 MET cc_start: 0.6981 (mtt) cc_final: 0.6567 (mtt) REVERT: A 300 MET cc_start: 0.7119 (ttm) cc_final: 0.6650 (tpp) REVERT: B 23 LEU cc_start: 0.7076 (mp) cc_final: 0.6756 (mt) REVERT: B 95 LYS cc_start: 0.8321 (mmmt) cc_final: 0.8078 (mmtm) REVERT: B 99 CYS cc_start: 0.7904 (p) cc_final: 0.7429 (m) REVERT: B 119 GLN cc_start: 0.8281 (tp40) cc_final: 0.8070 (mm-40) REVERT: B 225 ARG cc_start: 0.8138 (mmm-85) cc_final: 0.7757 (mmm160) REVERT: C 49 ARG cc_start: 0.8220 (mpt180) cc_final: 0.8007 (mtt90) REVERT: C 52 ARG cc_start: 0.8188 (mtt-85) cc_final: 0.7896 (mtt-85) REVERT: C 117 LEU cc_start: 0.8136 (mt) cc_final: 0.7727 (mt) REVERT: C 150 ARG cc_start: 0.8164 (mmt-90) cc_final: 0.7949 (mmt-90) REVERT: C 188 MET cc_start: 0.7418 (mmm) cc_final: 0.7168 (mmm) REVERT: C 234 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6617 (m-80) REVERT: C 258 ASP cc_start: 0.5957 (t0) cc_final: 0.5359 (t0) REVERT: C 277 SER cc_start: 0.7710 (t) cc_final: 0.7003 (m) REVERT: C 298 ASP cc_start: 0.7641 (t0) cc_final: 0.7314 (t0) REVERT: E 34 MET cc_start: 0.6965 (mmm) cc_final: 0.6573 (mmm) outliers start: 30 outliers final: 25 residues processed: 169 average time/residue: 0.1051 time to fit residues: 23.3327 Evaluate side-chains 178 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE 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 93 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 196 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 39 optimal weight: 0.9990 chunk 90 optimal weight: 0.0980 chunk 41 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 57 optimal weight: 0.2980 chunk 6 optimal weight: 0.0980 chunk 28 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.148047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.129052 restraints weight = 12458.210| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.18 r_work: 0.3598 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 8321 Z= 0.106 Angle : 0.517 10.377 11343 Z= 0.267 Chirality : 0.042 0.130 1346 Planarity : 0.004 0.044 1422 Dihedral : 7.657 149.450 1236 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.66 % Allowed : 14.53 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.27), residues: 1065 helix: 2.49 (0.29), residues: 357 sheet: 1.05 (0.30), residues: 300 loop : 0.17 (0.32), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 169 TYR 0.011 0.001 TYR E 178 PHE 0.022 0.001 PHE E 227 TRP 0.015 0.001 TRP A 130 HIS 0.004 0.001 HIS E 220 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 8318) covalent geometry : angle 0.51737 (11339) SS BOND : bond 0.00406 ( 2) SS BOND : angle 0.64194 ( 4) hydrogen bonds : bond 0.03729 ( 389) hydrogen bonds : angle 3.97749 ( 1098) Misc. bond : bond 0.00030 ( 1) *********************** 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 181 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.238 Fit side-chains revert: symmetry clash REVERT: A 107 MET cc_start: 0.7046 (mtt) cc_final: 0.6631 (mtt) REVERT: A 300 MET cc_start: 0.7138 (ttm) cc_final: 0.6719 (tpp) REVERT: B 23 LEU cc_start: 0.7095 (mp) cc_final: 0.6757 (mt) REVERT: B 95 LYS cc_start: 0.8313 (mmmt) cc_final: 0.8057 (mmtm) REVERT: B 99 CYS cc_start: 0.7913 (p) cc_final: 0.7444 (m) REVERT: B 119 GLN cc_start: 0.8279 (tp40) cc_final: 0.8074 (mm-40) REVERT: B 149 LEU cc_start: 0.7179 (tp) cc_final: 0.6867 (tp) REVERT: B 225 ARG cc_start: 0.8123 (mmm-85) cc_final: 0.7750 (mmm160) REVERT: C 52 ARG cc_start: 0.8247 (mtt-85) cc_final: 0.7963 (mtt-85) REVERT: C 61 MET cc_start: 0.7636 (tmm) cc_final: 0.7378 (ppp) REVERT: C 68 ARG cc_start: 0.7322 (mtp180) cc_final: 0.6949 (mtp180) REVERT: C 117 LEU cc_start: 0.8114 (mt) cc_final: 0.7734 (mt) REVERT: C 150 ARG cc_start: 0.8144 (mmt-90) cc_final: 0.7914 (mmt-90) REVERT: C 188 MET cc_start: 0.7406 (mmm) cc_final: 0.7118 (mmm) REVERT: C 234 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6672 (m-80) REVERT: C 258 ASP cc_start: 0.5990 (t0) cc_final: 0.5387 (t0) REVERT: C 277 SER cc_start: 0.7712 (t) cc_final: 0.7064 (m) REVERT: C 298 ASP cc_start: 0.7585 (t0) cc_final: 0.7263 (t0) REVERT: E 34 MET cc_start: 0.6951 (mmm) cc_final: 0.6587 (mmm) outliers start: 30 outliers final: 23 residues processed: 169 average time/residue: 0.1075 time to fit residues: 23.8608 Evaluate side-chains 172 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 148 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 VAL 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 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 93 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 196 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 103 optimal weight: 2.9990 chunk 12 optimal weight: 0.0000 chunk 55 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 8 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.147224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.128267 restraints weight = 12473.082| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 2.17 r_work: 0.3602 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8321 Z= 0.124 Angle : 0.546 10.603 11343 Z= 0.280 Chirality : 0.043 0.146 1346 Planarity : 0.004 0.045 1422 Dihedral : 7.691 149.288 1236 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.17 % Allowed : 15.38 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.27), residues: 1065 helix: 2.41 (0.29), residues: 358 sheet: 1.03 (0.30), residues: 300 loop : 0.07 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 169 TYR 0.016 0.001 TYR E 59 PHE 0.020 0.002 PHE E 227 TRP 0.013 0.001 TRP A 130 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 8318) covalent geometry : angle 0.54566 (11339) SS BOND : bond 0.00337 ( 2) SS BOND : angle 0.68113 ( 4) hydrogen bonds : bond 0.04065 ( 389) hydrogen bonds : angle 4.00865 ( 1098) Misc. bond : bond 0.00037 ( 1) ********************** 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 178 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 107 MET cc_start: 0.6979 (mtt) cc_final: 0.6572 (mtt) REVERT: A 300 MET cc_start: 0.7173 (ttm) cc_final: 0.6742 (tpp) REVERT: B 23 LEU cc_start: 0.7065 (mp) cc_final: 0.6732 (mt) REVERT: B 95 LYS cc_start: 0.8296 (mmmt) cc_final: 0.8076 (mmtm) REVERT: B 99 CYS cc_start: 0.7871 (p) cc_final: 0.7424 (m) REVERT: B 119 GLN cc_start: 0.8286 (tp40) cc_final: 0.8077 (mm-40) REVERT: B 149 LEU cc_start: 0.7244 (tp) cc_final: 0.6904 (tp) REVERT: B 225 ARG cc_start: 0.8155 (mmm-85) cc_final: 0.7804 (mmm160) REVERT: C 52 ARG cc_start: 0.8221 (mtt-85) cc_final: 0.7920 (mtt-85) REVERT: C 117 LEU cc_start: 0.8112 (mt) cc_final: 0.7698 (mt) REVERT: C 150 ARG cc_start: 0.8166 (mmt-90) cc_final: 0.7952 (mmt-90) REVERT: C 188 MET cc_start: 0.7431 (mmm) cc_final: 0.7166 (mmm) REVERT: C 234 PHE cc_start: 0.7300 (OUTLIER) cc_final: 0.6627 (m-80) REVERT: C 258 ASP cc_start: 0.6022 (t0) cc_final: 0.5431 (t0) REVERT: C 277 SER cc_start: 0.7701 (t) cc_final: 0.7005 (m) REVERT: E 98 ARG cc_start: 0.7819 (ttp-170) cc_final: 0.7545 (ttp-170) outliers start: 26 outliers final: 23 residues processed: 168 average time/residue: 0.1065 time to fit residues: 23.4131 Evaluate side-chains 174 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 208 VAL 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 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 93 ILE Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 196 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 29 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 0 optimal weight: 8.9990 chunk 90 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 86 optimal weight: 0.0000 chunk 92 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 overall best weight: 0.6786 ------------------------------------------------------------------------------- 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 = 0.3951 r_free = 0.3951 target = 0.146638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.127707 restraints weight = 12471.860| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 2.19 r_work: 0.3589 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3440 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3440 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7097 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8321 Z= 0.131 Angle : 0.554 10.588 11343 Z= 0.287 Chirality : 0.043 0.172 1346 Planarity : 0.004 0.047 1422 Dihedral : 7.734 149.346 1236 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.30 % Allowed : 15.87 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.58 (0.27), residues: 1065 helix: 2.35 (0.29), residues: 359 sheet: 1.01 (0.30), residues: 295 loop : -0.05 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 169 TYR 0.017 0.001 TYR E 59 PHE 0.021 0.002 PHE E 227 TRP 0.013 0.001 TRP A 130 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8318) covalent geometry : angle 0.55416 (11339) SS BOND : bond 0.00349 ( 2) SS BOND : angle 0.69348 ( 4) hydrogen bonds : bond 0.04236 ( 389) hydrogen bonds : angle 4.04248 ( 1098) Misc. bond : bond 0.00032 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2472.71 seconds wall clock time: 42 minutes 59.81 seconds (2579.81 seconds total)