Starting phenix.real_space_refine on Fri Aug 22 22:44:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpg_27634/08_2025/8dpg_27634_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpg_27634/08_2025/8dpg_27634.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8dpg_27634/08_2025/8dpg_27634_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpg_27634/08_2025/8dpg_27634_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8dpg_27634/08_2025/8dpg_27634.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpg_27634/08_2025/8dpg_27634.map" } resolution = 3.6 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= 0.028 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 5237 2.51 5 N 1369 2.21 5 O 1500 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: 8162 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 1939 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: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1683 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 122 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 101 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 9, 'ASP:plan': 7, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 88 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: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'91Q': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.94, per 1000 atoms: 0.24 Number of scatterers: 8162 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: 4 Type Number sf(0) S 56 16.00 O 1500 8.00 N 1369 7.00 C 5237 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: 0.64 Conformation dependent library (CDL) restraints added in 356.7 milliseconds Enol-peptide restraints added in 238.4 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 39.2% alpha, 26.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 61 through 80 removed outlier: 3.520A pdb=" N ILE A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N SER A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 106 removed outlier: 5.010A pdb=" N PHE A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU A 92 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET A 93 " --> pdb=" O ASN A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 117 removed outlier: 3.561A pdb=" N LEU A 112 " --> pdb=" O PRO A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 158 removed outlier: 4.210A pdb=" N SER A 132 " --> pdb=" O PRO A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 166 Processing helix chain 'A' and resid 167 through 185 removed outlier: 3.693A pdb=" N ALA A 171 " --> pdb=" O SER A 167 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET A 173 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY A 184 " --> pdb=" O ALA A 180 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 194 removed outlier: 3.928A pdb=" N VAL A 191 " --> pdb=" O VAL A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 201 removed outlier: 4.006A pdb=" N VAL A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 removed outlier: 4.454A pdb=" N ILE A 217 " --> pdb=" O ASN A 213 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N SER A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N PHE A 220 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N VAL A 221 " --> pdb=" O ILE A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 245 removed outlier: 3.502A pdb=" N ALA A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 337 removed outlier: 4.329A pdb=" N GLU A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LYS A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N SER A 310 " --> pdb=" O GLU A 306 " (cutoff:3.500A) Proline residue: A 326 - end of helix removed outlier: 3.584A pdb=" N ILE A 329 " --> pdb=" O CYS A 325 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 360 removed outlier: 3.753A pdb=" N VAL A 352 " --> pdb=" O LYS A 348 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N TRP A 355 " --> pdb=" O ASN A 351 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 357 " --> pdb=" O PHE A 353 " (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: 3.895A pdb=" N GLU B 28 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS B 29 " --> pdb=" O GLU B 25 " (cutoff:3.500A) removed outlier: 3.609A 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: 3.590A pdb=" N CYS B 99 " --> pdb=" O TRP B 96 " (cutoff:3.500A) removed outlier: 3.837A 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: 4.099A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 removed outlier: 3.626A 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 203 removed outlier: 3.957A pdb=" N ALA B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER B 201 " --> pdb=" O PHE B 197 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 203 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 removed outlier: 3.591A pdb=" N ARG B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) removed outlier: 3.540A 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: 3.526A 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: 3.595A pdb=" N ASN D 24 " --> pdb=" O LYS D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 44 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: 3.581A 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: 3.583A pdb=" N PHE B 74 " --> pdb=" O PHE B 81 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLY B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 10.062A pdb=" N ALA B 105 " --> pdb=" O THR B 33 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ARG B 35 " --> pdb=" O ALA B 105 " (cutoff:3.500A) removed outlier: 8.407A pdb=" N ILE B 107 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU B 37 " --> pdb=" O ILE B 107 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL B 109 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU B 39 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 9.204A pdb=" N ASP B 111 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.716A 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: 6.846A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA C 328 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LEU C 318 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 6.366A 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: 4.006A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS C 91 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 6.106A 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: 7.030A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.533A 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: 6.911A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.197A 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: 3.983A pdb=" N SER C 189 " --> pdb=" O GLY C 202 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA C 203 " --> pdb=" O SER C 207 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 3.727A pdb=" N ALA C 231 " --> pdb=" O GLY C 244 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 4.150A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.573A 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: 3.845A 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: 6.180A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 3.745A 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: 6.180A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU E 117 " --> pdb=" O ALA E 92 " (cutoff:3.500A) removed outlier: 4.681A 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: 3.521A 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: 3.796A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.911A 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: 3.796A pdb=" N GLY E 213 " --> pdb=" O LEU E 233 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN E 219 " --> pdb=" O THR E 226 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THR E 226 " --> pdb=" O GLN E 219 " (cutoff:3.500A) 407 hydrogen bonds defined for protein. 1125 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: 1.00 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2619 1.34 - 1.46: 2014 1.46 - 1.58: 3614 1.58 - 1.70: 0 1.70 - 1.81: 83 Bond restraints: 8330 Sorted by residual: bond pdb=" C6 91Q A 501 " pdb=" N2 91Q A 501 " ideal model delta sigma weight residual 1.368 1.310 0.058 2.00e-02 2.50e+03 8.34e+00 bond pdb=" C7 91Q A 501 " pdb=" C8 91Q A 501 " ideal model delta sigma weight residual 1.412 1.357 0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" C9 91Q A 501 " pdb=" O1 91Q A 501 " ideal model delta sigma weight residual 1.349 1.394 -0.045 2.00e-02 2.50e+03 5.13e+00 bond pdb=" C4 91Q A 501 " pdb=" C5 91Q A 501 " ideal model delta sigma weight residual 1.494 1.522 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C5 91Q A 501 " pdb=" C8 91Q A 501 " ideal model delta sigma weight residual 1.437 1.412 0.025 2.00e-02 2.50e+03 1.56e+00 ... (remaining 8325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.30: 11286 2.30 - 4.60: 59 4.60 - 6.89: 7 6.89 - 9.19: 0 9.19 - 11.49: 2 Bond angle restraints: 11354 Sorted by residual: angle pdb=" C1 91Q A 501 " pdb=" N1 91Q A 501 " pdb=" C3 91Q A 501 " ideal model delta sigma weight residual 111.25 122.74 -11.49 3.00e+00 1.11e-01 1.47e+01 angle pdb=" CA LEU A 370 " pdb=" CB LEU A 370 " pdb=" CG LEU A 370 " ideal model delta sigma weight residual 116.30 126.12 -9.82 3.50e+00 8.16e-02 7.88e+00 angle pdb=" N VAL A 352 " pdb=" CA VAL A 352 " pdb=" C VAL A 352 " ideal model delta sigma weight residual 113.53 110.85 2.68 9.80e-01 1.04e+00 7.50e+00 angle pdb=" C ALA E 131 " pdb=" N THR E 132 " pdb=" CA THR E 132 " ideal model delta sigma weight residual 121.54 125.73 -4.19 1.91e+00 2.74e-01 4.82e+00 angle pdb=" N MET E 180 " pdb=" CA MET E 180 " pdb=" C MET E 180 " ideal model delta sigma weight residual 110.80 115.46 -4.66 2.13e+00 2.20e-01 4.79e+00 ... (remaining 11349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.60: 4860 28.60 - 57.21: 44 57.21 - 85.81: 7 85.81 - 114.42: 0 114.42 - 143.02: 2 Dihedral angle restraints: 4913 sinusoidal: 1749 harmonic: 3164 Sorted by residual: dihedral pdb=" C1 91Q A 501 " pdb=" C3 91Q A 501 " pdb=" N1 91Q A 501 " pdb=" C4 91Q A 501 " ideal model delta sinusoidal sigma weight residual -162.00 -18.98 -143.02 1 3.00e+01 1.11e-03 1.92e+01 dihedral pdb=" C2 91Q A 501 " pdb=" C3 91Q A 501 " pdb=" N1 91Q A 501 " pdb=" C4 91Q A 501 " ideal model delta sinusoidal sigma weight residual 73.77 -152.43 -133.80 1 3.00e+01 1.11e-03 1.80e+01 dihedral pdb=" CA PHE A 223 " pdb=" C PHE A 223 " pdb=" N PHE A 224 " pdb=" CA PHE A 224 " ideal model delta harmonic sigma weight residual -180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 4910 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 941 0.038 - 0.075: 295 0.075 - 0.113: 89 0.113 - 0.150: 19 0.150 - 0.188: 1 Chirality restraints: 1345 Sorted by residual: chirality pdb=" C17 CLR A 502 " pdb=" C13 CLR A 502 " pdb=" C16 CLR A 502 " pdb=" C20 CLR A 502 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.19 2.00e-01 2.50e+01 8.82e-01 chirality pdb=" CA ILE B 140 " pdb=" N ILE B 140 " pdb=" C ILE B 140 " pdb=" CB ILE B 140 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE C 273 " pdb=" N ILE C 273 " pdb=" C ILE C 273 " pdb=" CB ILE C 273 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 ... (remaining 1342 not shown) Planarity restraints: 1424 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " -0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO C 236 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 364 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO A 365 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C10 91Q A 501 " 0.003 2.00e-02 2.50e+03 6.35e-03 1.11e+00 pdb=" C11 91Q A 501 " 0.013 2.00e-02 2.50e+03 pdb=" C12 91Q A 501 " -0.005 2.00e-02 2.50e+03 pdb=" C4 91Q A 501 " 0.004 2.00e-02 2.50e+03 pdb=" C5 91Q A 501 " 0.008 2.00e-02 2.50e+03 pdb=" C6 91Q A 501 " 0.001 2.00e-02 2.50e+03 pdb=" C7 91Q A 501 " -0.006 2.00e-02 2.50e+03 pdb=" C8 91Q A 501 " -0.001 2.00e-02 2.50e+03 pdb=" C9 91Q A 501 " -0.008 2.00e-02 2.50e+03 pdb=" N2 91Q A 501 " -0.004 2.00e-02 2.50e+03 pdb=" O1 91Q A 501 " -0.006 2.00e-02 2.50e+03 ... (remaining 1421 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 130 2.70 - 3.25: 7506 3.25 - 3.80: 11937 3.80 - 4.35: 15434 4.35 - 4.90: 27077 Nonbonded interactions: 62084 Sorted by model distance: nonbonded pdb=" OG SER C 245 " pdb=" OD1 ASP C 247 " model vdw 2.151 3.040 nonbonded pdb=" OD2 ASP A 151 " pdb=" OH TYR B 243 " model vdw 2.201 3.040 nonbonded pdb=" OG SER C 161 " pdb=" OD1 ASP C 163 " model vdw 2.221 3.040 nonbonded pdb=" NH1 ARG B 93 " pdb=" OD1 ASP B 124 " model vdw 2.264 3.120 nonbonded pdb=" OG SER C 74 " pdb=" OD1 ASP C 76 " model vdw 2.264 3.040 ... (remaining 62079 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 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: 0.020 Process input model: 8.170 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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: 10.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6624 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.231 8333 Z= 0.277 Angle : 0.487 11.489 11358 Z= 0.260 Chirality : 0.041 0.188 1345 Planarity : 0.003 0.035 1424 Dihedral : 9.689 143.022 2859 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.61 % Allowed : 1.59 % Favored : 97.80 % 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: 1.82 (0.26), residues: 1065 helix: 2.15 (0.29), residues: 332 sheet: 1.44 (0.30), residues: 292 loop : 0.40 (0.30), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 157 TYR 0.008 0.001 TYR E 102 PHE 0.009 0.001 PHE C 199 TRP 0.011 0.001 TRP A 130 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 8330) covalent geometry : angle 0.48664 (11354) SS BOND : bond 0.00140 ( 2) SS BOND : angle 0.84401 ( 4) hydrogen bonds : bond 0.21935 ( 399) hydrogen bonds : angle 6.10371 ( 1125) Misc. bond : bond 0.23092 ( 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 183 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 178 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: B 195 LYS cc_start: 0.7304 (tttt) cc_final: 0.7033 (tttt) REVERT: C 61 MET cc_start: 0.7443 (tmm) cc_final: 0.6947 (tmm) REVERT: C 68 ARG cc_start: 0.7583 (mtp180) cc_final: 0.6620 (mtp180) REVERT: C 70 LEU cc_start: 0.6940 (tt) cc_final: 0.6707 (tp) REVERT: C 86 THR cc_start: 0.7691 (p) cc_final: 0.7400 (p) REVERT: C 130 GLU cc_start: 0.7079 (mp0) cc_final: 0.6756 (mp0) REVERT: C 135 VAL cc_start: 0.7991 (t) cc_final: 0.7752 (p) REVERT: C 243 THR cc_start: 0.7434 (t) cc_final: 0.7209 (p) REVERT: C 292 PHE cc_start: 0.7578 (m-10) cc_final: 0.7361 (m-80) REVERT: C 334 SER cc_start: 0.8135 (m) cc_final: 0.7466 (t) REVERT: E 98 ARG cc_start: 0.7723 (ttp-170) cc_final: 0.7256 (ptt180) REVERT: E 106 SER cc_start: 0.8469 (t) cc_final: 0.8073 (p) REVERT: E 162 LEU cc_start: 0.8462 (tp) cc_final: 0.8149 (tp) outliers start: 5 outliers final: 1 residues processed: 182 average time/residue: 0.0785 time to fit residues: 19.4384 Evaluate side-chains 140 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 132 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.0000 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN C 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.146906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128442 restraints weight = 11716.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.130739 restraints weight = 7768.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.132492 restraints weight = 5828.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.132969 restraints weight = 4713.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.133536 restraints weight = 4313.094| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8333 Z= 0.127 Angle : 0.534 7.126 11358 Z= 0.286 Chirality : 0.043 0.147 1345 Planarity : 0.004 0.038 1424 Dihedral : 6.801 81.119 1231 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.44 % Allowed : 7.44 % Favored : 90.12 % 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: 1.98 (0.27), residues: 1065 helix: 2.31 (0.30), residues: 347 sheet: 1.67 (0.31), residues: 274 loop : 0.32 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 18 TYR 0.014 0.001 TYR E 178 PHE 0.011 0.002 PHE A 317 TRP 0.011 0.001 TRP A 130 HIS 0.006 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 8330) covalent geometry : angle 0.53343 (11354) SS BOND : bond 0.00635 ( 2) SS BOND : angle 1.47772 ( 4) hydrogen bonds : bond 0.04710 ( 399) hydrogen bonds : angle 4.37777 ( 1125) Misc. bond : bond 0.00005 ( 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 166 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 146 time to evaluate : 0.271 Fit side-chains REVERT: B 195 LYS cc_start: 0.7249 (tttt) cc_final: 0.6993 (tttt) REVERT: C 61 MET cc_start: 0.7423 (tmm) cc_final: 0.6859 (tmm) REVERT: C 68 ARG cc_start: 0.7440 (mtp180) cc_final: 0.6605 (mtp180) REVERT: C 135 VAL cc_start: 0.8041 (t) cc_final: 0.7820 (p) REVERT: C 292 PHE cc_start: 0.7386 (m-10) cc_final: 0.7127 (m-80) REVERT: C 303 ASP cc_start: 0.6907 (t0) cc_final: 0.6690 (m-30) REVERT: E 98 ARG cc_start: 0.7564 (ttp-170) cc_final: 0.7142 (ptt180) REVERT: E 106 SER cc_start: 0.8512 (t) cc_final: 0.8176 (p) REVERT: E 162 LEU cc_start: 0.8372 (tp) cc_final: 0.8100 (tp) outliers start: 20 outliers final: 9 residues processed: 154 average time/residue: 0.0887 time to fit residues: 18.3672 Evaluate side-chains 148 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 187 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN C 88 ASN C 119 ASN C 230 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 = 0.3787 r_free = 0.3787 target = 0.140960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.121876 restraints weight = 11542.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.124419 restraints weight = 7286.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.126096 restraints weight = 5308.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.127155 restraints weight = 4288.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.127938 restraints weight = 3717.957| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8333 Z= 0.188 Angle : 0.601 10.553 11358 Z= 0.319 Chirality : 0.045 0.158 1345 Planarity : 0.004 0.040 1424 Dihedral : 6.755 69.791 1230 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.80 % Allowed : 10.73 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.25 (0.29), residues: 343 sheet: 1.44 (0.31), residues: 278 loop : -0.01 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 219 TYR 0.018 0.002 TYR E 59 PHE 0.022 0.003 PHE C 199 TRP 0.017 0.002 TRP C 211 HIS 0.008 0.002 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 8330) covalent geometry : angle 0.60006 (11354) SS BOND : bond 0.00746 ( 2) SS BOND : angle 1.50743 ( 4) hydrogen bonds : bond 0.05824 ( 399) hydrogen bonds : angle 4.29320 ( 1125) Misc. bond : bond 0.00009 ( 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 170 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.211 Fit side-chains revert: symmetry clash REVERT: A 350 LEU cc_start: 0.7073 (mt) cc_final: 0.6827 (tt) REVERT: C 61 MET cc_start: 0.7344 (tmm) cc_final: 0.6864 (tmm) REVERT: C 68 ARG cc_start: 0.7419 (mtp180) cc_final: 0.6416 (mtp180) REVERT: C 135 VAL cc_start: 0.8160 (t) cc_final: 0.7863 (p) REVERT: C 255 LEU cc_start: 0.7340 (mt) cc_final: 0.6940 (mp) REVERT: C 292 PHE cc_start: 0.7412 (m-10) cc_final: 0.7090 (m-10) REVERT: E 18 ARG cc_start: 0.6838 (mmm-85) cc_final: 0.6596 (mmm-85) REVERT: E 98 ARG cc_start: 0.7576 (ttp-170) cc_final: 0.6966 (ptt180) REVERT: E 106 SER cc_start: 0.8578 (t) cc_final: 0.8251 (p) REVERT: E 181 SER cc_start: 0.8276 (m) cc_final: 0.8049 (m) outliers start: 23 outliers final: 15 residues processed: 164 average time/residue: 0.0897 time to fit residues: 20.0213 Evaluate side-chains 154 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 187 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 38 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.0870 chunk 59 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 17 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.142741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.124495 restraints weight = 11764.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.126813 restraints weight = 7731.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.128153 restraints weight = 5790.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.129249 restraints weight = 4800.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129569 restraints weight = 4219.184| |-----------------------------------------------------------------------------| r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6885 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8333 Z= 0.121 Angle : 0.511 7.974 11358 Z= 0.272 Chirality : 0.042 0.157 1345 Planarity : 0.003 0.036 1424 Dihedral : 5.950 53.790 1230 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.56 % Allowed : 12.20 % Favored : 85.24 % 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 (0.26), residues: 1065 helix: 2.34 (0.29), residues: 347 sheet: 1.51 (0.31), residues: 274 loop : -0.03 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 18 TYR 0.013 0.001 TYR E 178 PHE 0.013 0.001 PHE C 199 TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8330) covalent geometry : angle 0.51069 (11354) SS BOND : bond 0.00476 ( 2) SS BOND : angle 0.95673 ( 4) hydrogen bonds : bond 0.04280 ( 399) hydrogen bonds : angle 4.01444 ( 1125) Misc. bond : bond 0.00016 ( 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 159 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 93 MET cc_start: 0.6518 (tpp) cc_final: 0.6084 (tpt) REVERT: B 195 LYS cc_start: 0.7191 (tttt) cc_final: 0.6946 (tttt) REVERT: C 61 MET cc_start: 0.7384 (tmm) cc_final: 0.7050 (tmm) REVERT: C 68 ARG cc_start: 0.7356 (mtp180) cc_final: 0.6347 (mtp180) REVERT: C 135 VAL cc_start: 0.8146 (t) cc_final: 0.7837 (p) REVERT: C 252 LEU cc_start: 0.8740 (tt) cc_final: 0.8491 (tp) REVERT: C 255 LEU cc_start: 0.7437 (mt) cc_final: 0.7025 (mp) REVERT: C 292 PHE cc_start: 0.7448 (m-10) cc_final: 0.7148 (m-10) REVERT: E 18 ARG cc_start: 0.6858 (mmm-85) cc_final: 0.6557 (mmm-85) REVERT: E 98 ARG cc_start: 0.7543 (ttp-170) cc_final: 0.6947 (ttt180) REVERT: E 106 SER cc_start: 0.8555 (t) cc_final: 0.8171 (p) outliers start: 21 outliers final: 16 residues processed: 152 average time/residue: 0.0846 time to fit residues: 17.4837 Evaluate side-chains 152 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 136 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 263 THR Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 0.1980 chunk 82 optimal weight: 0.1980 chunk 83 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 104 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 3.9990 chunk 2 optimal weight: 0.0570 chunk 71 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.142942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.124911 restraints weight = 11692.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127224 restraints weight = 7693.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.128472 restraints weight = 5822.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.129631 restraints weight = 4821.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.130065 restraints weight = 4184.366| |-----------------------------------------------------------------------------| r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8333 Z= 0.109 Angle : 0.493 9.663 11358 Z= 0.262 Chirality : 0.042 0.154 1345 Planarity : 0.003 0.035 1424 Dihedral : 5.641 53.379 1230 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.80 % Allowed : 13.54 % Favored : 83.66 % 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: 1.78 (0.26), residues: 1065 helix: 2.43 (0.29), residues: 347 sheet: 1.56 (0.31), residues: 274 loop : -0.05 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 18 TYR 0.015 0.001 TYR E 178 PHE 0.013 0.001 PHE C 199 TRP 0.010 0.001 TRP C 211 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 8330) covalent geometry : angle 0.49272 (11354) SS BOND : bond 0.00440 ( 2) SS BOND : angle 0.92411 ( 4) hydrogen bonds : bond 0.03964 ( 399) hydrogen bonds : angle 3.89696 ( 1125) Misc. bond : bond 0.00020 ( 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 159 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 136 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: A 93 MET cc_start: 0.6469 (tpp) cc_final: 0.5930 (tpt) REVERT: C 61 MET cc_start: 0.7442 (tmm) cc_final: 0.7158 (tmm) REVERT: C 68 ARG cc_start: 0.7332 (mtp180) cc_final: 0.6377 (mtp180) REVERT: C 135 VAL cc_start: 0.8154 (t) cc_final: 0.7787 (p) REVERT: C 255 LEU cc_start: 0.7414 (mt) cc_final: 0.6975 (mp) REVERT: C 292 PHE cc_start: 0.7429 (m-10) cc_final: 0.7109 (m-10) REVERT: E 98 ARG cc_start: 0.7519 (ttp-170) cc_final: 0.6895 (ttt180) REVERT: E 106 SER cc_start: 0.8547 (t) cc_final: 0.8127 (p) REVERT: E 132 THR cc_start: 0.6653 (OUTLIER) cc_final: 0.6373 (m) REVERT: E 218 MET cc_start: 0.7575 (ttt) cc_final: 0.7310 (ttt) outliers start: 23 outliers final: 17 residues processed: 151 average time/residue: 0.0858 time to fit residues: 17.5931 Evaluate side-chains 154 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 100 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 166 ASN C 119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.142470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.124463 restraints weight = 11612.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.126644 restraints weight = 7650.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.128237 restraints weight = 5731.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.129221 restraints weight = 4650.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.129496 restraints weight = 4075.866| |-----------------------------------------------------------------------------| r_work (final): 0.3629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6895 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8333 Z= 0.123 Angle : 0.504 9.710 11358 Z= 0.268 Chirality : 0.042 0.151 1345 Planarity : 0.003 0.037 1424 Dihedral : 5.564 54.175 1230 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.56 % Allowed : 14.27 % Favored : 83.17 % 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: 2.45 (0.29), residues: 347 sheet: 1.55 (0.31), residues: 274 loop : -0.09 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 18 TYR 0.015 0.001 TYR E 178 PHE 0.015 0.002 PHE C 199 TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8330) covalent geometry : angle 0.50393 (11354) SS BOND : bond 0.00488 ( 2) SS BOND : angle 0.99549 ( 4) hydrogen bonds : bond 0.04234 ( 399) hydrogen bonds : angle 3.85811 ( 1125) Misc. bond : bond 0.00019 ( 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 154 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 93 MET cc_start: 0.6407 (tpp) cc_final: 0.5612 (tpt) REVERT: A 332 ILE cc_start: 0.7678 (mm) cc_final: 0.7163 (tt) REVERT: C 61 MET cc_start: 0.7420 (tmm) cc_final: 0.6850 (tmm) REVERT: C 68 ARG cc_start: 0.7354 (mtp180) cc_final: 0.6425 (mtp180) REVERT: C 135 VAL cc_start: 0.8164 (t) cc_final: 0.7810 (p) REVERT: C 255 LEU cc_start: 0.7461 (mt) cc_final: 0.6989 (mp) REVERT: C 292 PHE cc_start: 0.7417 (m-10) cc_final: 0.7094 (m-10) REVERT: E 18 ARG cc_start: 0.6557 (mmm-85) cc_final: 0.6353 (mmm-85) REVERT: E 106 SER cc_start: 0.8542 (t) cc_final: 0.8174 (p) REVERT: E 132 THR cc_start: 0.6592 (OUTLIER) cc_final: 0.6328 (m) REVERT: E 218 MET cc_start: 0.7674 (ttt) cc_final: 0.7466 (ttp) outliers start: 21 outliers final: 19 residues processed: 147 average time/residue: 0.0866 time to fit residues: 17.5031 Evaluate side-chains 151 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 181 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN C 119 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.141429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.123387 restraints weight = 11579.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.125591 restraints weight = 7653.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.127180 restraints weight = 5724.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.128082 restraints weight = 4716.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128559 restraints weight = 4139.606| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.3587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8333 Z= 0.137 Angle : 0.526 9.119 11358 Z= 0.278 Chirality : 0.043 0.155 1345 Planarity : 0.004 0.045 1424 Dihedral : 5.592 54.096 1230 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.56 % Allowed : 14.88 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.72 (0.27), residues: 1065 helix: 2.44 (0.29), residues: 347 sheet: 1.52 (0.31), residues: 276 loop : -0.15 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 18 TYR 0.012 0.001 TYR E 178 PHE 0.016 0.002 PHE C 199 TRP 0.011 0.001 TRP C 211 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 8330) covalent geometry : angle 0.52534 (11354) SS BOND : bond 0.00522 ( 2) SS BOND : angle 1.03557 ( 4) hydrogen bonds : bond 0.04528 ( 399) hydrogen bonds : angle 3.91631 ( 1125) Misc. bond : bond 0.00014 ( 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 161 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 0.303 Fit side-chains REVERT: A 332 ILE cc_start: 0.7712 (mm) cc_final: 0.7213 (tt) REVERT: C 61 MET cc_start: 0.7357 (tmm) cc_final: 0.6854 (tmm) REVERT: C 68 ARG cc_start: 0.7355 (mtp180) cc_final: 0.6420 (mtp180) REVERT: C 135 VAL cc_start: 0.8158 (t) cc_final: 0.7780 (p) REVERT: C 255 LEU cc_start: 0.7391 (mt) cc_final: 0.6966 (mp) REVERT: C 292 PHE cc_start: 0.7381 (m-10) cc_final: 0.7057 (m-10) REVERT: C 296 VAL cc_start: 0.8383 (t) cc_final: 0.8176 (m) REVERT: E 18 ARG cc_start: 0.6525 (mmm-85) cc_final: 0.6278 (mmm-85) REVERT: E 98 ARG cc_start: 0.7551 (ttp-170) cc_final: 0.7073 (ttt180) REVERT: E 106 SER cc_start: 0.8490 (t) cc_final: 0.8138 (p) REVERT: E 132 THR cc_start: 0.6696 (OUTLIER) cc_final: 0.6475 (m) outliers start: 21 outliers final: 17 residues processed: 154 average time/residue: 0.0850 time to fit residues: 17.9983 Evaluate side-chains 157 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 236 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 78 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 50 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 225 HIS C 237 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.140697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.123365 restraints weight = 11605.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.124859 restraints weight = 8078.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.125164 restraints weight = 6122.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.127167 restraints weight = 5730.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.127248 restraints weight = 4645.372| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8333 Z= 0.152 Angle : 0.545 9.593 11358 Z= 0.290 Chirality : 0.043 0.142 1345 Planarity : 0.004 0.045 1424 Dihedral : 5.679 53.344 1230 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.80 % Allowed : 15.73 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.64 (0.27), residues: 1065 helix: 2.40 (0.29), residues: 347 sheet: 1.47 (0.31), residues: 276 loop : -0.22 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 18 TYR 0.016 0.002 TYR E 178 PHE 0.017 0.002 PHE C 199 TRP 0.012 0.002 TRP C 211 HIS 0.005 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 8330) covalent geometry : angle 0.54466 (11354) SS BOND : bond 0.00563 ( 2) SS BOND : angle 1.15667 ( 4) hydrogen bonds : bond 0.04729 ( 399) hydrogen bonds : angle 3.93133 ( 1125) Misc. bond : bond 0.00012 ( 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 165 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 142 time to evaluate : 0.181 Fit side-chains REVERT: A 332 ILE cc_start: 0.7719 (mm) cc_final: 0.7227 (tt) REVERT: C 61 MET cc_start: 0.7348 (tmm) cc_final: 0.6823 (tmm) REVERT: C 68 ARG cc_start: 0.7322 (mtp180) cc_final: 0.6432 (mtp180) REVERT: C 135 VAL cc_start: 0.8124 (t) cc_final: 0.7774 (p) REVERT: C 255 LEU cc_start: 0.7449 (mt) cc_final: 0.7004 (mp) REVERT: C 292 PHE cc_start: 0.7394 (m-10) cc_final: 0.7082 (m-10) REVERT: E 18 ARG cc_start: 0.6618 (mmm-85) cc_final: 0.6331 (mmm-85) REVERT: E 98 ARG cc_start: 0.7550 (ttp-170) cc_final: 0.7317 (ttp-170) REVERT: E 106 SER cc_start: 0.8486 (t) cc_final: 0.8133 (p) REVERT: E 109 ASP cc_start: 0.6665 (p0) cc_final: 0.6456 (p0) REVERT: E 132 THR cc_start: 0.6653 (OUTLIER) cc_final: 0.6441 (m) outliers start: 23 outliers final: 20 residues processed: 156 average time/residue: 0.0804 time to fit residues: 17.1203 Evaluate side-chains 158 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 261 LEU Chi-restraints excluded: chain C residue 322 ASP Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 103 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 40 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 86 optimal weight: 0.0270 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN C 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.141579 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.124621 restraints weight = 11583.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.125259 restraints weight = 8411.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.125889 restraints weight = 6987.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.126453 restraints weight = 6146.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.126638 restraints weight = 5482.785| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8333 Z= 0.120 Angle : 0.518 9.588 11358 Z= 0.275 Chirality : 0.042 0.143 1345 Planarity : 0.004 0.041 1424 Dihedral : 5.546 52.957 1230 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.20 % Allowed : 16.46 % Favored : 81.34 % 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: 1.72 (0.27), residues: 1065 helix: 2.44 (0.29), residues: 347 sheet: 1.51 (0.31), residues: 276 loop : -0.15 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 157 TYR 0.015 0.001 TYR E 178 PHE 0.013 0.001 PHE C 199 TRP 0.010 0.001 TRP B 96 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8330) covalent geometry : angle 0.51789 (11354) SS BOND : bond 0.00443 ( 2) SS BOND : angle 0.93647 ( 4) hydrogen bonds : bond 0.04133 ( 399) hydrogen bonds : angle 3.82396 ( 1125) Misc. bond : bond 0.00013 ( 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 152 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 134 time to evaluate : 0.322 Fit side-chains REVERT: A 332 ILE cc_start: 0.7727 (mm) cc_final: 0.7258 (tt) REVERT: C 61 MET cc_start: 0.7374 (tmm) cc_final: 0.6978 (tmm) REVERT: C 68 ARG cc_start: 0.7263 (mtp180) cc_final: 0.6451 (mtp180) REVERT: C 135 VAL cc_start: 0.8133 (t) cc_final: 0.7793 (p) REVERT: C 255 LEU cc_start: 0.7485 (mt) cc_final: 0.6979 (mp) REVERT: C 292 PHE cc_start: 0.7391 (m-10) cc_final: 0.7128 (m-10) REVERT: E 18 ARG cc_start: 0.6574 (mmm-85) cc_final: 0.6273 (mmm-85) REVERT: E 98 ARG cc_start: 0.7525 (ttp-170) cc_final: 0.7302 (ttp-170) REVERT: E 106 SER cc_start: 0.8477 (t) cc_final: 0.8110 (p) REVERT: E 218 MET cc_start: 0.7665 (ttt) cc_final: 0.7406 (ttt) outliers start: 18 outliers final: 16 residues processed: 145 average time/residue: 0.0912 time to fit residues: 17.9002 Evaluate side-chains 148 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 132 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 110 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 83 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 80 optimal weight: 0.0770 chunk 55 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 78 optimal weight: 4.9990 chunk 13 optimal weight: 0.2980 overall best weight: 0.4938 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.142111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.125080 restraints weight = 11571.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.125950 restraints weight = 8510.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.126645 restraints weight = 6991.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.127172 restraints weight = 6224.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.127359 restraints weight = 5440.195| |-----------------------------------------------------------------------------| r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8333 Z= 0.113 Angle : 0.515 9.944 11358 Z= 0.273 Chirality : 0.042 0.152 1345 Planarity : 0.004 0.040 1424 Dihedral : 5.489 53.040 1230 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.20 % Allowed : 16.59 % Favored : 81.22 % 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: 1.78 (0.27), residues: 1065 helix: 2.51 (0.29), residues: 347 sheet: 1.52 (0.31), residues: 276 loop : -0.12 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 157 TYR 0.017 0.001 TYR E 178 PHE 0.012 0.001 PHE C 199 TRP 0.010 0.001 TRP B 96 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 8330) covalent geometry : angle 0.51508 (11354) SS BOND : bond 0.00405 ( 2) SS BOND : angle 0.90172 ( 4) hydrogen bonds : bond 0.03978 ( 399) hydrogen bonds : angle 3.78492 ( 1125) Misc. bond : bond 0.00012 ( 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 151 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.266 Fit side-chains REVERT: A 332 ILE cc_start: 0.7733 (mm) cc_final: 0.7275 (tt) REVERT: C 61 MET cc_start: 0.7397 (tmm) cc_final: 0.7047 (tmm) REVERT: C 68 ARG cc_start: 0.7272 (mtp180) cc_final: 0.6487 (mtp180) REVERT: C 135 VAL cc_start: 0.8127 (t) cc_final: 0.7779 (p) REVERT: C 255 LEU cc_start: 0.7563 (mt) cc_final: 0.7046 (mp) REVERT: C 292 PHE cc_start: 0.7403 (m-10) cc_final: 0.7158 (m-10) REVERT: E 18 ARG cc_start: 0.6557 (mmm-85) cc_final: 0.6265 (mmm-85) REVERT: E 98 ARG cc_start: 0.7506 (ttp-170) cc_final: 0.7102 (ptt180) REVERT: E 106 SER cc_start: 0.8451 (t) cc_final: 0.8089 (p) REVERT: E 218 MET cc_start: 0.7628 (ttt) cc_final: 0.7342 (ttt) outliers start: 18 outliers final: 14 residues processed: 145 average time/residue: 0.0846 time to fit residues: 16.6018 Evaluate side-chains 147 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 133 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 336 LEU Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 210 ILE Chi-restraints excluded: chain B residue 219 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain E residue 78 THR Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 187 VAL Chi-restraints excluded: chain E residue 212 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 13 optimal weight: 0.4980 chunk 56 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 0.0010 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 61 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 8 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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 = 0.3785 r_free = 0.3785 target = 0.141056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.121386 restraints weight = 11778.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.124097 restraints weight = 7357.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.125607 restraints weight = 5303.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.126952 restraints weight = 4296.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127532 restraints weight = 3673.494| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8333 Z= 0.106 Angle : 0.496 8.660 11358 Z= 0.263 Chirality : 0.042 0.150 1345 Planarity : 0.003 0.039 1424 Dihedral : 5.379 52.930 1230 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.46 % Allowed : 17.68 % Favored : 80.85 % 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: 1.88 (0.27), residues: 1065 helix: 2.62 (0.29), residues: 348 sheet: 1.52 (0.31), residues: 277 loop : -0.05 (0.31), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 157 TYR 0.015 0.001 TYR E 178 PHE 0.012 0.001 PHE C 199 TRP 0.010 0.001 TRP B 96 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8330) covalent geometry : angle 0.49599 (11354) SS BOND : bond 0.00371 ( 2) SS BOND : angle 0.83879 ( 4) hydrogen bonds : bond 0.03682 ( 399) hydrogen bonds : angle 3.69545 ( 1125) Misc. bond : bond 0.00014 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1317.72 seconds wall clock time: 23 minutes 21.50 seconds (1401.50 seconds total)