Starting phenix.real_space_refine on Fri Mar 6 12:04:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d43_30568/03_2026/7d43_30568.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d43_30568/03_2026/7d43_30568.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7d43_30568/03_2026/7d43_30568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d43_30568/03_2026/7d43_30568.map" model { file = "/net/cci-nas-00/data/ceres_data/7d43_30568/03_2026/7d43_30568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d43_30568/03_2026/7d43_30568.cif" } resolution = 4.3 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= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 142 5.16 5 C 19492 2.51 5 N 5519 2.21 5 O 5854 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31009 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2262 Classifications: {'peptide': 293} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "B" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2249 Classifications: {'peptide': 291} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 2} Link IDs: {'PTRANS': 9, 'TRANS': 281} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'TYR:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 2476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2476 Classifications: {'peptide': 317} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 302} Chain breaks: 1 Chain: "D" Number of atoms: 2538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2538 Classifications: {'peptide': 324} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 309} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2438 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 10, 'TRANS': 333} Chain breaks: 4 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 99 Chain: "F" Number of atoms: 2430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2430 Classifications: {'peptide': 343} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 10, 'TRANS': 332} Chain breaks: 4 Unresolved non-hydrogen bonds: 248 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4, 'ASN:plan1': 6} Unresolved non-hydrogen planarities: 99 Chain: "G" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "H" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2750 Classifications: {'peptide': 353} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 334} Chain: "I" Number of atoms: 3358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3358 Classifications: {'peptide': 427} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 408} Chain: "J" Number of atoms: 3371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3371 Classifications: {'peptide': 429} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 409} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 2 Chain: "K" Number of atoms: 1309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1309 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 225} Link IDs: {'PTRANS': 7, 'TRANS': 252} Unresolved chain links: 1 Unresolved chain link angles: 5 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 813 Unresolved non-hydrogen angles: 1032 Unresolved non-hydrogen dihedrals: 659 Unresolved non-hydrogen chiralities: 79 Planarities with less than four sites: {'ARG:plan': 19, 'PHE:plan': 7, 'TYR:plan': 12, 'GLN:plan1': 4, 'HIS:plan': 3, 'GLU:plan': 27, 'ASP:plan': 14, 'ASN:plan1': 13, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 450 Chain: "L" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 889 Classifications: {'peptide': 176} Incomplete info: {'truncation_to_alanine': 158} Link IDs: {'PTRANS': 4, 'TRANS': 171} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 585 Unresolved non-hydrogen angles: 743 Unresolved non-hydrogen dihedrals: 481 Unresolved non-hydrogen chiralities: 50 Planarities with less than four sites: {'ARG:plan': 14, 'PHE:plan': 6, 'TYR:plan': 9, 'GLN:plan1': 3, 'HIS:plan': 3, 'GLU:plan': 18, 'ASP:plan': 12, 'ASN:plan1': 9, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 340 Chain: "M" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 56 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASP:plan': 1, 'TYR:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 2, 'ARG:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "P" Number of atoms: 2109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 2109 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 332} Link IDs: {'PTRANS': 22, 'TRANS': 398} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1128 Unresolved non-hydrogen angles: 1429 Unresolved non-hydrogen dihedrals: 906 Unresolved non-hydrogen chiralities: 135 Planarities with less than four sites: {'ASN:plan1': 14, 'HIS:plan': 9, 'ARG:plan': 19, 'PHE:plan': 11, 'GLU:plan': 27, 'TYR:plan': 8, 'ASP:plan': 18, 'GLN:plan1': 13, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 536 Time building chain proxies: 7.32, per 1000 atoms: 0.24 Number of scatterers: 31009 At special positions: 0 Unit cell: (161.7, 174.93, 217.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 142 16.00 P 2 15.00 O 5854 8.00 N 5519 7.00 C 19492 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=0, symmetry=0 Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.8 seconds 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8214 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 47 sheets defined 37.8% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.12 Creating SS restraints... Processing helix chain 'A' and resid 3 through 17 removed outlier: 4.069A pdb=" N ILE A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 36 removed outlier: 3.606A pdb=" N ALA A 25 " --> pdb=" O ALA A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 57 WARNING: missing atoms! Processing helix chain 'A' and resid 62 through 77 removed outlier: 3.942A pdb=" N SER A 66 " --> pdb=" O SER A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 4.143A pdb=" N ARG A 108 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N ASN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS A 116 " --> pdb=" O ALA A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 132 through 144 removed outlier: 3.549A pdb=" N ARG A 136 " --> pdb=" O ARG A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 removed outlier: 4.017A pdb=" N LYS A 163 " --> pdb=" O LEU A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 179 through 189 removed outlier: 4.318A pdb=" N ILE A 186 " --> pdb=" O VAL A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 247 through 252 removed outlier: 4.071A pdb=" N TYR A 252 " --> pdb=" O ASP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'B' and resid 2 through 16 removed outlier: 3.587A pdb=" N LEU B 6 " --> pdb=" O ASP B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 36 Processing helix chain 'B' and resid 42 through 60 WARNING: missing atoms! Processing helix chain 'B' and resid 62 through 75 removed outlier: 3.981A pdb=" N SER B 66 " --> pdb=" O SER B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 116 removed outlier: 4.681A pdb=" N ARG B 108 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ASN B 109 " --> pdb=" O SER B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 144 Processing helix chain 'B' and resid 160 through 169 Processing helix chain 'B' and resid 170 through 172 No H-bonds generated for 'chain 'B' and resid 170 through 172' Processing helix chain 'B' and resid 179 through 181 No H-bonds generated for 'chain 'B' and resid 179 through 181' Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.701A pdb=" N ILE B 186 " --> pdb=" O ALA B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 222 Processing helix chain 'B' and resid 231 through 235 removed outlier: 3.615A pdb=" N LYS B 234 " --> pdb=" O GLU B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 305 removed outlier: 4.230A pdb=" N LEU B 305 " --> pdb=" O ILE B 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 9 through 25 removed outlier: 4.183A pdb=" N GLY C 25 " --> pdb=" O THR C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 48 Processing helix chain 'C' and resid 53 through 72 removed outlier: 3.945A pdb=" N LEU C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 96 Processing helix chain 'C' and resid 128 through 159 removed outlier: 3.856A pdb=" N ASN C 132 " --> pdb=" O GLN C 128 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N MET C 148 " --> pdb=" O LEU C 144 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLU C 149 " --> pdb=" O GLU C 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 153 " --> pdb=" O GLU C 149 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N GLU C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N HIS C 158 " --> pdb=" O GLN C 154 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 171 through 182 Processing helix chain 'C' and resid 201 through 210 Processing helix chain 'C' and resid 218 through 220 No H-bonds generated for 'chain 'C' and resid 218 through 220' Processing helix chain 'C' and resid 221 through 226 Processing helix chain 'C' and resid 227 through 229 No H-bonds generated for 'chain 'C' and resid 227 through 229' Processing helix chain 'C' and resid 251 through 262 Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 301 through 304 Processing helix chain 'C' and resid 317 through 321 Processing helix chain 'C' and resid 334 through 343 removed outlier: 4.112A pdb=" N ARG C 338 " --> pdb=" O SER C 334 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU C 339 " --> pdb=" O TYR C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 349 Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 30 through 49 removed outlier: 3.921A pdb=" N MET D 34 " --> pdb=" O SER D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 72 removed outlier: 3.997A pdb=" N GLN D 72 " --> pdb=" O MET D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 98 removed outlier: 4.273A pdb=" N GLY D 79 " --> pdb=" O GLU D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 146 removed outlier: 3.928A pdb=" N GLY D 146 " --> pdb=" O VAL D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 155 Processing helix chain 'D' and resid 156 through 158 No H-bonds generated for 'chain 'D' and resid 156 through 158' Processing helix chain 'D' and resid 171 through 182 Processing helix chain 'D' and resid 199 through 211 removed outlier: 3.900A pdb=" N MET D 203 " --> pdb=" O GLN D 199 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 226 removed outlier: 3.516A pdb=" N VAL D 225 " --> pdb=" O ALA D 221 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N MET D 226 " --> pdb=" O ILE D 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 221 through 226' Processing helix chain 'D' and resid 227 through 229 No H-bonds generated for 'chain 'D' and resid 227 through 229' Processing helix chain 'D' and resid 250 through 260 Processing helix chain 'D' and resid 296 through 300 removed outlier: 4.169A pdb=" N GLY D 300 " --> pdb=" O PHE D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 317 through 321 removed outlier: 3.899A pdb=" N LEU D 320 " --> pdb=" O PRO D 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 343 removed outlier: 4.198A pdb=" N TYR D 337 " --> pdb=" O PRO D 333 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N ARG D 338 " --> pdb=" O SER D 334 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N LEU D 339 " --> pdb=" O TYR D 335 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET D 340 " --> pdb=" O ILE D 336 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N SER D 341 " --> pdb=" O TYR D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 350 removed outlier: 3.876A pdb=" N VAL D 350 " --> pdb=" O ASP D 347 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 45 removed outlier: 4.132A pdb=" N LEU E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 68 Processing helix chain 'E' and resid 85 through 94 removed outlier: 3.770A pdb=" N SER E 89 " --> pdb=" O GLY E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 114 through 122 removed outlier: 3.773A pdb=" N VAL E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 176 Processing helix chain 'E' and resid 183 through 188 removed outlier: 4.064A pdb=" N LEU E 187 " --> pdb=" O LYS E 183 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 217 removed outlier: 3.640A pdb=" N ASP E 213 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLU E 217 " --> pdb=" O ASP E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 236 removed outlier: 4.813A pdb=" N ILE E 229 " --> pdb=" O ARG E 225 " (cutoff:3.500A) Proline residue: E 230 - end of helix Processing helix chain 'E' and resid 281 through 292 removed outlier: 3.703A pdb=" N CYS E 285 " --> pdb=" O CYS E 281 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N TRP E 290 " --> pdb=" O ARG E 286 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP E 292 " --> pdb=" O ASP E 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 46 removed outlier: 3.517A pdb=" N VAL F 46 " --> pdb=" O LEU F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 69 Processing helix chain 'F' and resid 85 through 94 Processing helix chain 'F' and resid 95 through 97 No H-bonds generated for 'chain 'F' and resid 95 through 97' Processing helix chain 'F' and resid 114 through 124 Processing helix chain 'F' and resid 183 through 190 removed outlier: 4.153A pdb=" N LEU F 187 " --> pdb=" O LYS F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 208 through 218 removed outlier: 3.528A pdb=" N ASN F 218 " --> pdb=" O PHE F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 235 Processing helix chain 'F' and resid 280 through 292 removed outlier: 4.016A pdb=" N ALA F 284 " --> pdb=" O ALA F 280 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ARG F 289 " --> pdb=" O CYS F 285 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TRP F 290 " --> pdb=" O ARG F 286 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLU F 291 " --> pdb=" O GLY F 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 177 through 182 removed outlier: 4.469A pdb=" N HIS G 182 " --> pdb=" O LEU G 179 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 195 removed outlier: 3.588A pdb=" N PHE G 195 " --> pdb=" O LEU G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 216 removed outlier: 3.608A pdb=" N GLN G 216 " --> pdb=" O LEU G 212 " (cutoff:3.500A) Processing helix chain 'G' and resid 221 through 240 Processing helix chain 'G' and resid 247 through 267 removed outlier: 3.955A pdb=" N VAL G 253 " --> pdb=" O SER G 249 " (cutoff:3.500A) Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 270 through 285 Processing helix chain 'G' and resid 292 through 312 Processing helix chain 'G' and resid 314 through 325 removed outlier: 4.598A pdb=" N GLN G 325 " --> pdb=" O ARG G 321 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 352 Processing helix chain 'G' and resid 368 through 378 removed outlier: 4.243A pdb=" N THR G 372 " --> pdb=" O GLU G 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 390 through 395 removed outlier: 3.974A pdb=" N VAL G 394 " --> pdb=" O ALA G 390 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU G 395 " --> pdb=" O ALA G 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 390 through 395' Processing helix chain 'G' and resid 420 through 431 Processing helix chain 'G' and resid 439 through 443 Processing helix chain 'G' and resid 459 through 464 removed outlier: 3.606A pdb=" N ASP G 462 " --> pdb=" O ASP G 459 " (cutoff:3.500A) Processing helix chain 'G' and resid 511 through 518 removed outlier: 4.030A pdb=" N VAL G 515 " --> pdb=" O SER G 511 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 181 Processing helix chain 'H' and resid 191 through 195 removed outlier: 3.828A pdb=" N GLN H 194 " --> pdb=" O SER H 191 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE H 195 " --> pdb=" O LEU H 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 191 through 195' Processing helix chain 'H' and resid 204 through 216 Processing helix chain 'H' and resid 221 through 240 Processing helix chain 'H' and resid 247 through 267 removed outlier: 4.808A pdb=" N VAL H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) Proline residue: H 258 - end of helix Processing helix chain 'H' and resid 270 through 286 Processing helix chain 'H' and resid 292 through 313 Processing helix chain 'H' and resid 314 through 324 Processing helix chain 'H' and resid 339 through 351 Processing helix chain 'H' and resid 369 through 378 Processing helix chain 'H' and resid 390 through 395 removed outlier: 4.027A pdb=" N VAL H 394 " --> pdb=" O ALA H 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 420 through 430 Processing helix chain 'H' and resid 439 through 443 Processing helix chain 'H' and resid 511 through 518 removed outlier: 4.033A pdb=" N VAL H 515 " --> pdb=" O SER H 511 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL H 518 " --> pdb=" O VAL H 514 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 86 Processing helix chain 'I' and resid 98 through 107 removed outlier: 3.529A pdb=" N ILE I 102 " --> pdb=" O LYS I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 130 through 141 removed outlier: 3.894A pdb=" N VAL I 134 " --> pdb=" O SER I 130 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 174 Processing helix chain 'I' and resid 228 through 234 removed outlier: 3.579A pdb=" N SER I 234 " --> pdb=" O LEU I 230 " (cutoff:3.500A) Processing helix chain 'I' and resid 254 through 262 Processing helix chain 'I' and resid 268 through 279 Processing helix chain 'I' and resid 302 through 314 Processing helix chain 'I' and resid 322 through 326 Processing helix chain 'I' and resid 330 through 334 Processing helix chain 'I' and resid 338 through 340 No H-bonds generated for 'chain 'I' and resid 338 through 340' Processing helix chain 'J' and resid 58 through 63 removed outlier: 3.637A pdb=" N GLN J 63 " --> pdb=" O ILE J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 98 through 107 Processing helix chain 'J' and resid 108 through 113 removed outlier: 7.110A pdb=" N TRP J 111 " --> pdb=" O LYS J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 130 through 141 Processing helix chain 'J' and resid 161 through 175 Processing helix chain 'J' and resid 228 through 234 removed outlier: 3.848A pdb=" N SER J 234 " --> pdb=" O LEU J 230 " (cutoff:3.500A) Processing helix chain 'J' and resid 253 through 262 Processing helix chain 'J' and resid 268 through 278 Processing helix chain 'J' and resid 302 through 314 Processing helix chain 'J' and resid 338 through 342 removed outlier: 3.765A pdb=" N ASN J 341 " --> pdb=" O SER J 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 80 removed outlier: 3.686A pdb=" N LYS K 79 " --> pdb=" O ASP K 76 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 118 Processing helix chain 'K' and resid 123 through 141 Processing helix chain 'K' and resid 145 through 158 removed outlier: 3.645A pdb=" N TYR K 149 " --> pdb=" O GLY K 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 158 through 163 Processing helix chain 'K' and resid 168 through 180 removed outlier: 3.920A pdb=" N ARG K 172 " --> pdb=" O ASN K 168 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ILE K 179 " --> pdb=" O LEU K 175 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASN K 180 " --> pdb=" O ILE K 176 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 223 Processing helix chain 'K' and resid 245 through 249 removed outlier: 3.555A pdb=" N LEU K 248 " --> pdb=" O THR K 245 " (cutoff:3.500A) Processing helix chain 'K' and resid 253 through 260 Processing helix chain 'K' and resid 261 through 265 removed outlier: 3.979A pdb=" N GLU K 264 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LYS K 265 " --> pdb=" O ILE K 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 261 through 265' Processing helix chain 'L' and resid 90 through 118 Processing helix chain 'L' and resid 123 through 140 removed outlier: 4.388A pdb=" N LYS L 140 " --> pdb=" O VAL L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 145 through 155 removed outlier: 4.373A pdb=" N TYR L 149 " --> pdb=" O GLY L 145 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 165 removed outlier: 3.633A pdb=" N SER L 164 " --> pdb=" O ILE L 161 " (cutoff:3.500A) Processing helix chain 'L' and resid 168 through 180 removed outlier: 4.203A pdb=" N ARG L 172 " --> pdb=" O ASN L 168 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN L 180 " --> pdb=" O ILE L 176 " (cutoff:3.500A) Processing helix chain 'M' and resid 175 through 183 Processing helix chain 'P' and resid 143 through 148 Processing helix chain 'P' and resid 149 through 152 Processing helix chain 'P' and resid 204 through 209 Processing helix chain 'P' and resid 233 through 237 Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 126 removed outlier: 7.078A pdb=" N ILE A 125 " --> pdb=" O TYR A 151 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N THR A 153 " --> pdb=" O ILE A 125 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL A 150 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL A 178 " --> pdb=" O VAL A 150 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 152 " --> pdb=" O VAL A 178 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 196 removed outlier: 6.685A pdb=" N VAL A 193 " --> pdb=" O TYR A 227 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N VAL A 229 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL A 195 " --> pdb=" O VAL A 229 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 200 through 201 removed outlier: 6.088A pdb=" N VAL A 200 " --> pdb=" O VAL A 236 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 206 through 209 Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 126 removed outlier: 5.881A pdb=" N ILE B 125 " --> pdb=" O TYR B 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 207 through 209 Processing sheet with id=AA7, first strand: chain 'C' and resid 164 through 167 removed outlier: 6.268A pdb=" N ILE C 165 " --> pdb=" O ILE C 190 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 232 through 234 removed outlier: 6.833A pdb=" N VAL C 232 " --> pdb=" O ILE C 266 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 246 through 248 Processing sheet with id=AB1, first strand: chain 'C' and resid 306 through 308 removed outlier: 7.231A pdb=" N SER C 307 " --> pdb=" O TYR G 385 " (cutoff:3.500A) removed outlier: 9.505A pdb=" N LEU G 387 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N VAL G 335 " --> pdb=" O VAL G 361 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 214 through 218 removed outlier: 6.005A pdb=" N ILE D 165 " --> pdb=" O ILE D 190 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA D 192 " --> pdb=" O ILE D 165 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL D 164 " --> pdb=" O LYS D 231 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE D 233 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N MET D 166 " --> pdb=" O ILE D 233 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N VAL D 232 " --> pdb=" O ILE D 266 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 238 through 239 Processing sheet with id=AB4, first strand: chain 'D' and resid 306 through 307 removed outlier: 7.016A pdb=" N SER D 307 " --> pdb=" O TYR H 385 " (cutoff:3.500A) removed outlier: 9.242A pdb=" N LEU H 387 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP H 362 " --> pdb=" O LEU H 386 " (cutoff:3.500A) removed outlier: 6.067A pdb=" N ILE H 333 " --> pdb=" O VAL H 359 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL H 361 " --> pdb=" O ILE H 333 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL H 335 " --> pdb=" O VAL H 361 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 52 through 54 Processing sheet with id=AB6, first strand: chain 'E' and resid 129 through 133 removed outlier: 7.051A pdb=" N MET E 130 " --> pdb=" O PHE E 266 " (cutoff:3.500A) removed outlier: 7.984A pdb=" N LYS E 268 " --> pdb=" O MET E 130 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N MET E 132 " --> pdb=" O LYS E 268 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 167 through 169 removed outlier: 5.822A pdb=" N GLY E 159 " --> pdb=" O LEU E 168 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N HIS E 196 " --> pdb=" O ILE E 158 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE E 193 " --> pdb=" O VAL J 240 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL J 238 " --> pdb=" O PHE E 195 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL J 202 " --> pdb=" O PHE J 215 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N PHE J 215 " --> pdb=" O VAL J 202 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA J 204 " --> pdb=" O LEU J 213 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 379 through 381 Processing sheet with id=AB9, first strand: chain 'E' and resid 413 through 414 Processing sheet with id=AC1, first strand: chain 'F' and resid 52 through 54 removed outlier: 6.732A pdb=" N VAL F 53 " --> pdb=" O ILE F 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'F' and resid 108 through 109 removed outlier: 3.507A pdb=" N ILE F 109 " --> pdb=" O THR F 272 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR F 272 " --> pdb=" O ILE F 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'F' and resid 200 through 201 removed outlier: 6.509A pdb=" N MET F 132 " --> pdb=" O LYS F 268 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 169 through 170 removed outlier: 4.133A pdb=" N VAL I 238 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N VAL I 202 " --> pdb=" O PHE I 215 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHE I 215 " --> pdb=" O VAL I 202 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ALA I 204 " --> pdb=" O LEU I 213 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 391 through 392 removed outlier: 7.361A pdb=" N LEU F 391 " --> pdb=" O ILE F 409 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 396 through 397 removed outlier: 3.672A pdb=" N THR F 397 " --> pdb=" O ALA F 413 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'F' and resid 425 through 426 removed outlier: 5.911A pdb=" N LEU F 425 " --> pdb=" O VAL F 444 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'G' and resid 414 through 417 Processing sheet with id=AC9, first strand: chain 'G' and resid 435 through 437 removed outlier: 6.307A pdb=" N VAL G 436 " --> pdb=" O ILE G 501 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE G 507 " --> pdb=" O VAL G 500 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'H' and resid 407 through 408 removed outlier: 3.762A pdb=" N ALA H 407 " --> pdb=" O MET H 415 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 435 through 437 removed outlier: 6.619A pdb=" N VAL H 436 " --> pdb=" O ILE H 501 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 44 through 46 removed outlier: 6.571A pdb=" N ALA I 45 " --> pdb=" O PHE I 92 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 155 through 156 Processing sheet with id=AD5, first strand: chain 'I' and resid 184 through 186 removed outlier: 6.799A pdb=" N PHE I 185 " --> pdb=" O THR I 292 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'I' and resid 342 through 344 removed outlier: 6.799A pdb=" N TYR I 343 " --> pdb=" O LEU I 362 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'I' and resid 391 through 392 removed outlier: 3.983A pdb=" N ASP I 392 " --> pdb=" O ILE I 408 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD7 Processing sheet with id=AD8, first strand: chain 'I' and resid 401 through 402 removed outlier: 6.551A pdb=" N ARG I 401 " --> pdb=" O VAL I 419 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'J' and resid 44 through 45 Processing sheet with id=AE1, first strand: chain 'J' and resid 94 through 95 removed outlier: 3.784A pdb=" N CYS J 95 " --> pdb=" O ILE J 123 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'J' and resid 155 through 157 Processing sheet with id=AE3, first strand: chain 'J' and resid 182 through 186 removed outlier: 3.554A pdb=" N THR J 292 " --> pdb=" O PHE J 185 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'J' and resid 373 through 375 removed outlier: 5.991A pdb=" N VAL J 390 " --> pdb=" O ILE J 408 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'J' and resid 384 through 385 removed outlier: 6.709A pdb=" N HIS J 384 " --> pdb=" O VAL J 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'K' and resid 41 through 46 Processing sheet with id=AE7, first strand: chain 'K' and resid 192 through 193 Processing sheet with id=AE8, first strand: chain 'L' and resid 19 through 25 removed outlier: 7.196A pdb=" N TYR L 32 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 8.350A pdb=" N LEU L 84 " --> pdb=" O GLU L 42 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N MET L 44 " --> pdb=" O LEU L 84 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'P' and resid 279 through 281 Processing sheet with id=AF1, first strand: chain 'P' and resid 371 through 373 Processing sheet with id=AF2, first strand: chain 'P' and resid 405 through 408 1119 hydrogen bonds defined for protein. 3135 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: 5.20 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10596 1.34 - 1.46: 5348 1.46 - 1.58: 15337 1.58 - 1.70: 9 1.70 - 1.82: 216 Bond restraints: 31506 Sorted by residual: bond pdb=" CA PRO P 94 " pdb=" C PRO P 94 " ideal model delta sigma weight residual 1.520 1.617 -0.098 1.42e-02 4.96e+03 4.76e+01 bond pdb=" CA SER P 95 " pdb=" C SER P 95 " ideal model delta sigma weight residual 1.521 1.574 -0.053 1.23e-02 6.61e+03 1.86e+01 bond pdb=" CA SER G 399 " pdb=" C SER G 399 " ideal model delta sigma weight residual 1.522 1.465 0.057 1.40e-02 5.10e+03 1.64e+01 bond pdb=" CA HIS H 430 " pdb=" C HIS H 430 " ideal model delta sigma weight residual 1.524 1.461 0.064 1.66e-02 3.63e+03 1.47e+01 bond pdb=" CA LEU C 303 " pdb=" C LEU C 303 " ideal model delta sigma weight residual 1.524 1.447 0.076 2.25e-02 1.98e+03 1.15e+01 ... (remaining 31501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.97: 42163 2.97 - 5.93: 670 5.93 - 8.90: 66 8.90 - 11.86: 8 11.86 - 14.83: 1 Bond angle restraints: 42908 Sorted by residual: angle pdb=" N PRO P 94 " pdb=" CA PRO P 94 " pdb=" C PRO P 94 " ideal model delta sigma weight residual 112.47 127.30 -14.83 2.06e+00 2.36e-01 5.18e+01 angle pdb=" N GLU P 439 " pdb=" CA GLU P 439 " pdb=" C GLU P 439 " ideal model delta sigma weight residual 110.50 120.43 -9.93 1.41e+00 5.03e-01 4.96e+01 angle pdb=" C GLN H 477 " pdb=" N ASN H 478 " pdb=" CA ASN H 478 " ideal model delta sigma weight residual 120.63 131.78 -11.15 1.61e+00 3.86e-01 4.80e+01 angle pdb=" C LEU A 238 " pdb=" N PHE A 239 " pdb=" CA PHE A 239 " ideal model delta sigma weight residual 122.37 116.19 6.18 9.30e-01 1.16e+00 4.42e+01 angle pdb=" O ASP P 93 " pdb=" C ASP P 93 " pdb=" N PRO P 94 " ideal model delta sigma weight residual 122.06 116.22 5.84 1.02e+00 9.61e-01 3.28e+01 ... (remaining 42903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 17141 17.94 - 35.88: 1626 35.88 - 53.82: 248 53.82 - 71.76: 32 71.76 - 89.70: 24 Dihedral angle restraints: 19071 sinusoidal: 6448 harmonic: 12623 Sorted by residual: dihedral pdb=" CA PRO P 94 " pdb=" C PRO P 94 " pdb=" N SER P 95 " pdb=" CA SER P 95 " ideal model delta harmonic sigma weight residual 180.00 110.55 69.45 0 5.00e+00 4.00e-02 1.93e+02 dihedral pdb=" CA TYR D 126 " pdb=" C TYR D 126 " pdb=" N ALA D 127 " pdb=" CA ALA D 127 " ideal model delta harmonic sigma weight residual 180.00 -145.02 -34.98 0 5.00e+00 4.00e-02 4.90e+01 dihedral pdb=" CA MET K 223 " pdb=" C MET K 223 " pdb=" N PRO K 224 " pdb=" CA PRO K 224 " ideal model delta harmonic sigma weight residual 180.00 146.78 33.22 0 5.00e+00 4.00e-02 4.41e+01 ... (remaining 19068 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 4419 0.075 - 0.150: 695 0.150 - 0.225: 19 0.225 - 0.300: 2 0.300 - 0.375: 1 Chirality restraints: 5136 Sorted by residual: chirality pdb=" CA PRO P 94 " pdb=" N PRO P 94 " pdb=" C PRO P 94 " pdb=" CB PRO P 94 " both_signs ideal model delta sigma weight residual False 2.72 2.34 0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CA TYR F 38 " pdb=" N TYR F 38 " pdb=" C TYR F 38 " pdb=" CB TYR F 38 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CB ILE G 312 " pdb=" CA ILE G 312 " pdb=" CG1 ILE G 312 " pdb=" CG2 ILE G 312 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 ... (remaining 5133 not shown) Planarity restraints: 5626 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL P 437 " 0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C VAL P 437 " -0.056 2.00e-02 2.50e+03 pdb=" O VAL P 437 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY P 438 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP P 93 " 0.015 2.00e-02 2.50e+03 2.74e-02 7.49e+00 pdb=" C ASP P 93 " -0.047 2.00e-02 2.50e+03 pdb=" O ASP P 93 " 0.017 2.00e-02 2.50e+03 pdb=" N PRO P 94 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS I 192 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.47e+00 pdb=" N PRO I 193 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO I 193 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO I 193 " 0.038 5.00e-02 4.00e+02 ... (remaining 5623 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 624 2.59 - 3.17: 31521 3.17 - 3.75: 48901 3.75 - 4.32: 64637 4.32 - 4.90: 102516 Nonbonded interactions: 248199 Sorted by model distance: nonbonded pdb=" OG SER H 200 " pdb=" O ILE H 203 " model vdw 2.018 3.040 nonbonded pdb=" OH TYR E 38 " pdb=" OD2 ASP E 288 " model vdw 2.079 3.040 nonbonded pdb=" O TYR B 86 " pdb=" NZ LYS B 90 " model vdw 2.114 3.120 nonbonded pdb=" O THR F 56 " pdb=" NH1 ARG F 57 " model vdw 2.128 3.120 nonbonded pdb=" ND2 ASN H 455 " pdb=" O TYR H 489 " model vdw 2.141 3.120 ... (remaining 248194 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 253 or resid 268 through 305)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 8 through 343 or (resid 344 and (name N or name CA or name \ C or name O or name CB or name CG or name CD1 or name CD2 or name CE1 or name C \ E2 or name CZ )) or resid 345 through 351)) selection = (chain 'D' and (resid 8 through 98 or resid 126 through 351)) } ncs_group { reference = (chain 'E' and (resid 1 through 27 or resid 29 through 444)) selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = (chain 'I' and (resid 41 through 170 or (resid 171 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name NE or name CZ )) or resid \ 172 through 467)) selection = (chain 'J' and resid 41 through 467) } 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: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.640 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: 0.020 Extract box with map and model: 0.420 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.190 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 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 : 0.006 0.098 31506 Z= 0.313 Angle : 0.987 14.829 42908 Z= 0.583 Chirality : 0.051 0.375 5136 Planarity : 0.005 0.068 5626 Dihedral : 14.617 89.701 10857 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 28.44 Ramachandran Plot: Outliers : 0.09 % Allowed : 18.29 % Favored : 81.62 % Rotamer: Outliers : 0.31 % Allowed : 9.65 % Favored : 90.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.12 % 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 are not related in a simple way. whole: -6.11 (0.09), residues: 4287 helix: -3.22 (0.10), residues: 1406 sheet: -4.28 (0.18), residues: 483 loop : -4.75 (0.09), residues: 2398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 301 TYR 0.024 0.002 TYR H 214 PHE 0.022 0.002 PHE D 278 TRP 0.019 0.003 TRP H 350 HIS 0.013 0.002 HIS B 128 Details of bonding type rmsd covalent geometry : bond 0.00645 (31506) covalent geometry : angle 0.98659 (42908) hydrogen bonds : bond 0.16655 ( 1119) hydrogen bonds : angle 7.55505 ( 3135) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 281 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7557 (mmp) cc_final: 0.7161 (mmt) REVERT: A 20 MET cc_start: 0.7577 (mmp) cc_final: 0.7295 (mmm) REVERT: C 11 LEU cc_start: 0.9103 (tp) cc_final: 0.8843 (tp) REVERT: C 304 GLU cc_start: 0.6810 (pp20) cc_final: 0.6285 (pp20) REVERT: D 58 MET cc_start: 0.8428 (tmm) cc_final: 0.8047 (tmm) REVERT: D 128 GLN cc_start: 0.7775 (tt0) cc_final: 0.7367 (mm-40) REVERT: E 90 LEU cc_start: 0.9343 (mt) cc_final: 0.8854 (tt) REVERT: E 282 TRP cc_start: 0.8449 (t-100) cc_final: 0.7977 (t-100) REVERT: F 8 MET cc_start: 0.5170 (tpt) cc_final: 0.4693 (tpp) REVERT: F 132 MET cc_start: 0.7863 (mtt) cc_final: 0.7590 (mtp) REVERT: F 205 TYR cc_start: 0.8049 (m-80) cc_final: 0.7415 (m-80) REVERT: G 229 LEU cc_start: 0.9262 (tp) cc_final: 0.8994 (tt) REVERT: G 422 GLN cc_start: 0.8874 (tt0) cc_final: 0.8671 (tp40) REVERT: G 495 GLU cc_start: 0.7830 (pt0) cc_final: 0.7626 (mm-30) REVERT: I 395 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7215 (m-80) outliers start: 9 outliers final: 4 residues processed: 290 average time/residue: 0.1926 time to fit residues: 89.4377 Evaluate side-chains 198 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 193 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 197 optimal weight: 0.5980 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.6980 chunk 207 optimal weight: 0.9980 chunk 401 optimal weight: 50.0000 chunk 424 optimal weight: 30.0000 chunk 155 optimal weight: 10.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 ASN C 132 ASN C 138 ASN C 150 ASN ** C 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 HIS C 261 HIS ** D 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 150 ASN ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 203 HIS E 271 ASN F 274 ASN G 185 GLN G 213 GLN G 254 ASN G 281 ASN G 411 ASN G 431 ASN G 479 HIS H 213 GLN ** H 281 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 455 ASN H 470 HIS H 479 HIS I 105 HIS I 200 ASN I 376 ASN J 177 ASN J 232 GLN J 255 GLN J 263 ASN ** J 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 359 ASN J 384 HIS J 434 GLN J 440 ASN J 452 HIS Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.087528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.069992 restraints weight = 118336.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.070231 restraints weight = 86626.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.070520 restraints weight = 65781.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.070943 restraints weight = 57267.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.071107 restraints weight = 48756.730| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 31506 Z= 0.172 Angle : 0.757 11.531 42908 Z= 0.394 Chirality : 0.049 0.269 5136 Planarity : 0.005 0.072 5626 Dihedral : 6.771 88.820 4610 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.25 % Favored : 87.73 % Rotamer: Outliers : 0.14 % Allowed : 7.39 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % 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 are not related in a simple way. whole: -4.51 (0.11), residues: 4287 helix: -1.58 (0.12), residues: 1446 sheet: -3.94 (0.18), residues: 526 loop : -3.85 (0.11), residues: 2315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 145 TYR 0.028 0.002 TYR E 38 PHE 0.018 0.002 PHE J 185 TRP 0.018 0.002 TRP E 290 HIS 0.007 0.001 HIS D 125 Details of bonding type rmsd covalent geometry : bond 0.00384 (31506) covalent geometry : angle 0.75662 (42908) hydrogen bonds : bond 0.04913 ( 1119) hydrogen bonds : angle 5.78243 ( 3135) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 296 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7529 (mmp) cc_final: 0.7009 (mmt) REVERT: A 135 LEU cc_start: 0.8456 (mt) cc_final: 0.7983 (mm) REVERT: A 187 MET cc_start: 0.9026 (tpp) cc_final: 0.8696 (tpt) REVERT: B 278 PRO cc_start: 0.9260 (Cg_endo) cc_final: 0.9014 (Cg_exo) REVERT: C 44 GLN cc_start: 0.8493 (tm-30) cc_final: 0.8026 (tm-30) REVERT: C 45 ILE cc_start: 0.8084 (mt) cc_final: 0.7441 (mt) REVERT: C 217 MET cc_start: 0.7589 (ttp) cc_final: 0.7307 (ttt) REVERT: D 128 GLN cc_start: 0.8162 (tt0) cc_final: 0.7300 (tp40) REVERT: D 139 GLU cc_start: 0.8014 (tm-30) cc_final: 0.7754 (tm-30) REVERT: D 166 MET cc_start: 0.7603 (mtm) cc_final: 0.7329 (mtp) REVERT: E 90 LEU cc_start: 0.9351 (mt) cc_final: 0.8915 (tt) REVERT: E 132 MET cc_start: 0.8992 (mmm) cc_final: 0.8759 (mmm) REVERT: E 216 MET cc_start: 0.7629 (tmm) cc_final: 0.7048 (tmm) REVERT: F 8 MET cc_start: 0.4635 (tpt) cc_final: 0.4379 (tpp) REVERT: F 132 MET cc_start: 0.7803 (mtt) cc_final: 0.7585 (mtp) REVERT: F 205 TYR cc_start: 0.7642 (m-80) cc_final: 0.7109 (m-80) REVERT: G 229 LEU cc_start: 0.9025 (tp) cc_final: 0.8800 (tt) REVERT: G 273 MET cc_start: 0.7989 (mtm) cc_final: 0.7418 (mtt) REVERT: G 422 GLN cc_start: 0.8537 (tt0) cc_final: 0.8215 (tp40) REVERT: G 497 VAL cc_start: 0.8640 (p) cc_final: 0.8424 (p) REVERT: H 273 MET cc_start: 0.8788 (mtm) cc_final: 0.8503 (mtm) outliers start: 4 outliers final: 1 residues processed: 300 average time/residue: 0.1781 time to fit residues: 87.1934 Evaluate side-chains 205 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 231 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 212 optimal weight: 1.9990 chunk 287 optimal weight: 0.9990 chunk 146 optimal weight: 0.0870 chunk 213 optimal weight: 3.9990 chunk 292 optimal weight: 0.6980 chunk 243 optimal weight: 2.9990 chunk 331 optimal weight: 5.9990 chunk 394 optimal weight: 9.9990 chunk 158 optimal weight: 0.1980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 243 GLN C 188 HIS D 125 HIS ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN ** I 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 333 GLN I 340 HIS J 72 ASN J 168 HIS J 384 HIS J 440 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.090092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.072193 restraints weight = 115844.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.072484 restraints weight = 79621.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.073112 restraints weight = 63248.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.073768 restraints weight = 47295.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.073819 restraints weight = 39819.614| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31506 Z= 0.136 Angle : 0.688 11.631 42908 Z= 0.355 Chirality : 0.047 0.270 5136 Planarity : 0.005 0.080 5626 Dihedral : 6.162 88.185 4610 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.54 % Favored : 90.44 % Rotamer: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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 are not related in a simple way. whole: -3.55 (0.12), residues: 4287 helix: -0.57 (0.13), residues: 1452 sheet: -3.53 (0.19), residues: 531 loop : -3.40 (0.12), residues: 2304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 299 TYR 0.030 0.001 TYR E 38 PHE 0.016 0.002 PHE I 52 TRP 0.029 0.002 TRP H 366 HIS 0.015 0.001 HIS I 214 Details of bonding type rmsd covalent geometry : bond 0.00299 (31506) covalent geometry : angle 0.68785 (42908) hydrogen bonds : bond 0.04155 ( 1119) hydrogen bonds : angle 5.20099 ( 3135) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7924 (mmp) cc_final: 0.7612 (mmt) REVERT: B 14 MET cc_start: 0.9054 (ptt) cc_final: 0.8795 (ptp) REVERT: B 278 PRO cc_start: 0.9165 (Cg_endo) cc_final: 0.8930 (Cg_exo) REVERT: C 42 LEU cc_start: 0.9008 (mt) cc_final: 0.8703 (pp) REVERT: C 203 MET cc_start: 0.8286 (tpt) cc_final: 0.7951 (tpp) REVERT: D 96 LEU cc_start: 0.9064 (tp) cc_final: 0.8675 (tp) REVERT: D 128 GLN cc_start: 0.7992 (tt0) cc_final: 0.7026 (tp40) REVERT: D 139 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7484 (tm-30) REVERT: D 166 MET cc_start: 0.7301 (mtm) cc_final: 0.7008 (mtp) REVERT: E 132 MET cc_start: 0.8931 (mmm) cc_final: 0.8674 (mmm) REVERT: E 204 LEU cc_start: 0.8775 (tp) cc_final: 0.8420 (tt) REVERT: E 207 LEU cc_start: 0.8474 (mp) cc_final: 0.8260 (mp) REVERT: E 290 TRP cc_start: 0.8470 (m-90) cc_final: 0.8157 (m-90) REVERT: F 8 MET cc_start: 0.4084 (tpt) cc_final: 0.3758 (tpp) REVERT: F 84 MET cc_start: 0.3950 (ppp) cc_final: 0.2264 (mtt) REVERT: F 94 TYR cc_start: 0.8487 (t80) cc_final: 0.7652 (t80) REVERT: F 120 LEU cc_start: 0.7205 (tp) cc_final: 0.6982 (tp) REVERT: F 205 TYR cc_start: 0.7353 (m-80) cc_final: 0.6980 (m-80) REVERT: G 229 LEU cc_start: 0.8884 (tp) cc_final: 0.8655 (tt) REVERT: G 273 MET cc_start: 0.7569 (mtm) cc_final: 0.7267 (mmm) REVERT: G 448 GLN cc_start: 0.7992 (tt0) cc_final: 0.7722 (tp-100) REVERT: G 465 CYS cc_start: 0.8169 (t) cc_final: 0.7918 (t) REVERT: H 260 MET cc_start: 0.8424 (mmp) cc_final: 0.7884 (mmp) REVERT: H 273 MET cc_start: 0.8910 (mtm) cc_final: 0.8685 (mtm) REVERT: I 187 GLU cc_start: 0.8209 (tt0) cc_final: 0.7993 (tp30) REVERT: I 296 TYR cc_start: 0.8331 (t80) cc_final: 0.8049 (t80) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.1631 time to fit residues: 89.8075 Evaluate side-chains 232 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 279 optimal weight: 5.9990 chunk 271 optimal weight: 0.6980 chunk 342 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 155 optimal weight: 10.0000 chunk 99 optimal weight: 0.5980 chunk 243 optimal weight: 0.8980 chunk 419 optimal weight: 20.0000 chunk 226 optimal weight: 0.8980 chunk 192 optimal weight: 0.3980 chunk 195 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 HIS ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 470 HIS I 452 HIS J 168 HIS J 384 HIS J 440 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.090575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.072676 restraints weight = 114856.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.073508 restraints weight = 78971.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.074018 restraints weight = 57218.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.074531 restraints weight = 45884.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.074548 restraints weight = 36555.268| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31506 Z= 0.130 Angle : 0.664 11.148 42908 Z= 0.339 Chirality : 0.046 0.232 5136 Planarity : 0.005 0.083 5626 Dihedral : 5.865 87.989 4610 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.31 % Favored : 90.67 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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 are not related in a simple way. whole: -3.04 (0.12), residues: 4287 helix: -0.08 (0.14), residues: 1439 sheet: -3.35 (0.18), residues: 566 loop : -3.07 (0.12), residues: 2282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 299 TYR 0.023 0.001 TYR E 38 PHE 0.020 0.001 PHE H 452 TRP 0.017 0.002 TRP B 272 HIS 0.007 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00293 (31506) covalent geometry : angle 0.66374 (42908) hydrogen bonds : bond 0.03818 ( 1119) hydrogen bonds : angle 4.92312 ( 3135) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7468 (mmp) cc_final: 0.7200 (mmt) REVERT: A 187 MET cc_start: 0.9052 (tpp) cc_final: 0.8661 (mmm) REVERT: B 14 MET cc_start: 0.9051 (ptt) cc_final: 0.8824 (ptp) REVERT: B 278 PRO cc_start: 0.9120 (Cg_endo) cc_final: 0.8776 (Cg_exo) REVERT: C 11 LEU cc_start: 0.9041 (tp) cc_final: 0.8705 (tp) REVERT: C 45 ILE cc_start: 0.7937 (mt) cc_final: 0.7710 (mt) REVERT: C 203 MET cc_start: 0.8305 (tpt) cc_final: 0.7968 (tpp) REVERT: C 217 MET cc_start: 0.7612 (ttp) cc_final: 0.7356 (ttp) REVERT: D 96 LEU cc_start: 0.9091 (tp) cc_final: 0.8690 (tp) REVERT: D 128 GLN cc_start: 0.7990 (tt0) cc_final: 0.7017 (tp40) REVERT: D 139 GLU cc_start: 0.7732 (tm-30) cc_final: 0.7407 (tm-30) REVERT: E 197 THR cc_start: 0.5869 (t) cc_final: 0.5403 (t) REVERT: E 204 LEU cc_start: 0.8739 (tp) cc_final: 0.8404 (tt) REVERT: E 216 MET cc_start: 0.7869 (tmm) cc_final: 0.7363 (tmm) REVERT: E 290 TRP cc_start: 0.8632 (m-90) cc_final: 0.8426 (m-90) REVERT: F 86 THR cc_start: 0.5338 (p) cc_final: 0.5083 (p) REVERT: F 205 TYR cc_start: 0.7475 (m-80) cc_final: 0.6980 (m-80) REVERT: G 448 GLN cc_start: 0.8007 (tt0) cc_final: 0.7706 (tp-100) REVERT: G 465 CYS cc_start: 0.8132 (t) cc_final: 0.7876 (t) REVERT: H 196 MET cc_start: 0.7846 (ppp) cc_final: 0.7539 (ppp) REVERT: H 260 MET cc_start: 0.8617 (mmp) cc_final: 0.8143 (mmp) REVERT: H 273 MET cc_start: 0.8847 (mtm) cc_final: 0.8563 (mtm) REVERT: I 187 GLU cc_start: 0.8326 (tt0) cc_final: 0.7801 (tp30) REVERT: I 228 LEU cc_start: 0.8763 (tp) cc_final: 0.8456 (tt) REVERT: I 289 MET cc_start: 0.9071 (tpp) cc_final: 0.8784 (tpp) REVERT: I 426 LYS cc_start: 0.8278 (mttm) cc_final: 0.7652 (mttm) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.1708 time to fit residues: 89.7834 Evaluate side-chains 225 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 225 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 82 optimal weight: 10.0000 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 73 optimal weight: 1.9990 chunk 153 optimal weight: 7.9990 chunk 272 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 372 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 163 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 188 HIS ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 ASN J 384 HIS J 440 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.089899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.072878 restraints weight = 116814.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.073753 restraints weight = 80345.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.074608 restraints weight = 55363.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.074650 restraints weight = 47869.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.074709 restraints weight = 36913.122| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31506 Z= 0.136 Angle : 0.659 12.668 42908 Z= 0.336 Chirality : 0.046 0.273 5136 Planarity : 0.005 0.087 5626 Dihedral : 5.735 87.724 4610 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.40 % Favored : 90.58 % Rotamer: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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 are not related in a simple way. whole: -2.79 (0.12), residues: 4287 helix: 0.13 (0.14), residues: 1437 sheet: -3.23 (0.18), residues: 572 loop : -2.91 (0.12), residues: 2278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 95 TYR 0.020 0.001 TYR H 214 PHE 0.050 0.002 PHE E 157 TRP 0.015 0.001 TRP E 282 HIS 0.007 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00314 (31506) covalent geometry : angle 0.65862 (42908) hydrogen bonds : bond 0.03666 ( 1119) hydrogen bonds : angle 4.79777 ( 3135) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 295 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7883 (mmp) cc_final: 0.7638 (mmt) REVERT: B 278 PRO cc_start: 0.9209 (Cg_endo) cc_final: 0.8915 (Cg_exo) REVERT: C 203 MET cc_start: 0.8320 (tpt) cc_final: 0.7957 (tpp) REVERT: C 217 MET cc_start: 0.7452 (ttp) cc_final: 0.7225 (ttp) REVERT: C 226 MET cc_start: 0.8617 (tpt) cc_final: 0.8217 (tpp) REVERT: D 128 GLN cc_start: 0.7971 (tt0) cc_final: 0.7445 (pm20) REVERT: D 139 GLU cc_start: 0.7686 (tm-30) cc_final: 0.7354 (tm-30) REVERT: D 226 MET cc_start: 0.8332 (tpt) cc_final: 0.7798 (tpt) REVERT: D 277 GLN cc_start: 0.8224 (mm110) cc_final: 0.7844 (mm-40) REVERT: E 38 TYR cc_start: 0.7433 (m-80) cc_final: 0.7020 (m-80) REVERT: E 68 LYS cc_start: 0.7015 (mmtt) cc_final: 0.6586 (mmtt) REVERT: E 204 LEU cc_start: 0.8804 (tp) cc_final: 0.8537 (tt) REVERT: F 92 TYR cc_start: 0.7506 (t80) cc_final: 0.7276 (t80) REVERT: F 109 ILE cc_start: 0.8603 (mp) cc_final: 0.8302 (mm) REVERT: F 205 TYR cc_start: 0.7428 (m-80) cc_final: 0.7121 (m-80) REVERT: G 409 LEU cc_start: 0.8352 (mt) cc_final: 0.8061 (mt) REVERT: G 448 GLN cc_start: 0.8110 (tt0) cc_final: 0.7566 (tt0) REVERT: G 465 CYS cc_start: 0.8177 (t) cc_final: 0.7957 (t) REVERT: H 260 MET cc_start: 0.8686 (mmp) cc_final: 0.8231 (mmp) REVERT: H 273 MET cc_start: 0.8930 (mtm) cc_final: 0.8371 (mtm) REVERT: I 228 LEU cc_start: 0.8698 (tp) cc_final: 0.8412 (tt) REVERT: I 289 MET cc_start: 0.9045 (tpp) cc_final: 0.8825 (tpp) outliers start: 0 outliers final: 0 residues processed: 295 average time/residue: 0.1673 time to fit residues: 83.2522 Evaluate side-chains 216 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 45 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 104 optimal weight: 0.0970 chunk 101 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 271 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 210 optimal weight: 4.9990 chunk 246 optimal weight: 0.2980 chunk 183 optimal weight: 30.0000 chunk 391 optimal weight: 30.0000 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS D 154 GLN ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 GLN H 431 ASN H 455 ASN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 ASN J 440 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.091154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.073976 restraints weight = 115555.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.074490 restraints weight = 78944.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.075167 restraints weight = 60433.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.075603 restraints weight = 45924.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.075691 restraints weight = 38395.434| |-----------------------------------------------------------------------------| r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.3377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 31506 Z= 0.123 Angle : 0.642 11.238 42908 Z= 0.326 Chirality : 0.046 0.242 5136 Planarity : 0.004 0.089 5626 Dihedral : 5.549 88.114 4610 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.70 % Favored : 91.28 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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 are not related in a simple way. whole: -2.53 (0.13), residues: 4287 helix: 0.27 (0.14), residues: 1440 sheet: -3.10 (0.19), residues: 559 loop : -2.70 (0.13), residues: 2288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 155 TYR 0.024 0.001 TYR E 38 PHE 0.015 0.001 PHE I 52 TRP 0.037 0.002 TRP H 366 HIS 0.008 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00272 (31506) covalent geometry : angle 0.64177 (42908) hydrogen bonds : bond 0.03486 ( 1119) hydrogen bonds : angle 4.64678 ( 3135) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 306 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4308 (mpp) cc_final: 0.3407 (mpt) REVERT: B 278 PRO cc_start: 0.9132 (Cg_endo) cc_final: 0.8899 (Cg_exo) REVERT: B 279 SER cc_start: 0.9056 (m) cc_final: 0.8779 (t) REVERT: C 44 GLN cc_start: 0.8573 (tm-30) cc_final: 0.8327 (tm-30) REVERT: C 203 MET cc_start: 0.8615 (tpt) cc_final: 0.8299 (tpp) REVERT: C 217 MET cc_start: 0.6902 (ttp) cc_final: 0.6669 (ttp) REVERT: D 128 GLN cc_start: 0.7888 (tt0) cc_final: 0.7463 (pm20) REVERT: E 38 TYR cc_start: 0.7625 (m-80) cc_final: 0.7327 (m-80) REVERT: E 68 LYS cc_start: 0.7089 (mmtt) cc_final: 0.6760 (mmtt) REVERT: E 204 LEU cc_start: 0.8861 (tp) cc_final: 0.8536 (tt) REVERT: F 86 THR cc_start: 0.4983 (p) cc_final: 0.4766 (p) REVERT: F 109 ILE cc_start: 0.8782 (mp) cc_final: 0.8444 (mm) REVERT: F 205 TYR cc_start: 0.7495 (m-80) cc_final: 0.7193 (m-80) REVERT: F 266 PHE cc_start: 0.7931 (t80) cc_final: 0.7598 (t80) REVERT: G 448 GLN cc_start: 0.8161 (tt0) cc_final: 0.7639 (tt0) REVERT: G 465 CYS cc_start: 0.8190 (t) cc_final: 0.7976 (t) REVERT: H 196 MET cc_start: 0.7869 (ppp) cc_final: 0.7623 (ppp) REVERT: H 254 ASN cc_start: 0.8519 (t0) cc_final: 0.8220 (t0) REVERT: H 260 MET cc_start: 0.8655 (mmp) cc_final: 0.8206 (mmp) REVERT: I 228 LEU cc_start: 0.8646 (tp) cc_final: 0.8359 (tt) REVERT: I 289 MET cc_start: 0.8974 (tpp) cc_final: 0.8765 (tpp) outliers start: 0 outliers final: 0 residues processed: 306 average time/residue: 0.1640 time to fit residues: 85.1628 Evaluate side-chains 226 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 283 optimal weight: 0.7980 chunk 374 optimal weight: 1.9990 chunk 309 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 106 optimal weight: 0.8980 chunk 236 optimal weight: 9.9990 chunk 83 optimal weight: 0.5980 chunk 190 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 160 optimal weight: 0.5980 chunk 250 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 ASN J 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.091127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.073451 restraints weight = 116108.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.074436 restraints weight = 75285.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.074950 restraints weight = 58898.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.075596 restraints weight = 43702.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.075831 restraints weight = 34398.511| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31506 Z= 0.124 Angle : 0.637 11.539 42908 Z= 0.323 Chirality : 0.046 0.228 5136 Planarity : 0.004 0.088 5626 Dihedral : 5.450 87.825 4610 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.61 % Favored : 91.37 % Rotamer: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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 are not related in a simple way. whole: -2.38 (0.13), residues: 4287 helix: 0.37 (0.14), residues: 1447 sheet: -2.94 (0.20), residues: 544 loop : -2.64 (0.13), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 145 TYR 0.023 0.001 TYR E 94 PHE 0.021 0.001 PHE A 250 TRP 0.021 0.001 TRP E 282 HIS 0.008 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00285 (31506) covalent geometry : angle 0.63749 (42908) hydrogen bonds : bond 0.03430 ( 1119) hydrogen bonds : angle 4.61291 ( 3135) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4347 (mpp) cc_final: 0.3430 (mpt) REVERT: B 278 PRO cc_start: 0.9140 (Cg_endo) cc_final: 0.8862 (Cg_exo) REVERT: B 279 SER cc_start: 0.9045 (m) cc_final: 0.8771 (t) REVERT: C 44 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8321 (tm-30) REVERT: D 277 GLN cc_start: 0.8091 (mm110) cc_final: 0.7883 (mm-40) REVERT: E 1 MET cc_start: 0.4956 (ttt) cc_final: 0.4119 (tpt) REVERT: E 38 TYR cc_start: 0.7682 (m-80) cc_final: 0.7413 (m-80) REVERT: E 204 LEU cc_start: 0.9023 (tp) cc_final: 0.8765 (tt) REVERT: F 86 THR cc_start: 0.4963 (p) cc_final: 0.3939 (p) REVERT: F 109 ILE cc_start: 0.8908 (mp) cc_final: 0.8422 (mm) REVERT: F 205 TYR cc_start: 0.7396 (m-80) cc_final: 0.6918 (m-80) REVERT: G 448 GLN cc_start: 0.8195 (tt0) cc_final: 0.7820 (tt0) REVERT: G 465 CYS cc_start: 0.8139 (t) cc_final: 0.7930 (t) REVERT: H 196 MET cc_start: 0.7854 (ppp) cc_final: 0.7218 (ppp) REVERT: H 254 ASN cc_start: 0.8540 (t0) cc_final: 0.8191 (t0) REVERT: I 228 LEU cc_start: 0.8516 (tp) cc_final: 0.8314 (tt) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.1633 time to fit residues: 83.2759 Evaluate side-chains 226 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 269 optimal weight: 0.0470 chunk 167 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 367 optimal weight: 5.9990 chunk 158 optimal weight: 1.9990 chunk 384 optimal weight: 5.9990 chunk 316 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 391 optimal weight: 30.0000 chunk 411 optimal weight: 50.0000 chunk 212 optimal weight: 0.6980 overall best weight: 0.8480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 4 GLN ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 ASN J 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.091123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.073590 restraints weight = 116527.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.074754 restraints weight = 76506.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.075196 restraints weight = 54458.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.075588 restraints weight = 46191.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.075633 restraints weight = 36154.181| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.3687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 31506 Z= 0.131 Angle : 0.659 12.059 42908 Z= 0.332 Chirality : 0.046 0.284 5136 Planarity : 0.004 0.088 5626 Dihedral : 5.416 87.653 4610 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.75 % Favored : 91.23 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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 are not related in a simple way. whole: -2.29 (0.13), residues: 4287 helix: 0.41 (0.14), residues: 1445 sheet: -2.80 (0.21), residues: 536 loop : -2.58 (0.13), residues: 2306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 269 TYR 0.029 0.001 TYR I 319 PHE 0.019 0.001 PHE D 324 TRP 0.021 0.001 TRP G 366 HIS 0.008 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00302 (31506) covalent geometry : angle 0.65854 (42908) hydrogen bonds : bond 0.03458 ( 1119) hydrogen bonds : angle 4.60567 ( 3135) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4342 (mpp) cc_final: 0.3346 (mpt) REVERT: B 93 MET cc_start: 0.8416 (tpp) cc_final: 0.8106 (mmt) REVERT: B 279 SER cc_start: 0.8992 (m) cc_final: 0.8691 (t) REVERT: C 203 MET cc_start: 0.8186 (tpt) cc_final: 0.7851 (tpp) REVERT: D 58 MET cc_start: 0.8051 (tmm) cc_final: 0.7840 (tmm) REVERT: D 226 MET cc_start: 0.8690 (tpt) cc_final: 0.8171 (tpt) REVERT: E 1 MET cc_start: 0.4884 (ttt) cc_final: 0.4429 (tpt) REVERT: E 38 TYR cc_start: 0.7759 (m-80) cc_final: 0.7408 (m-80) REVERT: E 158 ILE cc_start: 0.8708 (pt) cc_final: 0.8478 (pt) REVERT: E 204 LEU cc_start: 0.8968 (tp) cc_final: 0.8763 (tt) REVERT: F 109 ILE cc_start: 0.8897 (mp) cc_final: 0.8443 (mm) REVERT: F 205 TYR cc_start: 0.7377 (m-80) cc_final: 0.6988 (m-80) REVERT: F 266 PHE cc_start: 0.7726 (t80) cc_final: 0.7402 (t80) REVERT: G 448 GLN cc_start: 0.8216 (tt0) cc_final: 0.7778 (tt0) REVERT: G 465 CYS cc_start: 0.7972 (t) cc_final: 0.7732 (t) REVERT: H 196 MET cc_start: 0.7892 (ppp) cc_final: 0.7212 (ppp) REVERT: H 254 ASN cc_start: 0.8538 (t0) cc_final: 0.8199 (t0) REVERT: H 260 MET cc_start: 0.8387 (mmp) cc_final: 0.7641 (mmp) REVERT: H 274 HIS cc_start: 0.6552 (m-70) cc_final: 0.6246 (m-70) REVERT: I 187 GLU cc_start: 0.8207 (tt0) cc_final: 0.7978 (tp30) REVERT: I 243 ASP cc_start: 0.7207 (m-30) cc_final: 0.6996 (m-30) REVERT: J 191 SER cc_start: 0.8102 (m) cc_final: 0.7887 (t) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.1624 time to fit residues: 82.1916 Evaluate side-chains 233 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 293 optimal weight: 3.9990 chunk 268 optimal weight: 0.8980 chunk 405 optimal weight: 30.0000 chunk 339 optimal weight: 0.9990 chunk 67 optimal weight: 0.0000 chunk 353 optimal weight: 5.9990 chunk 355 optimal weight: 9.9990 chunk 418 optimal weight: 50.0000 chunk 12 optimal weight: 3.9990 chunk 236 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 349 HIS ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 ASN J 285 ASN J 388 ASN J 440 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.091658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.074166 restraints weight = 115623.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.074852 restraints weight = 75898.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.075260 restraints weight = 64461.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.075945 restraints weight = 47831.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.076241 restraints weight = 36545.010| |-----------------------------------------------------------------------------| r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 31506 Z= 0.122 Angle : 0.649 12.763 42908 Z= 0.326 Chirality : 0.046 0.278 5136 Planarity : 0.004 0.088 5626 Dihedral : 5.341 87.739 4610 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.14 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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 are not related in a simple way. whole: -2.19 (0.13), residues: 4287 helix: 0.48 (0.14), residues: 1443 sheet: -2.69 (0.21), residues: 541 loop : -2.52 (0.13), residues: 2303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 96 TYR 0.034 0.001 TYR I 319 PHE 0.016 0.001 PHE F 67 TRP 0.024 0.001 TRP E 282 HIS 0.008 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00281 (31506) covalent geometry : angle 0.64914 (42908) hydrogen bonds : bond 0.03362 ( 1119) hydrogen bonds : angle 4.55392 ( 3135) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4295 (mpp) cc_final: 0.3348 (mpt) REVERT: A 135 LEU cc_start: 0.8592 (mm) cc_final: 0.8330 (mm) REVERT: B 93 MET cc_start: 0.8450 (tpp) cc_final: 0.8105 (mmt) REVERT: B 279 SER cc_start: 0.9000 (m) cc_final: 0.8715 (t) REVERT: C 203 MET cc_start: 0.8128 (tpt) cc_final: 0.7798 (tpp) REVERT: D 58 MET cc_start: 0.7996 (tmm) cc_final: 0.7795 (tmm) REVERT: D 232 VAL cc_start: 0.8491 (m) cc_final: 0.7739 (p) REVERT: E 38 TYR cc_start: 0.7689 (m-80) cc_final: 0.7455 (m-80) REVERT: E 108 LEU cc_start: 0.7339 (mt) cc_final: 0.7086 (mt) REVERT: E 158 ILE cc_start: 0.8622 (pt) cc_final: 0.8397 (pt) REVERT: F 8 MET cc_start: 0.4169 (tpp) cc_final: 0.3753 (tmm) REVERT: F 66 GLU cc_start: 0.7733 (pm20) cc_final: 0.7359 (mm-30) REVERT: F 86 THR cc_start: 0.5427 (p) cc_final: 0.5126 (p) REVERT: F 109 ILE cc_start: 0.8872 (mp) cc_final: 0.8421 (mm) REVERT: F 205 TYR cc_start: 0.7213 (m-80) cc_final: 0.6837 (m-80) REVERT: F 266 PHE cc_start: 0.7831 (t80) cc_final: 0.7526 (t80) REVERT: G 448 GLN cc_start: 0.8223 (tt0) cc_final: 0.7871 (tt0) REVERT: H 196 MET cc_start: 0.7782 (ppp) cc_final: 0.7081 (ppp) REVERT: H 254 ASN cc_start: 0.8539 (t0) cc_final: 0.8179 (t0) REVERT: H 260 MET cc_start: 0.8381 (mmp) cc_final: 0.7599 (mmp) REVERT: H 314 LEU cc_start: 0.8670 (mm) cc_final: 0.8461 (mm) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1629 time to fit residues: 85.2745 Evaluate side-chains 233 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 65 optimal weight: 0.9980 chunk 346 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 409 optimal weight: 9.9990 chunk 110 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 311 optimal weight: 7.9990 chunk 286 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 202 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 277 GLN ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 ASN J 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.091249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.074023 restraints weight = 115849.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.075008 restraints weight = 81367.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.075247 restraints weight = 58693.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.075639 restraints weight = 50831.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.075720 restraints weight = 42197.194| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31506 Z= 0.134 Angle : 0.666 11.970 42908 Z= 0.334 Chirality : 0.046 0.337 5136 Planarity : 0.004 0.087 5626 Dihedral : 5.339 87.265 4610 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.84 % Favored : 91.14 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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 are not related in a simple way. whole: -2.13 (0.13), residues: 4287 helix: 0.50 (0.14), residues: 1438 sheet: -2.55 (0.21), residues: 548 loop : -2.48 (0.13), residues: 2301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG J 121 TYR 0.029 0.001 TYR I 319 PHE 0.016 0.001 PHE J 94 TRP 0.018 0.002 TRP G 366 HIS 0.008 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00313 (31506) covalent geometry : angle 0.66580 (42908) hydrogen bonds : bond 0.03399 ( 1119) hydrogen bonds : angle 4.54396 ( 3135) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8574 Ramachandran restraints generated. 4287 Oldfield, 0 Emsley, 4287 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4328 (mpp) cc_final: 0.3339 (mpt) REVERT: A 126 LEU cc_start: 0.8268 (tp) cc_final: 0.8012 (tp) REVERT: B 93 MET cc_start: 0.8492 (tpp) cc_final: 0.8137 (mmt) REVERT: B 279 SER cc_start: 0.9062 (m) cc_final: 0.8780 (t) REVERT: C 203 MET cc_start: 0.8150 (tpt) cc_final: 0.7809 (tpp) REVERT: D 226 MET cc_start: 0.8700 (tpt) cc_final: 0.8286 (tpt) REVERT: E 38 TYR cc_start: 0.7885 (m-80) cc_final: 0.7631 (m-80) REVERT: E 108 LEU cc_start: 0.7119 (mt) cc_final: 0.6918 (mt) REVERT: E 158 ILE cc_start: 0.8610 (pt) cc_final: 0.8386 (pt) REVERT: E 282 TRP cc_start: 0.7257 (m-90) cc_final: 0.6520 (m-90) REVERT: F 86 THR cc_start: 0.5241 (p) cc_final: 0.4848 (p) REVERT: F 109 ILE cc_start: 0.8881 (mp) cc_final: 0.8431 (mm) REVERT: F 205 TYR cc_start: 0.7173 (m-80) cc_final: 0.6836 (m-80) REVERT: F 216 MET cc_start: 0.7760 (tpp) cc_final: 0.7553 (tpp) REVERT: F 266 PHE cc_start: 0.7780 (t80) cc_final: 0.7483 (t80) REVERT: G 448 GLN cc_start: 0.8300 (tt0) cc_final: 0.7868 (tt0) REVERT: H 196 MET cc_start: 0.7796 (ppp) cc_final: 0.7161 (ppp) REVERT: H 254 ASN cc_start: 0.8701 (t0) cc_final: 0.8320 (t0) REVERT: H 260 MET cc_start: 0.8343 (mmp) cc_final: 0.7503 (mmp) REVERT: H 274 HIS cc_start: 0.6735 (m-70) cc_final: 0.6530 (m-70) REVERT: I 187 GLU cc_start: 0.8181 (tt0) cc_final: 0.7833 (tp30) REVERT: I 243 ASP cc_start: 0.7607 (m-30) cc_final: 0.7235 (m-30) outliers start: 0 outliers final: 0 residues processed: 302 average time/residue: 0.1627 time to fit residues: 83.3547 Evaluate side-chains 236 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 69 optimal weight: 3.9990 chunk 374 optimal weight: 0.0970 chunk 102 optimal weight: 0.9990 chunk 257 optimal weight: 0.6980 chunk 118 optimal weight: 0.0770 chunk 327 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 340 optimal weight: 10.0000 chunk 308 optimal weight: 0.0970 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 309 HIS ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 ASN J 440 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.092956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.075468 restraints weight = 115929.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.076316 restraints weight = 75127.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.076505 restraints weight = 63056.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.077244 restraints weight = 49224.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.077592 restraints weight = 36561.543| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 31506 Z= 0.114 Angle : 0.645 11.726 42908 Z= 0.322 Chirality : 0.046 0.320 5136 Planarity : 0.004 0.088 5626 Dihedral : 5.224 87.922 4610 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.67 % Favored : 92.30 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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 are not related in a simple way. whole: -2.00 (0.13), residues: 4287 helix: 0.57 (0.14), residues: 1450 sheet: -2.40 (0.21), residues: 567 loop : -2.41 (0.13), residues: 2270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 121 TYR 0.016 0.001 TYR G 441 PHE 0.029 0.001 PHE A 10 TRP 0.026 0.001 TRP G 366 HIS 0.009 0.001 HIS E 115 Details of bonding type rmsd covalent geometry : bond 0.00259 (31506) covalent geometry : angle 0.64485 (42908) hydrogen bonds : bond 0.03272 ( 1119) hydrogen bonds : angle 4.44489 ( 3135) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4094.00 seconds wall clock time: 72 minutes 15.49 seconds (4335.49 seconds total)