Starting phenix.real_space_refine on Thu Jun 26 18:25:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7d43_30568/06_2025/7d43_30568.cif Found real_map, /net/cci-nas-00/data/ceres_data/7d43_30568/06_2025/7d43_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_30568/06_2025/7d43_30568.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7d43_30568/06_2025/7d43_30568.map" model { file = "/net/cci-nas-00/data/ceres_data/7d43_30568/06_2025/7d43_30568.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7d43_30568/06_2025/7d43_30568.cif" } resolution = 4.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} 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, 'ASN:plan1': 6, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 4} 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: {'GLN:plan1': 4, 'ASP:plan': 14, 'TYR:plan': 12, 'ASN:plan1': 13, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 7, 'GLU:plan': 27, 'ARG:plan': 19} 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: {'GLN:plan1': 3, 'ASP:plan': 12, 'TYR:plan': 9, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 6, 'GLU:plan': 18, 'ARG:plan': 14} 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: {'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} 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: {'GLN:plan1': 13, 'ASP:plan': 18, 'TYR:plan': 8, 'ASN:plan1': 14, 'TRP:plan': 2, 'HIS:plan': 9, 'PHE:plan': 11, 'GLU:plan': 27, 'ARG:plan': 19} Unresolved non-hydrogen planarities: 536 Time building chain proxies: 17.96, per 1000 atoms: 0.58 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: 8.06 Conformation dependent library (CDL) restraints added in 4.1 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: 3.29 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: 10.94 Time building geometry restraints manager: 9.38 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: 1.510 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: 0.030 Extract box with map and model: 1.210 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 67.690 Find NCS groups from input model: 1.200 Set up NCS constraints: 0.160 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:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.510 ------------------------------------------------------------------------------- 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 : 28.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.11 (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 TRP 0.019 0.003 TRP H 350 HIS 0.013 0.002 HIS B 128 PHE 0.022 0.002 PHE D 278 TYR 0.024 0.002 TYR H 214 ARG 0.009 0.001 ARG H 301 Details of bonding type rmsd hydrogen bonds : bond 0.16655 ( 1119) hydrogen bonds : angle 7.55505 ( 3135) covalent geometry : bond 0.00645 (31506) covalent geometry : angle 0.98659 (42908) *********************** 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 : 3.759 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: 0.8855 (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: 0.7829 (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: 0.4316 time to fit residues: 200.5580 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 : 3.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 362 optimal weight: 7.9990 chunk 325 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 111 optimal weight: 1.9990 chunk 219 optimal weight: 6.9990 chunk 173 optimal weight: 9.9990 chunk 336 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 204 optimal weight: 0.9990 chunk 250 optimal weight: 3.9990 chunk 389 optimal weight: 40.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 GLN A 116 HIS ** A 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 HIS 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 190 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** H 213 GLN 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 393 GLN J 434 GLN J 452 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.085772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.068130 restraints weight = 119071.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.068077 restraints weight = 84693.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.068938 restraints weight = 71514.631| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 31506 Z= 0.223 Angle : 0.797 11.144 42908 Z= 0.415 Chirality : 0.050 0.272 5136 Planarity : 0.006 0.070 5626 Dihedral : 7.039 88.916 4610 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.02 % Allowed : 14.63 % Favored : 85.35 % Rotamer: Outliers : 0.10 % Allowed : 8.23 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.72 (0.11), residues: 4287 helix: -1.78 (0.12), residues: 1438 sheet: -3.98 (0.18), residues: 526 loop : -3.97 (0.11), residues: 2323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 282 HIS 0.009 0.002 HIS B 128 PHE 0.021 0.002 PHE G 443 TYR 0.026 0.002 TYR E 38 ARG 0.009 0.001 ARG J 145 Details of bonding type rmsd hydrogen bonds : bond 0.05203 ( 1119) hydrogen bonds : angle 6.02785 ( 3135) covalent geometry : bond 0.00505 (31506) covalent geometry : angle 0.79671 (42908) *********************** 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 277 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 274 time to evaluate : 3.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7590 (mmp) cc_final: 0.7039 (mmt) REVERT: A 20 MET cc_start: 0.7536 (mmp) cc_final: 0.7295 (ptt) REVERT: A 187 MET cc_start: 0.8815 (tpp) cc_final: 0.8534 (tpt) REVERT: C 44 GLN cc_start: 0.8454 (tm-30) cc_final: 0.7911 (tm-30) REVERT: C 45 ILE cc_start: 0.8247 (mt) cc_final: 0.7742 (mt) REVERT: C 217 MET cc_start: 0.7751 (ttp) cc_final: 0.7534 (ttt) REVERT: D 128 GLN cc_start: 0.8003 (tt0) cc_final: 0.7074 (tp40) REVERT: D 139 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7812 (tm-30) REVERT: D 166 MET cc_start: 0.7715 (mtm) cc_final: 0.7438 (mtp) REVERT: E 132 MET cc_start: 0.8970 (mmm) cc_final: 0.8658 (mmm) REVERT: E 216 MET cc_start: 0.7665 (tmm) cc_final: 0.7084 (tmm) REVERT: F 8 MET cc_start: 0.4935 (tpt) cc_final: 0.4601 (tpp) REVERT: F 132 MET cc_start: 0.7889 (mtt) cc_final: 0.7657 (mtp) REVERT: F 205 TYR cc_start: 0.7744 (m-80) cc_final: 0.7234 (m-80) REVERT: G 229 LEU cc_start: 0.9143 (tp) cc_final: 0.8796 (tt) REVERT: G 273 MET cc_start: 0.7945 (mtm) cc_final: 0.7471 (mtt) REVERT: G 422 GLN cc_start: 0.8781 (tt0) cc_final: 0.8520 (tp40) REVERT: G 497 VAL cc_start: 0.8794 (p) cc_final: 0.8573 (p) REVERT: H 273 MET cc_start: 0.8882 (mtm) cc_final: 0.8560 (mtm) REVERT: I 218 THR cc_start: 0.9154 (t) cc_final: 0.8928 (m) REVERT: J 175 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: K 63 ARG cc_start: 0.8810 (mtm110) cc_final: 0.8544 (ptm160) outliers start: 3 outliers final: 2 residues processed: 277 average time/residue: 0.4136 time to fit residues: 187.5272 Evaluate side-chains 197 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 194 time to evaluate : 3.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 338 optimal weight: 10.0000 chunk 355 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 239 optimal weight: 0.8980 chunk 261 optimal weight: 0.6980 chunk 55 optimal weight: 0.3980 chunk 144 optimal weight: 7.9990 chunk 272 optimal weight: 0.6980 chunk 157 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 335 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 132 ASN ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 245 ASN G 479 HIS I 200 ASN I 340 HIS J 72 ASN J 168 HIS J 384 HIS J 440 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.088889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.071199 restraints weight = 117064.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.071377 restraints weight = 78092.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.071803 restraints weight = 68581.493| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31506 Z= 0.156 Angle : 0.711 12.389 42908 Z= 0.368 Chirality : 0.047 0.269 5136 Planarity : 0.005 0.078 5626 Dihedral : 6.397 88.023 4610 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.66 % Favored : 89.32 % Rotamer: Outliers : 0.07 % Allowed : 5.94 % Favored : 94.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.12), residues: 4287 helix: -0.75 (0.13), residues: 1447 sheet: -3.60 (0.18), residues: 529 loop : -3.51 (0.12), residues: 2311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 366 HIS 0.006 0.001 HIS I 214 PHE 0.019 0.002 PHE J 224 TYR 0.030 0.002 TYR E 38 ARG 0.006 0.001 ARG E 286 Details of bonding type rmsd hydrogen bonds : bond 0.04359 ( 1119) hydrogen bonds : angle 5.37406 ( 3135) covalent geometry : bond 0.00333 (31506) covalent geometry : angle 0.71146 (42908) *********************** 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 301 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 299 time to evaluate : 3.407 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7520 (mmp) cc_final: 0.6836 (mmt) REVERT: A 135 LEU cc_start: 0.8660 (mm) cc_final: 0.8278 (mm) REVERT: A 187 MET cc_start: 0.9070 (tpp) cc_final: 0.8811 (tpt) REVERT: B 14 MET cc_start: 0.9070 (ptt) cc_final: 0.8775 (ptp) REVERT: C 44 GLN cc_start: 0.8778 (tm-30) cc_final: 0.8525 (tm-30) REVERT: C 203 MET cc_start: 0.8389 (tpt) cc_final: 0.8029 (tpp) REVERT: D 34 MET cc_start: 0.8530 (mmm) cc_final: 0.8269 (tpp) REVERT: D 96 LEU cc_start: 0.9038 (tp) cc_final: 0.8737 (tp) REVERT: D 128 GLN cc_start: 0.7920 (tt0) cc_final: 0.7083 (tp40) REVERT: D 139 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7555 (tm-30) REVERT: D 157 GLU cc_start: 0.7309 (tm-30) cc_final: 0.6886 (tm-30) REVERT: D 166 MET cc_start: 0.7423 (mtm) cc_final: 0.7119 (mtp) REVERT: E 44 GLU cc_start: 0.8103 (pt0) cc_final: 0.7840 (pt0) REVERT: E 132 MET cc_start: 0.8997 (mmm) cc_final: 0.8712 (mmm) REVERT: E 216 MET cc_start: 0.7665 (tmm) cc_final: 0.7084 (tpp) REVERT: E 290 TRP cc_start: 0.8674 (m-90) cc_final: 0.8353 (m-90) REVERT: F 8 MET cc_start: 0.4708 (tpt) cc_final: 0.4492 (tpp) REVERT: F 64 CYS cc_start: 0.7925 (m) cc_final: 0.7647 (t) REVERT: F 205 TYR cc_start: 0.7689 (m-80) cc_final: 0.7233 (m-80) REVERT: G 229 LEU cc_start: 0.9026 (tp) cc_final: 0.8620 (tt) REVERT: G 273 MET cc_start: 0.7784 (mtm) cc_final: 0.7380 (mtt) REVERT: G 448 GLN cc_start: 0.8077 (tt0) cc_final: 0.7748 (tp-100) REVERT: H 273 MET cc_start: 0.8723 (mtm) cc_final: 0.8448 (mtm) REVERT: I 149 LEU cc_start: 0.8468 (mt) cc_final: 0.8200 (mt) REVERT: I 187 GLU cc_start: 0.8282 (tt0) cc_final: 0.7834 (tp30) REVERT: I 214 HIS cc_start: 0.6524 (OUTLIER) cc_final: 0.6049 (m-70) REVERT: I 296 TYR cc_start: 0.8399 (t80) cc_final: 0.8054 (t80) REVERT: J 168 HIS cc_start: 0.8290 (OUTLIER) cc_final: 0.7785 (t-170) REVERT: K 63 ARG cc_start: 0.8844 (mtm110) cc_final: 0.8502 (ptm160) outliers start: 2 outliers final: 0 residues processed: 301 average time/residue: 0.3809 time to fit residues: 192.0070 Evaluate side-chains 218 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 216 time to evaluate : 3.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 212 optimal weight: 0.8980 chunk 396 optimal weight: 8.9990 chunk 183 optimal weight: 40.0000 chunk 242 optimal weight: 3.9990 chunk 307 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 334 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 173 optimal weight: 8.9990 chunk 193 optimal weight: 0.6980 chunk 198 optimal weight: 0.9980 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 HIS D 188 HIS ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 200 ASN J 168 HIS J 384 HIS J 434 GLN J 440 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.088928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.071099 restraints weight = 116166.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.071573 restraints weight = 79880.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.072109 restraints weight = 63928.886| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2496 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= 0.156 Angle : 0.691 11.842 42908 Z= 0.355 Chirality : 0.047 0.246 5136 Planarity : 0.005 0.081 5626 Dihedral : 6.173 87.428 4610 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.24 % Favored : 88.73 % Rotamer: Outliers : 0.03 % Allowed : 4.44 % Favored : 95.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.32 (0.12), residues: 4287 helix: -0.34 (0.13), residues: 1445 sheet: -3.47 (0.18), residues: 562 loop : -3.24 (0.12), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP G 366 HIS 0.014 0.001 HIS I 214 PHE 0.016 0.002 PHE H 452 TYR 0.023 0.002 TYR E 38 ARG 0.009 0.000 ARG J 299 Details of bonding type rmsd hydrogen bonds : bond 0.04064 ( 1119) hydrogen bonds : angle 5.12224 ( 3135) covalent geometry : bond 0.00356 (31506) covalent geometry : angle 0.69126 (42908) *********************** 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 300 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 299 time to evaluate : 3.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7964 (mmp) cc_final: 0.7673 (mmt) REVERT: B 14 MET cc_start: 0.9077 (ptt) cc_final: 0.8797 (ptp) REVERT: C 203 MET cc_start: 0.8448 (tpt) cc_final: 0.8038 (tpp) REVERT: C 217 MET cc_start: 0.7525 (ttp) cc_final: 0.7264 (ttp) REVERT: D 96 LEU cc_start: 0.9064 (tp) cc_final: 0.8701 (tp) REVERT: D 128 GLN cc_start: 0.7881 (tt0) cc_final: 0.7493 (pm20) REVERT: D 139 GLU cc_start: 0.7857 (tm-30) cc_final: 0.7478 (tm-30) REVERT: D 157 GLU cc_start: 0.7361 (tm-30) cc_final: 0.6970 (tm-30) REVERT: D 166 MET cc_start: 0.7465 (mtm) cc_final: 0.7163 (mtp) REVERT: E 44 GLU cc_start: 0.8093 (pt0) cc_final: 0.7695 (pt0) REVERT: E 132 MET cc_start: 0.8965 (mmm) cc_final: 0.8704 (mmm) REVERT: E 207 LEU cc_start: 0.8629 (mp) cc_final: 0.8387 (mp) REVERT: E 290 TRP cc_start: 0.8437 (m-90) cc_final: 0.8065 (m-90) REVERT: F 205 TYR cc_start: 0.7459 (m-80) cc_final: 0.7067 (m-80) REVERT: G 229 LEU cc_start: 0.9044 (tp) cc_final: 0.8613 (tt) REVERT: G 273 MET cc_start: 0.7545 (mtm) cc_final: 0.7200 (mtt) REVERT: G 409 LEU cc_start: 0.8249 (mt) cc_final: 0.8039 (mt) REVERT: G 415 MET cc_start: 0.9310 (ttm) cc_final: 0.9044 (tmm) REVERT: G 448 GLN cc_start: 0.8025 (tt0) cc_final: 0.7582 (tt0) REVERT: H 196 MET cc_start: 0.7987 (ppp) cc_final: 0.7726 (ppp) REVERT: H 273 MET cc_start: 0.8914 (mtm) cc_final: 0.8685 (mtm) REVERT: I 187 GLU cc_start: 0.8290 (tt0) cc_final: 0.7868 (tp30) REVERT: I 200 ASN cc_start: 0.8523 (m-40) cc_final: 0.8106 (m110) REVERT: I 218 THR cc_start: 0.8849 (m) cc_final: 0.8523 (t) REVERT: I 296 TYR cc_start: 0.8329 (t80) cc_final: 0.7979 (t80) outliers start: 1 outliers final: 1 residues processed: 300 average time/residue: 0.3909 time to fit residues: 197.4467 Evaluate side-chains 214 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 3.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 128 optimal weight: 0.9990 chunk 286 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 262 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 290 optimal weight: 1.9990 chunk 344 optimal weight: 20.0000 chunk 379 optimal weight: 7.9990 chunk 247 optimal weight: 0.9980 chunk 364 optimal weight: 0.1980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 97 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** H 194 GLN I 177 ASN I 333 GLN I 452 HIS J 384 HIS J 440 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.090448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.072954 restraints weight = 115126.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.073399 restraints weight = 79449.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.073241 restraints weight = 65906.209| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2912 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= 0.134 Angle : 0.668 11.669 42908 Z= 0.340 Chirality : 0.047 0.289 5136 Planarity : 0.005 0.085 5626 Dihedral : 5.864 87.623 4610 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.47 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.12), residues: 4287 helix: -0.00 (0.14), residues: 1436 sheet: -3.26 (0.19), residues: 555 loop : -2.96 (0.12), residues: 2296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 282 HIS 0.007 0.001 HIS E 115 PHE 0.022 0.002 PHE F 67 TYR 0.019 0.001 TYR E 38 ARG 0.007 0.000 ARG I 316 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 1119) hydrogen bonds : angle 4.89151 ( 3135) covalent geometry : bond 0.00301 (31506) covalent geometry : angle 0.66785 (42908) *********************** 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 312 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 MET cc_start: 0.7547 (mmp) cc_final: 0.7284 (mmt) REVERT: A 187 MET cc_start: 0.8982 (tpp) cc_final: 0.8569 (mmm) REVERT: B 14 MET cc_start: 0.9154 (ptt) cc_final: 0.8884 (ptp) REVERT: C 203 MET cc_start: 0.8416 (tpt) cc_final: 0.8026 (tpp) REVERT: C 217 MET cc_start: 0.7451 (ttp) cc_final: 0.6995 (ttt) REVERT: D 96 LEU cc_start: 0.9094 (tp) cc_final: 0.8714 (tp) REVERT: D 128 GLN cc_start: 0.7730 (tt0) cc_final: 0.7440 (pm20) REVERT: D 139 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7393 (tm-30) REVERT: D 157 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7102 (tm-30) REVERT: E 44 GLU cc_start: 0.8138 (pt0) cc_final: 0.7773 (pt0) REVERT: E 68 LYS cc_start: 0.6993 (mmtt) cc_final: 0.6578 (mmtt) REVERT: E 207 LEU cc_start: 0.8561 (mp) cc_final: 0.8335 (mp) REVERT: F 86 THR cc_start: 0.5074 (p) cc_final: 0.4746 (p) REVERT: F 205 TYR cc_start: 0.7272 (m-80) cc_final: 0.6781 (m-80) REVERT: G 229 LEU cc_start: 0.9025 (tp) cc_final: 0.8579 (tt) REVERT: G 409 LEU cc_start: 0.8284 (mt) cc_final: 0.8033 (mt) REVERT: G 415 MET cc_start: 0.9227 (ttm) cc_final: 0.8947 (tmm) REVERT: G 448 GLN cc_start: 0.7913 (tt0) cc_final: 0.7560 (tt0) REVERT: H 254 ASN cc_start: 0.8596 (t0) cc_final: 0.8317 (t0) REVERT: H 273 MET cc_start: 0.8778 (mtm) cc_final: 0.8073 (mtt) REVERT: I 228 LEU cc_start: 0.8831 (tp) cc_final: 0.8550 (tt) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.3963 time to fit residues: 206.3005 Evaluate side-chains 213 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 4.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 284 optimal weight: 7.9990 chunk 392 optimal weight: 50.0000 chunk 420 optimal weight: 0.7980 chunk 238 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 347 optimal weight: 9.9990 chunk 403 optimal weight: 3.9990 chunk 123 optimal weight: 0.0170 chunk 165 optimal weight: 7.9990 chunk 179 optimal weight: 20.0000 overall best weight: 1.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 188 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** 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 I 200 ASN ** J 248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3748 r_free = 0.3748 target = 0.089364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.072030 restraints weight = 117391.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.072547 restraints weight = 80497.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.072768 restraints weight = 66364.779| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 31506 Z= 0.147 Angle : 0.681 11.619 42908 Z= 0.346 Chirality : 0.047 0.248 5136 Planarity : 0.005 0.084 5626 Dihedral : 5.802 87.257 4610 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.98 % Favored : 89.99 % Rotamer: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.13), residues: 4287 helix: 0.11 (0.14), residues: 1442 sheet: -3.32 (0.19), residues: 564 loop : -2.84 (0.13), residues: 2281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP H 366 HIS 0.008 0.001 HIS E 115 PHE 0.028 0.002 PHE B 285 TYR 0.026 0.002 TYR E 38 ARG 0.008 0.000 ARG I 145 Details of bonding type rmsd hydrogen bonds : bond 0.03737 ( 1119) hydrogen bonds : angle 4.83698 ( 3135) covalent geometry : bond 0.00338 (31506) covalent geometry : angle 0.68107 (42908) *********************** 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 291 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 291 time to evaluate : 3.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 MET cc_start: 0.9145 (ptt) cc_final: 0.8901 (ptp) REVERT: C 44 GLN cc_start: 0.8565 (tm-30) cc_final: 0.8310 (tm-30) REVERT: C 203 MET cc_start: 0.8399 (tpt) cc_final: 0.8018 (tpp) REVERT: D 128 GLN cc_start: 0.7880 (tt0) cc_final: 0.7441 (pm20) REVERT: D 139 GLU cc_start: 0.7547 (tm-30) cc_final: 0.7335 (tm-30) REVERT: D 157 GLU cc_start: 0.7595 (tm-30) cc_final: 0.7123 (tm-30) REVERT: D 232 VAL cc_start: 0.8763 (m) cc_final: 0.8346 (m) REVERT: E 1 MET cc_start: 0.5309 (ttt) cc_final: 0.3900 (tpt) REVERT: E 8 MET cc_start: 0.7983 (ttm) cc_final: 0.7757 (ttm) REVERT: E 68 LYS cc_start: 0.6956 (mmtt) cc_final: 0.6560 (mmtt) REVERT: E 207 LEU cc_start: 0.8590 (mp) cc_final: 0.8342 (mp) REVERT: F 109 ILE cc_start: 0.8759 (mp) cc_final: 0.8348 (mm) REVERT: F 205 TYR cc_start: 0.7334 (m-80) cc_final: 0.6880 (m-80) REVERT: G 409 LEU cc_start: 0.8241 (mt) cc_final: 0.7960 (mt) REVERT: G 415 MET cc_start: 0.9283 (ttm) cc_final: 0.8910 (tmm) REVERT: G 448 GLN cc_start: 0.8050 (tt0) cc_final: 0.7634 (tt0) REVERT: H 196 MET cc_start: 0.7944 (ppp) cc_final: 0.7674 (ppp) REVERT: H 254 ASN cc_start: 0.8588 (t0) cc_final: 0.8299 (t0) REVERT: H 260 MET cc_start: 0.8450 (mmp) cc_final: 0.7975 (mmp) REVERT: H 273 MET cc_start: 0.8791 (mtm) cc_final: 0.8059 (mtt) REVERT: I 187 GLU cc_start: 0.8287 (tt0) cc_final: 0.7766 (tp30) REVERT: I 228 LEU cc_start: 0.8779 (tp) cc_final: 0.8485 (tt) REVERT: I 243 ASP cc_start: 0.6966 (m-30) cc_final: 0.6736 (m-30) outliers start: 0 outliers final: 0 residues processed: 291 average time/residue: 0.4090 time to fit residues: 201.6742 Evaluate side-chains 214 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 214 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 429 random chunks: chunk 185 optimal weight: 40.0000 chunk 399 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 348 optimal weight: 0.3980 chunk 302 optimal weight: 0.1980 chunk 243 optimal weight: 0.7980 chunk 137 optimal weight: 5.9990 chunk 323 optimal weight: 0.2980 chunk 105 optimal weight: 0.9980 chunk 283 optimal weight: 2.9990 chunk 331 optimal weight: 4.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 252 HIS C 261 HIS D 132 ASN ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 349 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 431 ASN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 ASN J 388 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 = 0.3780 r_free = 0.3780 target = 0.090963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.073667 restraints weight = 116185.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.074559 restraints weight = 75398.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.074681 restraints weight = 56481.231| |-----------------------------------------------------------------------------| r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3436 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= 0.123 Angle : 0.662 10.952 42908 Z= 0.334 Chirality : 0.046 0.283 5136 Planarity : 0.004 0.086 5626 Dihedral : 5.605 87.885 4610 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.37 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.65 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.13), residues: 4287 helix: 0.27 (0.14), residues: 1440 sheet: -3.15 (0.19), residues: 550 loop : -2.68 (0.13), residues: 2297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 272 HIS 0.008 0.001 HIS E 115 PHE 0.031 0.002 PHE F 67 TYR 0.024 0.001 TYR H 214 ARG 0.005 0.000 ARG E 45 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 1119) hydrogen bonds : angle 4.69276 ( 3135) covalent geometry : bond 0.00279 (31506) covalent geometry : angle 0.66161 (42908) *********************** 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 312 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 312 time to evaluate : 3.316 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.4364 (mpp) cc_final: 0.3335 (mpt) REVERT: B 14 MET cc_start: 0.9101 (ptt) cc_final: 0.8885 (ptp) REVERT: C 140 LEU cc_start: 0.9160 (tp) cc_final: 0.8766 (tp) REVERT: C 203 MET cc_start: 0.8615 (tpt) cc_final: 0.8174 (tpp) REVERT: D 58 MET cc_start: 0.8132 (tmm) cc_final: 0.7918 (tmm) REVERT: D 157 GLU cc_start: 0.7554 (tm-30) cc_final: 0.7055 (tm-30) REVERT: E 1 MET cc_start: 0.4700 (ttt) cc_final: 0.4199 (tpt) REVERT: E 8 MET cc_start: 0.7833 (ttm) cc_final: 0.7568 (ttm) REVERT: E 68 LYS cc_start: 0.7083 (mmtt) cc_final: 0.6779 (mmtt) REVERT: E 158 ILE cc_start: 0.8613 (pt) cc_final: 0.8389 (pt) REVERT: E 204 LEU cc_start: 0.8749 (tp) cc_final: 0.8357 (tt) REVERT: F 86 THR cc_start: 0.5149 (p) cc_final: 0.4289 (p) REVERT: F 109 ILE cc_start: 0.8692 (mp) cc_final: 0.8283 (mm) REVERT: F 205 TYR cc_start: 0.7099 (m-80) cc_final: 0.6710 (m-80) REVERT: G 273 MET cc_start: 0.7292 (mtt) cc_final: 0.6783 (mtt) REVERT: G 409 LEU cc_start: 0.8169 (mt) cc_final: 0.7960 (mt) REVERT: G 415 MET cc_start: 0.9113 (ttm) cc_final: 0.8734 (tmm) REVERT: G 448 GLN cc_start: 0.7974 (tt0) cc_final: 0.7614 (tt0) REVERT: H 196 MET cc_start: 0.7968 (ppp) cc_final: 0.7588 (ppp) REVERT: H 254 ASN cc_start: 0.8612 (t0) cc_final: 0.8283 (t0) REVERT: H 260 MET cc_start: 0.8536 (mmp) cc_final: 0.8013 (mmp) REVERT: H 314 LEU cc_start: 0.8793 (mm) cc_final: 0.8564 (mm) REVERT: H 420 THR cc_start: 0.8747 (t) cc_final: 0.8462 (t) REVERT: I 187 GLU cc_start: 0.8284 (tt0) cc_final: 0.7823 (tp30) REVERT: I 228 LEU cc_start: 0.8669 (tp) cc_final: 0.8397 (tt) REVERT: I 243 ASP cc_start: 0.7118 (m-30) cc_final: 0.6763 (m-30) outliers start: 0 outliers final: 0 residues processed: 312 average time/residue: 0.3784 time to fit residues: 198.2444 Evaluate side-chains 222 residues out of total 3792 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 3.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.8954 > 50: distance: 14 - 32: 22.752 distance: 18 - 41: 23.236 distance: 22 - 48: 13.732 distance: 28 - 32: 19.854 distance: 29 - 56: 21.264 distance: 32 - 33: 16.768 distance: 33 - 34: 39.675 distance: 33 - 36: 24.653 distance: 34 - 35: 36.778 distance: 34 - 41: 48.512 distance: 35 - 65: 38.370 distance: 36 - 37: 30.151 distance: 37 - 38: 26.458 distance: 38 - 39: 6.563 distance: 38 - 40: 6.938 distance: 41 - 42: 22.295 distance: 42 - 43: 12.298 distance: 42 - 45: 7.185 distance: 43 - 44: 8.512 distance: 43 - 48: 27.621 distance: 44 - 73: 30.542 distance: 45 - 46: 12.131 distance: 45 - 47: 16.244 distance: 48 - 49: 9.113 distance: 49 - 50: 22.625 distance: 49 - 52: 20.741 distance: 50 - 51: 19.334 distance: 50 - 56: 29.153 distance: 52 - 53: 28.835 distance: 52 - 54: 24.060 distance: 53 - 55: 18.192 distance: 56 - 57: 27.651 distance: 57 - 58: 23.367 distance: 57 - 60: 18.314 distance: 58 - 59: 19.762 distance: 58 - 65: 39.838 distance: 60 - 61: 26.754 distance: 61 - 62: 16.588 distance: 62 - 63: 14.216 distance: 62 - 64: 19.172 distance: 65 - 66: 15.769 distance: 66 - 67: 29.464 distance: 66 - 69: 14.672 distance: 67 - 68: 28.278 distance: 67 - 73: 19.516 distance: 69 - 70: 14.915 distance: 70 - 71: 12.158 distance: 70 - 72: 8.041 distance: 73 - 74: 18.159 distance: 74 - 75: 24.847 distance: 74 - 77: 15.041 distance: 75 - 76: 5.157 distance: 75 - 85: 19.161 distance: 77 - 78: 17.599 distance: 78 - 79: 14.371 distance: 78 - 80: 7.971 distance: 79 - 81: 14.523 distance: 80 - 82: 4.291 distance: 81 - 83: 4.242 distance: 82 - 83: 6.758 distance: 83 - 84: 9.115 distance: 85 - 86: 33.199 distance: 86 - 87: 6.088 distance: 86 - 89: 20.135 distance: 87 - 88: 41.452 distance: 87 - 92: 10.905 distance: 89 - 90: 16.199 distance: 89 - 91: 15.296 distance: 92 - 93: 12.807 distance: 93 - 94: 7.075 distance: 93 - 96: 24.200 distance: 94 - 95: 21.671 distance: 94 - 99: 32.204 distance: 96 - 97: 28.894 distance: 96 - 98: 18.659 distance: 99 - 100: 19.441 distance: 99 - 105: 40.260 distance: 100 - 101: 16.451 distance: 100 - 103: 14.876 distance: 101 - 102: 42.613 distance: 101 - 106: 34.273 distance: 103 - 104: 26.516 distance: 104 - 105: 34.786 distance: 106 - 107: 12.072 distance: 106 - 112: 27.717 distance: 107 - 108: 21.786 distance: 108 - 109: 16.853 distance: 108 - 113: 5.210 distance: 110 - 111: 23.603 distance: 111 - 112: 49.487