Starting phenix.real_space_refine on Fri Sep 27 02:50:50 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/09_2024/6u96_20694.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/09_2024/6u96_20694.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/09_2024/6u96_20694.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/09_2024/6u96_20694.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/09_2024/6u96_20694.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u96_20694/09_2024/6u96_20694.cif" } resolution = 3.8 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.007 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 10 5.49 5 S 110 5.16 5 C 9410 2.51 5 N 2510 2.21 5 O 2870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14910 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'CIS': 1, 'TRANS': 5} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1, 'ALO:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: F, I, H, J, C, B, E, D Time building chain proxies: 6.64, per 1000 atoms: 0.45 Number of scatterers: 14910 At special positions: 0 Unit cell: (87.74, 102.72, 204.37, 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 110 16.00 P 10 15.00 O 2870 8.00 N 2510 7.00 C 9410 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.99 Conformation dependent library (CDL) restraints added in 1.9 seconds 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3500 Finding SS restraints... Secondary structure from input PDB file: 105 helices and 25 sheets defined 42.8% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.568A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 91 removed outlier: 3.630A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR A 91 " --> pdb=" O HIS A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.801A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 114 through 125 removed outlier: 4.212A pdb=" N MET A 119 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR A 120 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN A 121 " --> pdb=" O GLU A 117 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE A 122 " --> pdb=" O LYS A 118 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET A 123 " --> pdb=" O MET A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 140 No H-bonds generated for 'chain 'A' and resid 138 through 140' Processing helix chain 'A' and resid 141 through 146 removed outlier: 3.652A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 4.172A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 182 through 193 removed outlier: 3.725A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 206 through 216 removed outlier: 3.989A pdb=" N ILE A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 233 removed outlier: 3.550A pdb=" N MET A 227 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 228 " --> pdb=" O GLU A 224 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 232 " --> pdb=" O ALA A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.658A pdb=" N THR A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU A 261 " --> pdb=" O PRO A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 removed outlier: 4.009A pdb=" N THR A 278 " --> pdb=" O ILE A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.977A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 3.947A pdb=" N MET A 305 " --> pdb=" O GLY A 302 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 306' Processing helix chain 'A' and resid 309 through 318 removed outlier: 3.576A pdb=" N MET A 313 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS A 315 " --> pdb=" O ASP A 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE A 317 " --> pdb=" O MET A 313 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 removed outlier: 3.566A pdb=" N GLY A 343 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 347 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER A 348 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.616A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 removed outlier: 3.735A pdb=" N TYR A 362 " --> pdb=" O THR A 358 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA A 365 " --> pdb=" O GLU A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 368 No H-bonds generated for 'chain 'A' and resid 366 through 368' Processing helix chain 'A' and resid 369 through 374 removed outlier: 3.770A pdb=" N CYS A 374 " --> pdb=" O VAL A 370 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.567A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.631A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR B 91 " --> pdb=" O HIS B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.801A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 114 through 125 removed outlier: 4.213A pdb=" N MET B 119 " --> pdb=" O ASN B 115 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN B 121 " --> pdb=" O GLU B 117 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET B 123 " --> pdb=" O MET B 119 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 140 No H-bonds generated for 'chain 'B' and resid 138 through 140' Processing helix chain 'B' and resid 141 through 146 removed outlier: 3.653A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 removed outlier: 4.173A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 182 through 193 removed outlier: 3.724A pdb=" N LYS B 191 " --> pdb=" O ASP B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 196 No H-bonds generated for 'chain 'B' and resid 194 through 196' Processing helix chain 'B' and resid 206 through 216 removed outlier: 3.988A pdb=" N ILE B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 233 removed outlier: 3.551A pdb=" N MET B 227 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA B 228 " --> pdb=" O GLU B 224 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER B 232 " --> pdb=" O ALA B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 262 removed outlier: 3.658A pdb=" N THR B 260 " --> pdb=" O CYS B 257 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU B 261 " --> pdb=" O PRO B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 removed outlier: 4.009A pdb=" N THR B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 295 removed outlier: 3.977A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 3.947A pdb=" N MET B 305 " --> pdb=" O GLY B 302 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 302 through 306' Processing helix chain 'B' and resid 309 through 318 removed outlier: 3.576A pdb=" N MET B 313 " --> pdb=" O ILE B 309 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS B 315 " --> pdb=" O ASP B 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE B 317 " --> pdb=" O MET B 313 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR B 318 " --> pdb=" O GLN B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 348 removed outlier: 3.566A pdb=" N GLY B 343 " --> pdb=" O VAL B 339 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE B 345 " --> pdb=" O ILE B 341 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA B 347 " --> pdb=" O GLY B 343 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER B 348 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.616A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 365 removed outlier: 3.735A pdb=" N TYR B 362 " --> pdb=" O THR B 358 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 368 No H-bonds generated for 'chain 'B' and resid 366 through 368' Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.770A pdb=" N CYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.567A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.630A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ILE C 85 " --> pdb=" O ASP C 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR C 91 " --> pdb=" O HIS C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.801A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 114 through 125 removed outlier: 4.212A pdb=" N MET C 119 " --> pdb=" O ASN C 115 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR C 120 " --> pdb=" O ARG C 116 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLN C 121 " --> pdb=" O GLU C 117 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 140 No H-bonds generated for 'chain 'C' and resid 138 through 140' Processing helix chain 'C' and resid 141 through 146 removed outlier: 3.653A pdb=" N SER C 145 " --> pdb=" O SER C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 4.173A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 182 through 193 removed outlier: 3.725A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 196 No H-bonds generated for 'chain 'C' and resid 194 through 196' Processing helix chain 'C' and resid 206 through 216 removed outlier: 3.989A pdb=" N ILE C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 233 removed outlier: 3.550A pdb=" N MET C 227 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER C 232 " --> pdb=" O ALA C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.658A pdb=" N THR C 260 " --> pdb=" O CYS C 257 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU C 261 " --> pdb=" O PRO C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 284 removed outlier: 4.010A pdb=" N THR C 278 " --> pdb=" O ILE C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 removed outlier: 3.976A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 3.947A pdb=" N MET C 305 " --> pdb=" O GLY C 302 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 302 through 306' Processing helix chain 'C' and resid 309 through 318 removed outlier: 3.576A pdb=" N MET C 313 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C 315 " --> pdb=" O ASP C 311 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE C 317 " --> pdb=" O MET C 313 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR C 318 " --> pdb=" O GLN C 314 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 348 removed outlier: 3.566A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE C 345 " --> pdb=" O ILE C 341 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA C 347 " --> pdb=" O GLY C 343 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.616A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 365 removed outlier: 3.735A pdb=" N TYR C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 368 No H-bonds generated for 'chain 'C' and resid 366 through 368' Processing helix chain 'C' and resid 369 through 374 removed outlier: 3.770A pdb=" N CYS C 374 " --> pdb=" O VAL C 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.567A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.630A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS D 84 " --> pdb=" O ASP D 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR D 91 " --> pdb=" O HIS D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.801A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 114 through 125 removed outlier: 4.212A pdb=" N MET D 119 " --> pdb=" O ASN D 115 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N THR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN D 121 " --> pdb=" O GLU D 117 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE D 122 " --> pdb=" O LYS D 118 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N MET D 123 " --> pdb=" O MET D 119 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 140 No H-bonds generated for 'chain 'D' and resid 138 through 140' Processing helix chain 'D' and resid 141 through 146 removed outlier: 3.653A pdb=" N SER D 145 " --> pdb=" O SER D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 removed outlier: 4.174A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 182 through 193 removed outlier: 3.725A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 196 No H-bonds generated for 'chain 'D' and resid 194 through 196' Processing helix chain 'D' and resid 206 through 216 removed outlier: 3.989A pdb=" N ILE D 212 " --> pdb=" O ILE D 208 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 233 removed outlier: 3.550A pdb=" N MET D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA D 231 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER D 232 " --> pdb=" O ALA D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 removed outlier: 3.658A pdb=" N THR D 260 " --> pdb=" O CYS D 257 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU D 261 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 273 through 284 removed outlier: 4.009A pdb=" N THR D 278 " --> pdb=" O ILE D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 295 removed outlier: 3.976A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 3.947A pdb=" N MET D 305 " --> pdb=" O GLY D 302 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 302 through 306' Processing helix chain 'D' and resid 309 through 318 removed outlier: 3.576A pdb=" N MET D 313 " --> pdb=" O ILE D 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 315 " --> pdb=" O ASP D 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE D 317 " --> pdb=" O MET D 313 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N THR D 318 " --> pdb=" O GLN D 314 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 348 removed outlier: 3.566A pdb=" N GLY D 343 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA D 347 " --> pdb=" O GLY D 343 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER D 348 " --> pdb=" O SER D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.616A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 358 through 365 removed outlier: 3.735A pdb=" N TYR D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 365 " --> pdb=" O GLU D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 368 No H-bonds generated for 'chain 'D' and resid 366 through 368' Processing helix chain 'D' and resid 369 through 374 removed outlier: 3.770A pdb=" N CYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.568A pdb=" N LYS E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.630A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TYR E 91 " --> pdb=" O HIS E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.801A pdb=" N GLU E 100 " --> pdb=" O ALA E 97 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 97 through 101' Processing helix chain 'E' and resid 114 through 125 removed outlier: 4.212A pdb=" N MET E 119 " --> pdb=" O ASN E 115 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N THR E 120 " --> pdb=" O ARG E 116 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN E 121 " --> pdb=" O GLU E 117 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE E 122 " --> pdb=" O LYS E 118 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET E 123 " --> pdb=" O MET E 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 140 No H-bonds generated for 'chain 'E' and resid 138 through 140' Processing helix chain 'E' and resid 141 through 146 removed outlier: 3.653A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 175 removed outlier: 4.173A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 182 through 193 removed outlier: 3.725A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 196 No H-bonds generated for 'chain 'E' and resid 194 through 196' Processing helix chain 'E' and resid 206 through 216 removed outlier: 3.988A pdb=" N ILE E 212 " --> pdb=" O ILE E 208 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS E 215 " --> pdb=" O ASP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 233 removed outlier: 3.551A pdb=" N MET E 227 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA E 228 " --> pdb=" O GLU E 224 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA E 231 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N SER E 232 " --> pdb=" O ALA E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 262 removed outlier: 3.658A pdb=" N THR E 260 " --> pdb=" O CYS E 257 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU E 261 " --> pdb=" O PRO E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 273 through 284 removed outlier: 4.009A pdb=" N THR E 278 " --> pdb=" O ILE E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 290 through 295 removed outlier: 3.977A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 302 through 306 removed outlier: 3.946A pdb=" N MET E 305 " --> pdb=" O GLY E 302 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 302 through 306' Processing helix chain 'E' and resid 309 through 318 removed outlier: 3.577A pdb=" N MET E 313 " --> pdb=" O ILE E 309 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ILE E 317 " --> pdb=" O MET E 313 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR E 318 " --> pdb=" O GLN E 314 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 348 removed outlier: 3.567A pdb=" N GLY E 343 " --> pdb=" O VAL E 339 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE E 345 " --> pdb=" O ILE E 341 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA E 347 " --> pdb=" O GLY E 343 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER E 348 " --> pdb=" O SER E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.616A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 365 removed outlier: 3.736A pdb=" N TYR E 362 " --> pdb=" O THR E 358 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E 365 " --> pdb=" O GLU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 366 through 368 No H-bonds generated for 'chain 'E' and resid 366 through 368' Processing helix chain 'E' and resid 369 through 374 removed outlier: 3.770A pdb=" N CYS E 374 " --> pdb=" O VAL E 370 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 12 removed outlier: 3.563A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 41 through 42 removed outlier: 4.421A pdb=" N GLN A 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 105 through 107 removed outlier: 7.119A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 151 removed outlier: 4.424A pdb=" N GLN E 41 " --> pdb=" O ALA A 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 162 removed outlier: 3.691A pdb=" N MET A 176 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 8 through 12 removed outlier: 3.564A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA B 29 " --> pdb=" O ALA B 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 105 through 107 removed outlier: 7.119A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 150 through 151 removed outlier: 4.533A pdb=" N GLN C 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 160 through 162 removed outlier: 3.691A pdb=" N MET B 176 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB3, first strand: chain 'C' and resid 8 through 12 removed outlier: 3.562A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA C 29 " --> pdb=" O ALA C 19 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 105 through 107 removed outlier: 7.119A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 150 through 151 Processing sheet with id=AB6, first strand: chain 'C' and resid 160 through 162 removed outlier: 3.691A pdb=" N MET C 176 " --> pdb=" O ASN C 162 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB8, first strand: chain 'D' and resid 8 through 12 removed outlier: 3.563A pdb=" N PHE D 31 " --> pdb=" O VAL D 17 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA D 29 " --> pdb=" O ALA D 19 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 105 through 107 removed outlier: 7.119A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 160 through 162 removed outlier: 3.691A pdb=" N MET D 176 " --> pdb=" O ASN D 162 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC3, first strand: chain 'E' and resid 8 through 12 removed outlier: 3.562A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA E 29 " --> pdb=" O ALA E 19 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 105 through 107 removed outlier: 7.119A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'E' and resid 150 through 151 Processing sheet with id=AC6, first strand: chain 'E' and resid 160 through 162 removed outlier: 3.692A pdb=" N MET E 176 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 238 through 241 316 hydrogen bonds defined for protein. 858 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: 4.14 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2486 1.31 - 1.44: 3934 1.44 - 1.57: 8615 1.57 - 1.70: 20 1.70 - 1.83: 190 Bond restraints: 15245 Sorted by residual: bond pdb=" C CYS H 4 " pdb=" N HYP H 5 " ideal model delta sigma weight residual 1.329 1.488 -0.159 1.40e-02 5.10e+03 1.28e+02 bond pdb=" C CYS J 4 " pdb=" N HYP J 5 " ideal model delta sigma weight residual 1.329 1.487 -0.158 1.40e-02 5.10e+03 1.27e+02 bond pdb=" C CYS G 4 " pdb=" N HYP G 5 " ideal model delta sigma weight residual 1.329 1.487 -0.158 1.40e-02 5.10e+03 1.27e+02 bond pdb=" C CYS I 4 " pdb=" N HYP I 5 " ideal model delta sigma weight residual 1.329 1.487 -0.158 1.40e-02 5.10e+03 1.27e+02 bond pdb=" C CYS F 4 " pdb=" N HYP F 5 " ideal model delta sigma weight residual 1.329 1.486 -0.157 1.40e-02 5.10e+03 1.26e+02 ... (remaining 15240 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 19847 2.49 - 4.98: 715 4.98 - 7.46: 113 7.46 - 9.95: 15 9.95 - 12.44: 15 Bond angle restraints: 20705 Sorted by residual: angle pdb=" CD1 TRP F 7 " pdb=" NE1 TRP F 7 " pdb=" CE2 TRP F 7 " ideal model delta sigma weight residual 108.90 120.67 -11.77 1.80e+00 3.09e-01 4.27e+01 angle pdb=" CD1 TRP H 7 " pdb=" NE1 TRP H 7 " pdb=" CE2 TRP H 7 " ideal model delta sigma weight residual 108.90 120.66 -11.76 1.80e+00 3.09e-01 4.27e+01 angle pdb=" CD1 TRP J 7 " pdb=" NE1 TRP J 7 " pdb=" CE2 TRP J 7 " ideal model delta sigma weight residual 108.90 120.66 -11.76 1.80e+00 3.09e-01 4.27e+01 angle pdb=" CD1 TRP I 7 " pdb=" NE1 TRP I 7 " pdb=" CE2 TRP I 7 " ideal model delta sigma weight residual 108.90 120.65 -11.75 1.80e+00 3.09e-01 4.26e+01 angle pdb=" CD1 TRP G 7 " pdb=" NE1 TRP G 7 " pdb=" CE2 TRP G 7 " ideal model delta sigma weight residual 108.90 120.62 -11.72 1.80e+00 3.09e-01 4.24e+01 ... (remaining 20700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.43: 8975 24.43 - 48.87: 190 48.87 - 73.30: 15 73.30 - 97.74: 10 97.74 - 122.17: 5 Dihedral angle restraints: 9195 sinusoidal: 3735 harmonic: 5460 Sorted by residual: dihedral pdb=" O1B ADP A 801 " pdb=" O3A ADP A 801 " pdb=" PB ADP A 801 " pdb=" PA ADP A 801 " ideal model delta sinusoidal sigma weight residual 300.00 177.82 122.17 1 2.00e+01 2.50e-03 3.68e+01 dihedral pdb=" O1B ADP B 801 " pdb=" O3A ADP B 801 " pdb=" PB ADP B 801 " pdb=" PA ADP B 801 " ideal model delta sinusoidal sigma weight residual 300.00 177.83 122.17 1 2.00e+01 2.50e-03 3.68e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 177.85 122.15 1 2.00e+01 2.50e-03 3.68e+01 ... (remaining 9192 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.157: 2258 0.157 - 0.313: 42 0.313 - 0.470: 0 0.470 - 0.626: 0 0.626 - 0.783: 5 Chirality restraints: 2305 Sorted by residual: chirality pdb=" CA HIC E 73 " pdb=" N HIC E 73 " pdb=" C HIC E 73 " pdb=" CB HIC E 73 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.53e+01 chirality pdb=" CA HIC D 73 " pdb=" N HIC D 73 " pdb=" C HIC D 73 " pdb=" CB HIC D 73 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.52e+01 chirality pdb=" CA HIC A 73 " pdb=" N HIC A 73 " pdb=" C HIC A 73 " pdb=" CB HIC A 73 " both_signs ideal model delta sigma weight residual False 2.51 1.73 0.78 2.00e-01 2.50e+01 1.52e+01 ... (remaining 2302 not shown) Planarity restraints: 2630 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 69 " -0.042 5.00e-02 4.00e+02 6.44e-02 6.63e+00 pdb=" N PRO A 70 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 70 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 70 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 69 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO E 70 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO E 70 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO E 70 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR B 69 " -0.042 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO B 70 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO B 70 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 70 " -0.036 5.00e-02 4.00e+02 ... (remaining 2627 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 40 2.45 - 3.06: 8363 3.06 - 3.68: 19943 3.68 - 4.29: 27494 4.29 - 4.90: 46955 Nonbonded interactions: 102795 Sorted by model distance: nonbonded pdb=" SG CYS I 4 " pdb=" CD1 TRP I 7 " model vdw 1.838 3.620 nonbonded pdb=" SG CYS J 4 " pdb=" CD1 TRP J 7 " model vdw 1.838 3.620 nonbonded pdb=" SG CYS G 4 " pdb=" CD1 TRP G 7 " model vdw 1.838 3.620 nonbonded pdb=" SG CYS H 4 " pdb=" CD1 TRP H 7 " model vdw 1.838 3.620 nonbonded pdb=" SG CYS F 4 " pdb=" CD1 TRP F 7 " model vdw 1.838 3.620 ... (remaining 102790 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.430 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 31.500 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.040 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 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 : 0.014 0.219 15245 Z= 0.881 Angle : 1.120 12.440 20705 Z= 0.579 Chirality : 0.071 0.783 2305 Planarity : 0.007 0.064 2630 Dihedral : 11.419 122.172 5695 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.83 % Favored : 93.17 % Rotamer: Outliers : 0.63 % Allowed : 4.13 % Favored : 95.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.97 (0.15), residues: 1830 helix: -4.52 (0.09), residues: 580 sheet: -1.96 (0.26), residues: 385 loop : -2.97 (0.17), residues: 865 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 340 HIS 0.004 0.002 HIS D 40 PHE 0.016 0.003 PHE B 262 TYR 0.024 0.002 TYR D 294 ARG 0.005 0.001 ARG C 372 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 230 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 358 THR cc_start: 0.9112 (p) cc_final: 0.8887 (t) REVERT: E 216 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8524 (pp) outliers start: 10 outliers final: 4 residues processed: 240 average time/residue: 0.2849 time to fit residues: 98.3192 Evaluate side-chains 122 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 117 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 216 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 156 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 145 optimal weight: 20.0000 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 168 optimal weight: 4.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 121 GLN B 137 GLN C 137 GLN D 360 GLN D 371 HIS E 121 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15245 Z= 0.311 Angle : 0.751 6.590 20705 Z= 0.368 Chirality : 0.051 0.178 2305 Planarity : 0.005 0.048 2630 Dihedral : 10.068 111.606 2210 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 1.33 % Allowed : 7.30 % Favored : 91.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.17), residues: 1830 helix: -3.16 (0.16), residues: 590 sheet: -1.75 (0.27), residues: 385 loop : -2.47 (0.18), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 340 HIS 0.004 0.001 HIS D 40 PHE 0.009 0.001 PHE C 200 TYR 0.013 0.001 TYR E 294 ARG 0.005 0.001 ARG E 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 134 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 244 ASP cc_start: 0.7904 (t0) cc_final: 0.7570 (t0) REVERT: A 283 MET cc_start: 0.9080 (tpp) cc_final: 0.8703 (tpp) REVERT: A 325 MET cc_start: 0.8682 (mtt) cc_final: 0.8461 (mtt) REVERT: B 355 MET cc_start: 0.8525 (mmm) cc_final: 0.8080 (mtp) REVERT: E 283 MET cc_start: 0.9012 (tpp) cc_final: 0.8652 (tpp) outliers start: 21 outliers final: 10 residues processed: 153 average time/residue: 0.2650 time to fit residues: 60.3496 Evaluate side-chains 119 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 269 MET Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 93 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 139 optimal weight: 0.5980 chunk 114 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 168 optimal weight: 2.9990 chunk 181 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 166 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 135 optimal weight: 20.0000 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 371 HIS ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8792 moved from start: 0.2726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15245 Z= 0.227 Angle : 0.656 6.323 20705 Z= 0.313 Chirality : 0.048 0.159 2305 Planarity : 0.004 0.040 2630 Dihedral : 9.196 105.246 2210 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.29 % Allowed : 8.57 % Favored : 89.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.18), residues: 1830 helix: -2.19 (0.19), residues: 595 sheet: -1.56 (0.27), residues: 355 loop : -2.24 (0.18), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 340 HIS 0.003 0.001 HIS D 275 PHE 0.007 0.001 PHE C 200 TYR 0.011 0.001 TYR C 294 ARG 0.004 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 120 time to evaluate : 1.879 Fit side-chains revert: symmetry clash REVERT: A 244 ASP cc_start: 0.7986 (t0) cc_final: 0.7727 (t0) REVERT: A 283 MET cc_start: 0.8954 (tpp) cc_final: 0.8642 (tpp) REVERT: B 82 MET cc_start: 0.8649 (tpp) cc_final: 0.8421 (mmm) REVERT: B 208 ILE cc_start: 0.9354 (OUTLIER) cc_final: 0.9142 (mt) REVERT: B 349 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8557 (mp) REVERT: B 355 MET cc_start: 0.8591 (mmm) cc_final: 0.8124 (mtp) REVERT: C 208 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8995 (mt) REVERT: C 349 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8617 (mp) REVERT: D 82 MET cc_start: 0.8656 (mmm) cc_final: 0.8256 (tpt) REVERT: E 236 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8727 (pt) REVERT: E 283 MET cc_start: 0.8961 (tpp) cc_final: 0.8544 (tpp) outliers start: 36 outliers final: 13 residues processed: 152 average time/residue: 0.2552 time to fit residues: 59.1322 Evaluate side-chains 123 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 375 PHE Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 166 optimal weight: 9.9990 chunk 126 optimal weight: 20.0000 chunk 87 optimal weight: 0.5980 chunk 18 optimal weight: 10.0000 chunk 80 optimal weight: 0.9980 chunk 113 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 48 optimal weight: 8.9990 overall best weight: 4.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 15245 Z= 0.229 Angle : 0.647 6.465 20705 Z= 0.305 Chirality : 0.048 0.165 2305 Planarity : 0.004 0.039 2630 Dihedral : 9.027 100.737 2210 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.35 % Allowed : 8.63 % Favored : 89.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.18), residues: 1830 helix: -1.91 (0.20), residues: 625 sheet: -1.60 (0.27), residues: 355 loop : -2.00 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 340 HIS 0.003 0.001 HIS B 275 PHE 0.008 0.001 PHE C 200 TYR 0.011 0.001 TYR A 294 ARG 0.003 0.000 ARG B 210 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 113 time to evaluate : 1.720 Fit side-chains REVERT: A 124 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8417 (m-10) REVERT: A 208 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8962 (mt) REVERT: A 283 MET cc_start: 0.8931 (tpp) cc_final: 0.8571 (tpp) REVERT: B 269 MET cc_start: 0.8849 (ttm) cc_final: 0.8543 (ttm) REVERT: B 283 MET cc_start: 0.8850 (tpp) cc_final: 0.8046 (tpp) REVERT: B 349 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8666 (mp) REVERT: B 355 MET cc_start: 0.8582 (mmm) cc_final: 0.8100 (mtp) REVERT: C 49 GLN cc_start: 0.8642 (pp30) cc_final: 0.8372 (tm-30) REVERT: C 72 GLU cc_start: 0.8009 (tp30) cc_final: 0.7582 (tp30) REVERT: E 236 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8723 (pt) REVERT: E 283 MET cc_start: 0.8912 (tpp) cc_final: 0.8616 (tpp) REVERT: E 349 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8587 (mp) outliers start: 37 outliers final: 21 residues processed: 148 average time/residue: 0.2516 time to fit residues: 56.8600 Evaluate side-chains 121 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 95 time to evaluate : 1.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 303 THR Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 208 ILE Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 374 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 185 random chunks: chunk 148 optimal weight: 30.0000 chunk 101 optimal weight: 3.9990 chunk 2 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 152 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 91 optimal weight: 8.9990 chunk 160 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 15245 Z= 0.359 Angle : 0.725 6.627 20705 Z= 0.347 Chirality : 0.051 0.170 2305 Planarity : 0.004 0.042 2630 Dihedral : 9.309 103.024 2210 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 2.54 % Allowed : 9.21 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.19), residues: 1830 helix: -1.68 (0.20), residues: 595 sheet: -1.69 (0.27), residues: 355 loop : -1.90 (0.20), residues: 880 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 340 HIS 0.005 0.001 HIS D 40 PHE 0.012 0.001 PHE A 200 TYR 0.012 0.001 TYR E 294 ARG 0.005 0.001 ARG B 183 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3660 Ramachandran restraints generated. 1830 Oldfield, 0 Emsley, 1830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 95 time to evaluate : 1.711 Fit side-chains REVERT: A 124 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8301 (m-10) REVERT: A 283 MET cc_start: 0.8936 (tpp) cc_final: 0.8690 (tpp) REVERT: B 244 ASP cc_start: 0.7610 (t0) cc_final: 0.7357 (m-30) REVERT: B 349 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8768 (mp) REVERT: C 124 PHE cc_start: 0.9074 (OUTLIER) cc_final: 0.8697 (m-10) REVERT: C 349 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8768 (mp) REVERT: D 82 MET cc_start: 0.8802 (mmm) cc_final: 0.8439 (tpt) REVERT: E 236 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8729 (pt) REVERT: E 283 MET cc_start: 0.8881 (tpp) cc_final: 0.8615 (tpp) outliers start: 40 outliers final: 22 residues processed: 132 average time/residue: 0.2307 time to fit residues: 48.0791 Evaluate side-chains 121 residues out of total 1575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 94 time to evaluate : 1.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 GLU Chi-restraints excluded: chain A residue 124 PHE Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 269 MET Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain B residue 124 PHE Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 190 MET Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 124 PHE Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 202 THR Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 349 LEU Chi-restraints excluded: chain D residue 124 PHE Chi-restraints excluded: chain D residue 202 THR Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 216 LEU Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain E residue 299 MET Chi-restraints excluded: chain E residue 303 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/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-5461/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-5461/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-5461/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-5461/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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-5461/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-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 64.6431 > 50: distance: 63 - 68: 20.313 distance: 68 - 69: 8.441 distance: 69 - 70: 35.161 distance: 69 - 72: 22.820 distance: 70 - 71: 19.364 distance: 70 - 75: 22.647 distance: 72 - 74: 8.979 distance: 75 - 76: 37.800 distance: 76 - 77: 22.494 distance: 76 - 79: 45.494 distance: 77 - 78: 6.297 distance: 77 - 83: 19.656 distance: 79 - 80: 45.301 distance: 80 - 81: 23.151 distance: 81 - 82: 24.734 distance: 83 - 84: 17.838 distance: 84 - 85: 25.011 distance: 84 - 87: 21.631 distance: 85 - 86: 18.435 distance: 85 - 95: 36.104 distance: 87 - 88: 24.881 distance: 88 - 89: 14.315 distance: 88 - 90: 8.243 distance: 89 - 91: 9.263 distance: 90 - 92: 19.998 distance: 91 - 93: 3.593 distance: 92 - 93: 12.669 distance: 93 - 94: 25.473 distance: 95 - 96: 9.136 distance: 95 - 101: 4.902 distance: 96 - 97: 38.245 distance: 96 - 99: 12.720 distance: 97 - 98: 13.617 distance: 97 - 102: 19.999 distance: 99 - 100: 15.252 distance: 100 - 101: 24.687 distance: 103 - 104: 40.972 distance: 104 - 105: 41.707 distance: 104 - 106: 29.206 distance: 106 - 107: 38.944 distance: 107 - 108: 29.458 distance: 107 - 110: 9.089 distance: 108 - 109: 9.985 distance: 108 - 114: 14.725 distance: 110 - 111: 58.606 distance: 110 - 112: 36.947 distance: 111 - 113: 25.418 distance: 114 - 115: 10.199 distance: 115 - 116: 27.244 distance: 115 - 118: 19.730 distance: 116 - 117: 26.923 distance: 116 - 119: 14.860 distance: 117 - 146: 19.774 distance: 119 - 120: 9.816 distance: 120 - 121: 10.758 distance: 120 - 123: 23.647 distance: 121 - 127: 8.050 distance: 123 - 124: 11.306 distance: 124 - 125: 41.817 distance: 124 - 126: 14.224 distance: 127 - 128: 6.489 distance: 128 - 129: 3.697 distance: 128 - 131: 5.357 distance: 129 - 130: 3.776 distance: 129 - 138: 4.211 distance: 130 - 159: 5.671 distance: 131 - 132: 13.886 distance: 132 - 133: 10.946 distance: 134 - 135: 9.304 distance: 135 - 137: 5.499 distance: 138 - 139: 4.797 distance: 139 - 140: 5.847 distance: 139 - 142: 11.715 distance: 140 - 141: 13.423 distance: 140 - 146: 8.474 distance: 142 - 143: 13.691 distance: 143 - 144: 6.820 distance: 144 - 145: 9.428