Starting phenix.real_space_refine on Thu Nov 16 15:55:45 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udt_26459/11_2023/7udt_26459_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udt_26459/11_2023/7udt_26459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udt_26459/11_2023/7udt_26459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udt_26459/11_2023/7udt_26459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udt_26459/11_2023/7udt_26459_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7udt_26459/11_2023/7udt_26459_updated.pdb" } resolution = 3.17 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= 0.003 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 103 5.16 5 C 10009 2.51 5 N 2690 2.21 5 O 2995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 15806 Number of models: 1 Model: "" Number of chains: 8 Chain: "G" Number of atoms: 1187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1187 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "A" Number of atoms: 2958 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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 Conformer: "B" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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 bond proxies already assigned to first conformer: 2938 Chain: "B" Number of atoms: 2958 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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 Conformer: "B" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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 bond proxies already assigned to first conformer: 2938 Chain: "C" Number of atoms: 2958 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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 Conformer: "B" Number of residues, atoms: 373, 2917 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 353} 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 bond proxies already assigned to first conformer: 2938 Chain: "D" Number of atoms: 5661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 701, 5661 Classifications: {'peptide': 701} Link IDs: {'PTRANS': 23, 'TRANS': 677} Chain breaks: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 18 residue: pdb=" N AVAL A 45 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 45 " occ=0.50 residue: pdb=" N AGLY A 46 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 46 " occ=0.50 residue: pdb=" N AMET A 47 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 47 " occ=0.50 residue: pdb=" N AGLY A 48 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 48 " occ=0.50 residue: pdb=" N AGLN A 49 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 49 " occ=0.50 residue: pdb=" N ALYS A 50 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 50 " occ=0.50 residue: pdb=" N AVAL B 45 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL B 45 " occ=0.50 residue: pdb=" N AGLY B 46 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 46 " occ=0.50 residue: pdb=" N AMET B 47 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET B 47 " occ=0.50 residue: pdb=" N AGLY B 48 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 48 " occ=0.50 residue: pdb=" N AGLN B 49 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 49 " occ=0.50 residue: pdb=" N ALYS B 50 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS B 50 " occ=0.50 ... (remaining 6 not shown) Time building chain proxies: 12.55, per 1000 atoms: 0.79 Number of scatterers: 15806 At special positions: 0 Unit cell: (114.33, 166.86, 166.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 6 15.00 Mg 3 11.99 O 2995 8.00 N 2690 7.00 C 10009 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 - 3.50 Amino acid : False - 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: 6.69 Conformation dependent library (CDL) restraints added in 4.6 seconds 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3708 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 94 helices and 16 sheets defined 46.0% alpha, 10.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.98 Creating SS restraints... Processing helix chain 'G' and resid 28 through 41 removed outlier: 4.484A pdb=" N GLN G 32 " --> pdb=" O GLN G 28 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N GLU G 33 " --> pdb=" O SER G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 58 Processing helix chain 'G' and resid 83 through 92 Processing helix chain 'G' and resid 100 through 109 Processing helix chain 'G' and resid 120 through 129 Processing helix chain 'G' and resid 136 through 143 Processing helix chain 'G' and resid 157 through 165 Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.736A pdb=" N SER A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 79 through 91 removed outlier: 3.609A pdb=" N GLU A 83 " --> pdb=" O TRP A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 100 No H-bonds generated for 'chain 'A' and resid 98 through 100' Processing helix chain 'A' and resid 113 through 125 Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 196 removed outlier: 4.012A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 216 removed outlier: 3.752A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 232 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.720A pdb=" N ARG A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 264 through 267 Processing helix chain 'A' and resid 274 through 283 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 303 through 305 No H-bonds generated for 'chain 'A' and resid 303 through 305' Processing helix chain 'A' and resid 309 through 320 Processing helix chain 'A' and resid 335 through 347 removed outlier: 3.552A pdb=" N SER A 338 " --> pdb=" O ARG A 335 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N VAL A 339 " --> pdb=" O LYS A 336 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA A 347 " --> pdb=" O SER A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 removed outlier: 3.775A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 359 through 373 Proline residue: A 367 - end of helix removed outlier: 5.388A pdb=" N VAL A 370 " --> pdb=" O GLY A 366 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N HIS A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 60 removed outlier: 3.737A pdb=" N SER B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 64 No H-bonds generated for 'chain 'B' and resid 62 through 64' Processing helix chain 'B' and resid 79 through 91 removed outlier: 3.611A pdb=" N GLU B 83 " --> pdb=" O TRP B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 100 No H-bonds generated for 'chain 'B' and resid 98 through 100' Processing helix chain 'B' and resid 113 through 125 Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 196 removed outlier: 4.012A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.752A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 252 through 256 removed outlier: 3.719A pdb=" N ARG B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 264 through 267 Processing helix chain 'B' and resid 274 through 283 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 303 through 305 No H-bonds generated for 'chain 'B' and resid 303 through 305' Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 335 through 347 removed outlier: 3.553A pdb=" N SER B 338 " --> pdb=" O ARG B 335 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL B 339 " --> pdb=" O LYS B 336 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA B 347 " --> pdb=" O SER B 344 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 354 removed outlier: 3.773A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 351 through 354' Processing helix chain 'B' and resid 359 through 373 Proline residue: B 367 - end of helix removed outlier: 5.389A pdb=" N VAL B 370 " --> pdb=" O GLY B 366 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N HIS B 371 " --> pdb=" O PRO B 367 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 60 removed outlier: 3.737A pdb=" N SER C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 64 No H-bonds generated for 'chain 'C' and resid 62 through 64' Processing helix chain 'C' and resid 79 through 91 removed outlier: 3.612A pdb=" N GLU C 83 " --> pdb=" O TRP C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 100 No H-bonds generated for 'chain 'C' and resid 98 through 100' Processing helix chain 'C' and resid 113 through 125 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 196 removed outlier: 4.011A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 203 through 216 removed outlier: 3.751A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 232 Processing helix chain 'C' and resid 252 through 256 removed outlier: 3.718A pdb=" N ARG C 256 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 264 through 267 Processing helix chain 'C' and resid 274 through 283 Processing helix chain 'C' and resid 290 through 294 Processing helix chain 'C' and resid 303 through 305 No H-bonds generated for 'chain 'C' and resid 303 through 305' Processing helix chain 'C' and resid 309 through 320 Processing helix chain 'C' and resid 335 through 347 removed outlier: 3.554A pdb=" N SER C 338 " --> pdb=" O ARG C 335 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N VAL C 339 " --> pdb=" O LYS C 336 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA C 347 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 351 through 354 removed outlier: 3.775A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 351 through 354' Processing helix chain 'C' and resid 359 through 373 Proline residue: C 367 - end of helix removed outlier: 5.387A pdb=" N VAL C 370 " --> pdb=" O GLY C 366 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N HIS C 371 " --> pdb=" O PRO C 367 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 1211 through 1213 No H-bonds generated for 'chain 'D' and resid 1211 through 1213' Processing helix chain 'D' and resid 1219 through 1231 Processing helix chain 'D' and resid 1257 through 1262 Processing helix chain 'D' and resid 1275 through 1289 Processing helix chain 'D' and resid 1305 through 1320 Processing helix chain 'D' and resid 1326 through 1332 Processing helix chain 'D' and resid 1335 through 1342 Processing helix chain 'D' and resid 1394 through 1402 Processing helix chain 'D' and resid 1405 through 1411 Processing helix chain 'D' and resid 1435 through 1448 Processing helix chain 'D' and resid 1453 through 1471 removed outlier: 3.765A pdb=" N ASN D1471 " --> pdb=" O LEU D1467 " (cutoff:3.500A) Processing helix chain 'D' and resid 1491 through 1500 Processing helix chain 'D' and resid 1504 through 1512 Processing helix chain 'D' and resid 1529 through 1559 Processing helix chain 'D' and resid 1584 through 1614 removed outlier: 3.751A pdb=" N LEU D1599 " --> pdb=" O ASN D1595 " (cutoff:3.500A) Processing helix chain 'D' and resid 1628 through 1635 Processing helix chain 'D' and resid 1641 through 1649 Processing helix chain 'D' and resid 1656 through 1667 Processing helix chain 'D' and resid 1709 through 1716 Processing helix chain 'D' and resid 1721 through 1733 Processing helix chain 'D' and resid 1754 through 1769 removed outlier: 3.519A pdb=" N MET D1769 " --> pdb=" O LEU D1765 " (cutoff:3.500A) Processing helix chain 'D' and resid 1793 through 1803 Processing helix chain 'D' and resid 1805 through 1812 Processing helix chain 'D' and resid 1823 through 1828 Processing helix chain 'D' and resid 1847 through 1854 Processing helix chain 'D' and resid 1872 through 1909 Processing helix chain 'D' and resid 1914 through 1921 Processing sheet with id= A, first strand: chain 'A' and resid 132 through 136 removed outlier: 6.645A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.425A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 34 through 38 Processing sheet with id= C, first strand: chain 'A' and resid 297 through 300 removed outlier: 6.265A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 238 through 241 Processing sheet with id= E, first strand: chain 'B' and resid 132 through 136 removed outlier: 6.644A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.392A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.426A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 34 through 38 Processing sheet with id= G, first strand: chain 'B' and resid 297 through 300 removed outlier: 6.265A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 238 through 241 Processing sheet with id= I, first strand: chain 'C' and resid 132 through 136 removed outlier: 6.644A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 34 through 38 Processing sheet with id= K, first strand: chain 'C' and resid 297 through 300 removed outlier: 6.266A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 238 through 241 Processing sheet with id= M, first strand: chain 'D' and resid 1237 through 1239 removed outlier: 3.501A pdb=" N ASN D1247 " --> pdb=" O LEU D1780 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN D1293 " --> pdb=" O SER D1567 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU D1566 " --> pdb=" O LEU D1363 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 1474 through 1478 Processing sheet with id= O, first strand: chain 'D' and resid 1513 through 1517 Processing sheet with id= P, first strand: chain 'D' and resid 1673 through 1675 625 hydrogen bonds defined for protein. 1692 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.10 Time building geometry restraints manager: 7.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2938 1.33 - 1.45: 3975 1.45 - 1.57: 9037 1.57 - 1.69: 9 1.69 - 1.81: 176 Bond restraints: 16135 Sorted by residual: bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.65e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.50e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.13e+00 bond pdb=" N GLU G 92 " pdb=" CA GLU G 92 " ideal model delta sigma weight residual 1.457 1.486 -0.029 1.25e-02 6.40e+03 5.46e+00 bond pdb=" C ASP D1618 " pdb=" O ASP D1618 " ideal model delta sigma weight residual 1.232 1.203 0.029 1.37e-02 5.33e+03 4.40e+00 ... (remaining 16130 not shown) Histogram of bond angle deviations from ideal: 99.79 - 107.07: 523 107.07 - 114.35: 9348 114.35 - 121.63: 8405 121.63 - 128.91: 3481 128.91 - 136.19: 86 Bond angle restraints: 21843 Sorted by residual: angle pdb=" N GLU G 92 " pdb=" CA GLU G 92 " pdb=" C GLU G 92 " ideal model delta sigma weight residual 112.93 123.25 -10.32 1.33e+00 5.65e-01 6.03e+01 angle pdb=" C VAL D1833 " pdb=" N ALA D1834 " pdb=" CA ALA D1834 " ideal model delta sigma weight residual 122.93 133.26 -10.33 1.51e+00 4.39e-01 4.68e+01 angle pdb=" N LYS G 93 " pdb=" CA LYS G 93 " pdb=" C LYS G 93 " ideal model delta sigma weight residual 110.80 119.47 -8.67 2.13e+00 2.20e-01 1.66e+01 angle pdb=" C GLU G 92 " pdb=" CA GLU G 92 " pdb=" CB GLU G 92 " ideal model delta sigma weight residual 110.08 104.13 5.95 1.57e+00 4.06e-01 1.44e+01 angle pdb=" N ILE C 64 " pdb=" CA ILE C 64 " pdb=" C ILE C 64 " ideal model delta sigma weight residual 113.20 109.70 3.50 9.60e-01 1.09e+00 1.33e+01 ... (remaining 21838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.91: 9425 28.91 - 57.83: 259 57.83 - 86.74: 47 86.74 - 115.65: 6 115.65 - 144.56: 6 Dihedral angle restraints: 9743 sinusoidal: 3976 harmonic: 5767 Sorted by residual: dihedral pdb=" O1B ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PB ADP A 401 " pdb=" PA ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 84.56 -144.56 1 2.00e+01 2.50e-03 4.36e+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 -60.00 84.56 -144.56 1 2.00e+01 2.50e-03 4.36e+01 dihedral pdb=" O1B ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PB ADP B 401 " pdb=" PA ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 84.49 -144.50 1 2.00e+01 2.50e-03 4.35e+01 ... (remaining 9740 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2170 0.071 - 0.143: 243 0.143 - 0.214: 1 0.214 - 0.285: 0 0.285 - 0.356: 2 Chirality restraints: 2416 Sorted by residual: chirality pdb=" CA LEU D1837 " pdb=" N LEU D1837 " pdb=" C LEU D1837 " pdb=" CB LEU D1837 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" CA LYS G 93 " pdb=" N LYS G 93 " pdb=" C LYS G 93 " pdb=" CB LYS G 93 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA PRO D1652 " pdb=" N PRO D1652 " pdb=" C PRO D1652 " pdb=" CB PRO D1652 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.15 2.00e-01 2.50e+01 5.67e-01 ... (remaining 2413 not shown) Planarity restraints: 2823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR D1612 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.94e+00 pdb=" C TYR D1612 " 0.030 2.00e-02 2.50e+03 pdb=" O TYR D1612 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE D1613 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D1884 " 0.097 9.50e-02 1.11e+02 4.47e-02 2.42e+00 pdb=" NE ARG D1884 " -0.012 2.00e-02 2.50e+03 pdb=" CZ ARG D1884 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG D1884 " -0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG D1884 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE D1651 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRO D1652 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO D1652 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO D1652 " -0.020 5.00e-02 4.00e+02 ... (remaining 2820 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1230 2.74 - 3.28: 15382 3.28 - 3.82: 26088 3.82 - 4.36: 31800 4.36 - 4.90: 54303 Nonbonded interactions: 128803 Sorted by model distance: nonbonded pdb=" O PHE G 38 " pdb=" N ASP G 42 " model vdw 2.197 2.520 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.207 2.170 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 2.207 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 2.208 2.170 nonbonded pdb=" OD2 ASP C 222 " pdb=" ND2 ASN C 225 " model vdw 2.211 2.520 ... (remaining 128798 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 44 or resid 51 through 375 or resid 401 through \ 402)) selection = (chain 'B' and (resid 3 through 44 or resid 51 through 375 or resid 401 through \ 402)) selection = (chain 'C' and (resid 3 through 44 or resid 51 through 375 or resid 401 through \ 402)) } 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=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 26.690 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 50.910 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6711 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16135 Z= 0.223 Angle : 0.594 10.331 21843 Z= 0.321 Chirality : 0.044 0.356 2416 Planarity : 0.004 0.046 2823 Dihedral : 14.888 144.565 6035 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.24 % Allowed : 0.41 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.38 (0.20), residues: 1967 helix: 1.13 (0.18), residues: 912 sheet: -0.44 (0.30), residues: 274 loop : -0.41 (0.23), residues: 781 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 409 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 410 average time/residue: 0.3124 time to fit residues: 184.5293 Evaluate side-chains 212 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 212 time to evaluate : 1.841 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.2453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 113 optimal weight: 0.0470 chunk 177 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 HIS A 162 ASN A 225 ASN A 353 GLN B 12 ASN B 121 GLN B 162 ASN B 360 GLN C 40 HIS C 87 HIS C 162 ASN C 314 GLN D1225 ASN ** D1343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1477 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1903 GLN D1905 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 16135 Z= 0.232 Angle : 0.631 8.011 21843 Z= 0.316 Chirality : 0.045 0.220 2416 Planarity : 0.005 0.049 2823 Dihedral : 9.479 143.180 2204 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.88 % Allowed : 9.60 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.42 (0.19), residues: 1967 helix: 1.04 (0.18), residues: 904 sheet: -0.29 (0.29), residues: 268 loop : -0.27 (0.23), residues: 795 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 229 time to evaluate : 1.909 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 17 residues processed: 249 average time/residue: 0.2795 time to fit residues: 104.2270 Evaluate side-chains 211 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 194 time to evaluate : 1.849 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1693 time to fit residues: 7.5712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 147 optimal weight: 7.9990 chunk 120 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 177 optimal weight: 0.9980 chunk 191 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 95 ASN A 128 ASN A 162 ASN B 12 ASN B 353 GLN B 354 GLN C 49 GLN B C 87 HIS ** D1343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1477 HIS D1590 ASN D1905 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6915 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16135 Z= 0.248 Angle : 0.605 9.805 21843 Z= 0.300 Chirality : 0.045 0.327 2416 Planarity : 0.004 0.044 2823 Dihedral : 9.221 146.388 2204 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.65 % Allowed : 10.78 % Favored : 87.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.38 (0.19), residues: 1967 helix: 1.06 (0.18), residues: 882 sheet: -0.11 (0.28), residues: 295 loop : -0.42 (0.23), residues: 790 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 215 time to evaluate : 1.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 17 residues processed: 232 average time/residue: 0.2677 time to fit residues: 96.0768 Evaluate side-chains 198 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 181 time to evaluate : 1.946 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1586 time to fit residues: 7.5319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 19 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 chunk 119 optimal weight: 0.8980 chunk 178 optimal weight: 0.6980 chunk 188 optimal weight: 7.9990 chunk 93 optimal weight: 0.5980 chunk 168 optimal weight: 0.0370 chunk 50 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 HIS C 297 ASN ** D1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1471 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6912 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16135 Z= 0.184 Angle : 0.580 9.217 21843 Z= 0.283 Chirality : 0.044 0.263 2416 Planarity : 0.004 0.041 2823 Dihedral : 8.923 150.802 2204 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.71 % Allowed : 12.19 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.47 (0.19), residues: 1967 helix: 1.16 (0.18), residues: 881 sheet: -0.04 (0.28), residues: 297 loop : -0.42 (0.23), residues: 789 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 194 time to evaluate : 1.841 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 199 average time/residue: 0.3187 time to fit residues: 98.3272 Evaluate side-chains 185 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 179 time to evaluate : 1.679 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.2405 time to fit residues: 5.6892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 0.0970 chunk 106 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 160 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 0 optimal weight: 70.0000 chunk 96 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 47 optimal weight: 0.0170 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN C 87 HIS ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1225 ASN ** D1343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6948 moved from start: 0.3569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16135 Z= 0.240 Angle : 0.595 9.216 21843 Z= 0.291 Chirality : 0.044 0.179 2416 Planarity : 0.004 0.043 2823 Dihedral : 8.708 150.362 2204 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.12 % Allowed : 13.02 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.40 (0.19), residues: 1967 helix: 1.07 (0.18), residues: 885 sheet: -0.01 (0.29), residues: 297 loop : -0.45 (0.23), residues: 785 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 191 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 199 average time/residue: 0.2769 time to fit residues: 86.0479 Evaluate side-chains 182 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 174 time to evaluate : 1.835 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1671 time to fit residues: 4.9962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 0.8980 chunk 169 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 110 optimal weight: 0.7980 chunk 46 optimal weight: 0.0370 chunk 188 optimal weight: 0.2980 chunk 156 optimal weight: 0.3980 chunk 87 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 overall best weight: 0.4258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS ** C 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1343 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16135 Z= 0.166 Angle : 0.562 9.419 21843 Z= 0.274 Chirality : 0.043 0.181 2416 Planarity : 0.004 0.039 2823 Dihedral : 8.475 148.154 2204 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.82 % Allowed : 13.37 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.53 (0.19), residues: 1967 helix: 1.16 (0.18), residues: 887 sheet: 0.11 (0.30), residues: 292 loop : -0.37 (0.23), residues: 788 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 184 time to evaluate : 1.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 5 residues processed: 191 average time/residue: 0.2776 time to fit residues: 81.8347 Evaluate side-chains 184 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 179 time to evaluate : 1.795 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1472 time to fit residues: 3.7636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 0.0030 chunk 21 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 0.1980 chunk 158 optimal weight: 0.7980 chunk 105 optimal weight: 1.9990 chunk 187 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 chunk 114 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 353 GLN C 87 HIS C 225 ASN ** D1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1905 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6930 moved from start: 0.3815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16135 Z= 0.177 Angle : 0.571 9.109 21843 Z= 0.275 Chirality : 0.043 0.210 2416 Planarity : 0.004 0.039 2823 Dihedral : 8.301 143.768 2204 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.00 % Allowed : 13.37 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.59 (0.20), residues: 1967 helix: 1.11 (0.18), residues: 895 sheet: 0.23 (0.30), residues: 290 loop : -0.27 (0.23), residues: 782 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 192 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 199 average time/residue: 0.2862 time to fit residues: 86.3500 Evaluate side-chains 190 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 181 time to evaluate : 1.826 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2089 time to fit residues: 6.1509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 17 optimal weight: 0.2980 chunk 147 optimal weight: 7.9990 chunk 170 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 87 HIS C 225 ASN D1280 ASN ** D1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6951 moved from start: 0.3968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16135 Z= 0.217 Angle : 0.594 9.878 21843 Z= 0.289 Chirality : 0.044 0.247 2416 Planarity : 0.004 0.043 2823 Dihedral : 8.273 148.730 2204 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.41 % Allowed : 13.90 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.55 (0.20), residues: 1967 helix: 1.07 (0.18), residues: 895 sheet: 0.21 (0.30), residues: 290 loop : -0.29 (0.23), residues: 782 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 180 time to evaluate : 1.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 181 average time/residue: 0.2842 time to fit residues: 78.7164 Evaluate side-chains 175 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 173 time to evaluate : 1.754 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1614 time to fit residues: 3.0470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 0.0670 chunk 164 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 0.1980 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 chunk 165 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN C 87 HIS C 314 GLN D1280 ASN ** D1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16135 Z= 0.190 Angle : 0.595 12.040 21843 Z= 0.286 Chirality : 0.043 0.253 2416 Planarity : 0.004 0.042 2823 Dihedral : 8.164 153.649 2204 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.47 % Allowed : 14.55 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.60 (0.20), residues: 1967 helix: 1.13 (0.18), residues: 893 sheet: 0.25 (0.30), residues: 290 loop : -0.27 (0.23), residues: 784 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 183 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 184 average time/residue: 0.2879 time to fit residues: 79.9375 Evaluate side-chains 181 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 177 time to evaluate : 1.710 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1617 time to fit residues: 3.7319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 0.9990 chunk 113 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 chunk 128 optimal weight: 0.0470 chunk 194 optimal weight: 30.0000 chunk 178 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 94 optimal weight: 1.9990 chunk 122 optimal weight: 0.0070 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 GLN C 87 HIS D1280 ASN ** D1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 moved from start: 0.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16135 Z= 0.172 Angle : 0.596 10.898 21843 Z= 0.285 Chirality : 0.043 0.256 2416 Planarity : 0.004 0.113 2823 Dihedral : 8.072 157.490 2204 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.41 % Allowed : 14.61 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.66 (0.20), residues: 1967 helix: 1.17 (0.18), residues: 891 sheet: 0.29 (0.30), residues: 290 loop : -0.24 (0.23), residues: 786 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3934 Ramachandran restraints generated. 1967 Oldfield, 0 Emsley, 1967 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 1.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 4 residues processed: 185 average time/residue: 0.3008 time to fit residues: 84.0313 Evaluate side-chains 178 residues out of total 1674 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 174 time to evaluate : 1.656 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2992 time to fit residues: 4.2857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 142 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 42 optimal weight: 0.0040 chunk 154 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 159 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 87 HIS ** D1320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.152033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.111767 restraints weight = 36467.897| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 2.97 r_work: 0.3155 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3010 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3010 r_free = 0.3010 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3010 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16135 Z= 0.190 Angle : 0.610 14.503 21843 Z= 0.292 Chirality : 0.043 0.255 2416 Planarity : 0.004 0.094 2823 Dihedral : 8.048 160.040 2204 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.35 % Allowed : 15.08 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.62 (0.20), residues: 1967 helix: 1.13 (0.18), residues: 894 sheet: 0.29 (0.30), residues: 290 loop : -0.27 (0.23), residues: 783 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4144.52 seconds wall clock time: 75 minutes 48.61 seconds (4548.61 seconds total)