Starting phenix.real_space_refine on Fri Feb 16 04:44:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r91_24322/02_2024/7r91_24322_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r91_24322/02_2024/7r91_24322.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r91_24322/02_2024/7r91_24322.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r91_24322/02_2024/7r91_24322.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r91_24322/02_2024/7r91_24322_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r91_24322/02_2024/7r91_24322_neut_updated.pdb" } resolution = 2.83 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= 0.004 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 94 5.16 5 C 9065 2.51 5 N 2437 2.21 5 O 2715 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 25": "OD1" <-> "OD2" Residue "A GLU 72": "OE1" <-> "OE2" Residue "A GLU 83": "OE1" <-> "OE2" Residue "A GLU 167": "OE1" <-> "OE2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "B PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B GLU 72": "OE1" <-> "OE2" Residue "B GLU 83": "OE1" <-> "OE2" Residue "B GLU 167": "OE1" <-> "OE2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B GLU 334": "OE1" <-> "OE2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C GLU 72": "OE1" <-> "OE2" Residue "C GLU 83": "OE1" <-> "OE2" Residue "C GLU 167": "OE1" <-> "OE2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C GLU 334": "OE1" <-> "OE2" Residue "D GLU 1219": "OE1" <-> "OE2" Residue "D PHE 1362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1454": "OE1" <-> "OE2" Residue "D TYR 1544": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 1610": "OE1" <-> "OE2" Residue "D PHE 1727": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14320 Number of models: 1 Model: "" Number of chains: 7 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: 5362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5362 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 23, 'TRANS': 643} 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: 11.81, per 1000 atoms: 0.82 Number of scatterers: 14320 At special positions: 0 Unit cell: (122.57, 144.2, 139.05, 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 94 16.00 P 6 15.00 Mg 3 11.99 O 2715 8.00 N 2437 7.00 C 9065 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: 5.57 Conformation dependent library (CDL) restraints added in 4.5 seconds 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3370 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 87 helices and 16 sheets defined 45.6% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.91 Creating SS restraints... Processing helix chain 'A' and resid 55 through 60 removed outlier: 3.737A 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: 3.610A 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: 3.751A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 3.808A 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: 3.719A 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: 5.527A 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: 3.774A 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: 4.206A 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: 4.011A 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: 3.751A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 3.808A 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: 5.526A 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: 5.388A 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: 3.736A 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: 3.553A 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: 3.572A 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: 5.388A 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: 3.750A 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 1822 through 1833 removed outlier: 3.668A pdb=" N ILE D1826 " --> pdb=" O PHE D1822 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG D1830 " --> pdb=" O ILE D1826 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N CYS D1831 " --> pdb=" O ASP D1827 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N LEU D1832 " --> pdb=" O ARG D1828 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N VAL D1833 " --> pdb=" O TYR D1829 " (cutoff:3.500A) Processing helix chain 'D' and resid 1844 through 1852 Processing helix chain 'D' and resid 1858 through 1860 No H-bonds generated for 'chain 'D' and resid 1858 through 1860' Processing helix chain 'D' and resid 1874 through 1888 removed outlier: 4.151A pdb=" N ARG D1888 " --> pdb=" O ARG D1884 " (cutoff:3.500A) 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: 7.883A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.676A 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: 8.426A 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: 6.102A 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: 7.883A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.676A 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: 7.667A 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: 3.569A 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 560 hydrogen bonds defined for protein. 1497 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: 4.99 Time building geometry restraints manager: 6.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4696 1.34 - 1.46: 2397 1.46 - 1.58: 7358 1.58 - 1.69: 9 1.69 - 1.81: 159 Bond restraints: 14619 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 7.67e+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 7.47e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.31e+00 bond pdb=" CG HIC B 73 " pdb=" CD2 HIC B 73 " ideal model delta sigma weight residual 1.369 1.410 -0.041 2.00e-02 2.50e+03 4.21e+00 bond pdb=" CG HIC A 73 " pdb=" CD2 HIC A 73 " ideal model delta sigma weight residual 1.369 1.410 -0.041 2.00e-02 2.50e+03 4.10e+00 ... (remaining 14614 not shown) Histogram of bond angle deviations from ideal: 99.81 - 107.09: 490 107.09 - 114.36: 8544 114.36 - 121.63: 7510 121.63 - 128.91: 3181 128.91 - 136.18: 83 Bond angle restraints: 19808 Sorted by residual: 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 angle pdb=" N ILE B 64 " pdb=" CA ILE B 64 " pdb=" C ILE B 64 " ideal model delta sigma weight residual 113.20 109.72 3.48 9.60e-01 1.09e+00 1.31e+01 angle pdb=" N ILE A 64 " pdb=" CA ILE A 64 " pdb=" C ILE A 64 " ideal model delta sigma weight residual 113.20 109.74 3.46 9.60e-01 1.09e+00 1.30e+01 angle pdb=" CA ARG D1322 " pdb=" CB ARG D1322 " pdb=" CG ARG D1322 " ideal model delta sigma weight residual 114.10 120.54 -6.44 2.00e+00 2.50e-01 1.04e+01 angle pdb=" CA ARG D1852 " pdb=" CB ARG D1852 " pdb=" CG ARG D1852 " ideal model delta sigma weight residual 114.10 120.20 -6.10 2.00e+00 2.50e-01 9.29e+00 ... (remaining 19803 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.91: 8545 28.91 - 57.82: 228 57.82 - 86.73: 46 86.73 - 115.64: 5 115.64 - 144.55: 6 Dihedral angle restraints: 8830 sinusoidal: 3585 harmonic: 5245 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 84.55 -144.55 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 84.53 -144.53 1 2.00e+01 2.50e-03 4.35e+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 84.48 -144.48 1 2.00e+01 2.50e-03 4.35e+01 ... (remaining 8827 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 1241 0.030 - 0.059: 633 0.059 - 0.089: 177 0.089 - 0.118: 136 0.118 - 0.148: 18 Chirality restraints: 2205 Sorted by residual: 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 5.45e-01 chirality pdb=" CA ILE D1239 " pdb=" N ILE D1239 " pdb=" C ILE D1239 " pdb=" CB ILE D1239 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA VAL D1559 " pdb=" N VAL D1559 " pdb=" C VAL D1559 " pdb=" CB VAL D1559 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.72e-01 ... (remaining 2202 not shown) Planarity restraints: 2550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D1651 " -0.024 5.00e-02 4.00e+02 3.71e-02 2.20e+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 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D1628 " -0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO D1629 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO D1629 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO D1629 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 242 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO C 243 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO C 243 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO C 243 " 0.018 5.00e-02 4.00e+02 ... (remaining 2547 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1435 2.75 - 3.28: 13501 3.28 - 3.82: 23638 3.82 - 4.36: 28924 4.36 - 4.90: 49703 Nonbonded interactions: 117201 Sorted by model distance: nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 2.207 2.170 nonbonded pdb=" O2B ADP C 401 " pdb="MG MG C 402 " model vdw 2.207 2.170 nonbonded pdb=" O2B ADP B 401 " pdb="MG MG B 402 " model vdw 2.207 2.170 nonbonded pdb=" OD2 ASP A 222 " pdb=" ND2 ASN A 225 " model vdw 2.212 2.520 nonbonded pdb=" OD2 ASP C 222 " pdb=" ND2 ASN C 225 " model vdw 2.212 2.520 ... (remaining 117196 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: 6.600 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: 27.350 Check model and map are aligned: 0.250 Set scattering table: 0.140 Process input model: 47.380 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 94.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 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 14619 Z= 0.218 Angle : 0.555 7.461 19808 Z= 0.293 Chirality : 0.044 0.148 2205 Planarity : 0.004 0.037 2550 Dihedral : 14.983 144.553 5460 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.19 % Allowed : 0.26 % Favored : 99.55 % 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: 0.49 (0.21), residues: 1789 helix: 1.11 (0.19), residues: 807 sheet: -0.44 (0.30), residues: 274 loop : -0.12 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 340 HIS 0.003 0.001 HIS A 161 PHE 0.010 0.001 PHE D1727 TYR 0.009 0.001 TYR D1574 ARG 0.007 0.000 ARG D1852 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 1.654 Fit side-chains REVERT: B 246 GLN cc_start: 0.8888 (mt0) cc_final: 0.8687 (mt0) REVERT: B 283 MET cc_start: 0.8769 (mmm) cc_final: 0.8556 (mmp) REVERT: B 372 ARG cc_start: 0.7968 (ptp90) cc_final: 0.7644 (ptt90) outliers start: 0 outliers final: 1 residues processed: 165 average time/residue: 1.7021 time to fit residues: 303.7712 Evaluate side-chains 102 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 101 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1884 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 74 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 138 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN A 115 ASN B 353 GLN C 12 ASN D1477 HIS D1875 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14619 Z= 0.218 Angle : 0.550 7.084 19808 Z= 0.273 Chirality : 0.044 0.146 2205 Planarity : 0.004 0.041 2550 Dihedral : 9.969 154.982 2010 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.36 % Allowed : 6.04 % Favored : 92.60 % 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: 1789 helix: 1.22 (0.19), residues: 787 sheet: -0.30 (0.29), residues: 274 loop : -0.05 (0.23), residues: 728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 340 HIS 0.003 0.001 HIS C 161 PHE 0.017 0.001 PHE D1825 TYR 0.009 0.001 TYR B 69 ARG 0.010 0.000 ARG D1852 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 108 time to evaluate : 1.663 Fit side-chains REVERT: A 176 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7406 (mmt) REVERT: B 276 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7564 (mt-10) REVERT: B 351 THR cc_start: 0.9191 (p) cc_final: 0.8938 (p) REVERT: C 132 MET cc_start: 0.8282 (OUTLIER) cc_final: 0.8058 (ttt) outliers start: 18 outliers final: 3 residues processed: 118 average time/residue: 1.5864 time to fit residues: 203.3294 Evaluate side-chains 106 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 100 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain D residue 1884 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 chunk 173 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 159 optimal weight: 0.0270 chunk 54 optimal weight: 0.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN D1477 HIS D1590 ASN D1875 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14619 Z= 0.400 Angle : 0.600 6.916 19808 Z= 0.301 Chirality : 0.047 0.163 2205 Planarity : 0.005 0.045 2550 Dihedral : 10.109 178.176 2010 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.01 % Allowed : 7.14 % Favored : 90.85 % 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: 0.33 (0.20), residues: 1789 helix: 0.82 (0.19), residues: 813 sheet: -0.30 (0.29), residues: 276 loop : -0.09 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 340 HIS 0.006 0.001 HIS C 161 PHE 0.009 0.001 PHE A 31 TYR 0.013 0.001 TYR B 69 ARG 0.005 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 102 time to evaluate : 1.699 Fit side-chains outliers start: 28 outliers final: 10 residues processed: 119 average time/residue: 1.5610 time to fit residues: 202.4584 Evaluate side-chains 108 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 98 time to evaluate : 1.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain D residue 1319 MET Chi-restraints excluded: chain D residue 1517 GLU Chi-restraints excluded: chain D residue 1884 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 161 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 84 optimal weight: 0.6980 chunk 153 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN D1477 HIS D1875 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14619 Z= 0.213 Angle : 0.535 7.886 19808 Z= 0.263 Chirality : 0.044 0.144 2205 Planarity : 0.004 0.042 2550 Dihedral : 9.727 179.243 2010 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.23 % Allowed : 8.11 % Favored : 90.66 % 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: 0.54 (0.20), residues: 1789 helix: 1.05 (0.19), residues: 790 sheet: -0.15 (0.30), residues: 274 loop : -0.05 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 340 HIS 0.004 0.001 HIS C 161 PHE 0.017 0.001 PHE D1825 TYR 0.010 0.001 TYR D1236 ARG 0.003 0.000 ARG D1884 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 1.770 Fit side-chains revert: symmetry clash REVERT: A 205 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7857 (mt-10) REVERT: B 351 THR cc_start: 0.9185 (p) cc_final: 0.8947 (p) outliers start: 16 outliers final: 5 residues processed: 116 average time/residue: 1.5431 time to fit residues: 194.9612 Evaluate side-chains 104 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 99 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 1252 PHE Chi-restraints excluded: chain D residue 1319 MET Chi-restraints excluded: chain D residue 1884 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 0.0980 chunk 97 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 127 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 118 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN D1477 HIS D1875 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 14619 Z= 0.358 Angle : 0.590 9.678 19808 Z= 0.292 Chirality : 0.046 0.157 2205 Planarity : 0.004 0.044 2550 Dihedral : 9.340 178.804 2010 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.69 % Allowed : 8.05 % Favored : 90.27 % 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: 0.43 (0.20), residues: 1789 helix: 1.00 (0.19), residues: 788 sheet: -0.24 (0.30), residues: 276 loop : -0.14 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 340 HIS 0.006 0.001 HIS C 161 PHE 0.013 0.001 PHE D1283 TYR 0.012 0.001 TYR B 69 ARG 0.004 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 100 time to evaluate : 1.744 Fit side-chains REVERT: B 355 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8165 (mtp) outliers start: 23 outliers final: 9 residues processed: 117 average time/residue: 1.5749 time to fit residues: 201.3699 Evaluate side-chains 106 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 96 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain A residue 353 GLN Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain B residue 355 MET Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 353 GLN Chi-restraints excluded: chain D residue 1319 MET Chi-restraints excluded: chain D residue 1884 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.7980 chunk 154 optimal weight: 0.0020 chunk 33 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 171 optimal weight: 9.9990 chunk 142 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 89 optimal weight: 0.3980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN D1477 HIS D1875 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14619 Z= 0.174 Angle : 0.537 11.499 19808 Z= 0.260 Chirality : 0.043 0.143 2205 Planarity : 0.004 0.042 2550 Dihedral : 8.478 163.695 2010 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.10 % Allowed : 8.89 % Favored : 90.01 % 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: 0.67 (0.20), residues: 1789 helix: 1.14 (0.19), residues: 782 sheet: -0.06 (0.30), residues: 276 loop : 0.03 (0.24), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 79 HIS 0.003 0.001 HIS C 161 PHE 0.017 0.001 PHE D1825 TYR 0.009 0.001 TYR D1236 ARG 0.005 0.000 ARG D1884 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 104 time to evaluate : 1.585 Fit side-chains REVERT: B 276 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7532 (mt-10) REVERT: B 351 THR cc_start: 0.9147 (p) cc_final: 0.8893 (p) outliers start: 14 outliers final: 3 residues processed: 113 average time/residue: 1.6162 time to fit residues: 198.7025 Evaluate side-chains 103 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 99 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 1884 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 97 optimal weight: 0.0040 chunk 125 optimal weight: 10.0000 chunk 96 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 170 optimal weight: 7.9990 chunk 106 optimal weight: 0.2980 chunk 104 optimal weight: 1.9990 chunk 78 optimal weight: 0.0060 overall best weight: 0.2808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 GLN D1477 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14619 Z= 0.128 Angle : 0.518 11.448 19808 Z= 0.248 Chirality : 0.042 0.140 2205 Planarity : 0.004 0.039 2550 Dihedral : 7.641 131.652 2010 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.71 % Allowed : 9.41 % Favored : 89.88 % 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: 0.82 (0.20), residues: 1789 helix: 1.23 (0.19), residues: 785 sheet: 0.17 (0.31), residues: 270 loop : 0.08 (0.24), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.002 0.001 HIS C 161 PHE 0.010 0.001 PHE B 255 TYR 0.008 0.001 TYR D1829 ARG 0.006 0.000 ARG D1884 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 108 time to evaluate : 1.551 Fit side-chains REVERT: B 351 THR cc_start: 0.9086 (p) cc_final: 0.8821 (p) REVERT: C 178 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8185 (tp) outliers start: 8 outliers final: 4 residues processed: 113 average time/residue: 1.5653 time to fit residues: 193.0350 Evaluate side-chains 106 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 1319 MET Chi-restraints excluded: chain D residue 1772 CYS Chi-restraints excluded: chain D residue 1884 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.8980 chunk 68 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 116 optimal weight: 6.9990 chunk 84 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 134 optimal weight: 5.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 ASN D1477 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 14619 Z= 0.400 Angle : 0.627 11.649 19808 Z= 0.307 Chirality : 0.048 0.182 2205 Planarity : 0.004 0.043 2550 Dihedral : 7.879 126.187 2010 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.97 % Allowed : 9.60 % Favored : 89.42 % 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: 0.58 (0.20), residues: 1789 helix: 1.07 (0.19), residues: 786 sheet: -0.01 (0.30), residues: 276 loop : -0.07 (0.23), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 340 HIS 0.007 0.001 HIS C 161 PHE 0.030 0.002 PHE D1439 TYR 0.013 0.001 TYR B 69 ARG 0.005 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 97 time to evaluate : 1.805 Fit side-chains REVERT: B 276 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7553 (mt-10) REVERT: B 351 THR cc_start: 0.9188 (p) cc_final: 0.8958 (p) outliers start: 12 outliers final: 6 residues processed: 106 average time/residue: 1.5763 time to fit residues: 183.2248 Evaluate side-chains 103 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 96 time to evaluate : 1.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 THR Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain B residue 286 ASP Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 1772 CYS Chi-restraints excluded: chain D residue 1884 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 6.9990 chunk 149 optimal weight: 0.9980 chunk 158 optimal weight: 0.0470 chunk 95 optimal weight: 0.5980 chunk 69 optimal weight: 0.0040 chunk 124 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 143 optimal weight: 0.8980 chunk 150 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 168 optimal weight: 7.9990 overall best weight: 0.4090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1477 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 14619 Z= 0.150 Angle : 0.550 11.989 19808 Z= 0.263 Chirality : 0.042 0.146 2205 Planarity : 0.004 0.041 2550 Dihedral : 7.437 111.448 2010 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.84 % Allowed : 9.73 % Favored : 89.42 % 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: 0.78 (0.20), residues: 1789 helix: 1.19 (0.19), residues: 783 sheet: 0.01 (0.32), residues: 252 loop : 0.13 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 79 HIS 0.003 0.001 HIS C 161 PHE 0.025 0.001 PHE D1439 TYR 0.009 0.001 TYR D1829 ARG 0.002 0.000 ARG D1852 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 1.688 Fit side-chains revert: symmetry clash REVERT: B 276 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7531 (mt-10) REVERT: B 351 THR cc_start: 0.9118 (p) cc_final: 0.8871 (p) REVERT: C 178 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8174 (tp) REVERT: D 1796 MET cc_start: 0.8265 (OUTLIER) cc_final: 0.8024 (mmm) outliers start: 10 outliers final: 3 residues processed: 111 average time/residue: 1.5351 time to fit residues: 185.4761 Evaluate side-chains 105 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 99 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 1772 CYS Chi-restraints excluded: chain D residue 1796 MET Chi-restraints excluded: chain D residue 1884 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 162 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 108 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 111 optimal weight: 10.0000 chunk 149 optimal weight: 0.5980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1477 HIS D1590 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14619 Z= 0.239 Angle : 0.585 12.000 19808 Z= 0.280 Chirality : 0.044 0.182 2205 Planarity : 0.004 0.040 2550 Dihedral : 7.491 109.375 2010 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 0.91 % Allowed : 9.80 % Favored : 89.29 % 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: 0.80 (0.20), residues: 1789 helix: 1.21 (0.19), residues: 783 sheet: 0.21 (0.31), residues: 270 loop : 0.07 (0.24), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 340 HIS 0.005 0.001 HIS C 161 PHE 0.023 0.001 PHE D1439 TYR 0.008 0.001 TYR B 69 ARG 0.006 0.000 ARG D1884 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 101 time to evaluate : 1.607 Fit side-chains revert: symmetry clash REVERT: B 276 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7548 (mt-10) REVERT: B 351 THR cc_start: 0.9142 (p) cc_final: 0.8904 (p) outliers start: 11 outliers final: 7 residues processed: 109 average time/residue: 1.6404 time to fit residues: 194.2146 Evaluate side-chains 106 residues out of total 1517 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 1.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 276 GLU Chi-restraints excluded: chain C residue 178 LEU Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain D residue 1722 VAL Chi-restraints excluded: chain D residue 1772 CYS Chi-restraints excluded: chain D residue 1796 MET Chi-restraints excluded: chain D residue 1873 HIS Chi-restraints excluded: chain D residue 1884 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 144 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 123 optimal weight: 0.0060 chunk 8 optimal weight: 0.5980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D1477 HIS D1590 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.139866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.087490 restraints weight = 38834.795| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.61 r_work: 0.2851 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14619 Z= 0.169 Angle : 0.556 12.006 19808 Z= 0.264 Chirality : 0.043 0.146 2205 Planarity : 0.004 0.041 2550 Dihedral : 7.335 106.142 2010 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.71 % Allowed : 10.12 % Favored : 89.16 % 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: 0.85 (0.20), residues: 1789 helix: 1.25 (0.19), residues: 783 sheet: 0.10 (0.33), residues: 252 loop : 0.14 (0.23), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 79 HIS 0.003 0.001 HIS C 161 PHE 0.021 0.001 PHE D1439 TYR 0.007 0.001 TYR D1236 ARG 0.002 0.000 ARG B 177 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4935.22 seconds wall clock time: 89 minutes 0.30 seconds (5340.30 seconds total)