Starting phenix.real_space_refine on Mon Aug 5 21:29:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb9_24400/08_2024/7rb9_24400.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb9_24400/08_2024/7rb9_24400.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb9_24400/08_2024/7rb9_24400.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb9_24400/08_2024/7rb9_24400.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb9_24400/08_2024/7rb9_24400.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rb9_24400/08_2024/7rb9_24400.cif" } resolution = 3.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 91 5.16 5 C 8988 2.51 5 N 2413 2.21 5 O 2692 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 80": "OD1" <-> "OD2" Residue "B ASP 211": "OD1" <-> "OD2" Residue "B GLU 276": "OE1" <-> "OE2" Residue "B GLU 364": "OE1" <-> "OE2" Residue "D TYR 1473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1869": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 80": "OD1" <-> "OD2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "C PHE 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 80": "OD1" <-> "OD2" Residue "C ASP 211": "OD1" <-> "OD2" Residue "C GLU 276": "OE1" <-> "OE2" Residue "C GLU 364": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 14193 Number of models: 1 Model: "" Number of chains: 7 Chain: "B" Number of atoms: 2917 Number of conformers: 1 Conformer: "" 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 Chain: "D" Number of atoms: 5358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 667, 5358 Classifications: {'peptide': 667} Link IDs: {'PTRANS': 23, 'TRANS': 643} Chain breaks: 2 Chain: "A" Number of atoms: 2917 Number of conformers: 1 Conformer: "" 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 Chain: "C" Number of atoms: 2917 Number of conformers: 1 Conformer: "" 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 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: "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: "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} Time building chain proxies: 8.95, per 1000 atoms: 0.63 Number of scatterers: 14193 At special positions: 0 Unit cell: (112.27, 148.32, 136.99, 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 91 16.00 P 6 15.00 Mg 3 11.99 O 2692 8.00 N 2413 7.00 C 8988 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: 5.10 Conformation dependent library (CDL) restraints added in 2.5 seconds 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3344 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 22 sheets defined 52.9% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.946A pdb=" N SER B 60 " --> pdb=" O ASP B 56 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 56 through 61' Processing helix chain 'B' and resid 79 through 95 removed outlier: 3.587A pdb=" N LYS B 84 " --> pdb=" O ASP B 80 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU B 93 " --> pdb=" O THR B 89 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.657A pdb=" N GLU B 100 " --> pdb=" O ALA B 97 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 97 through 101' Processing helix chain 'B' and resid 112 through 126 removed outlier: 3.857A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.653A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 removed outlier: 3.939A pdb=" N THR B 194 " --> pdb=" O MET B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.673A pdb=" N ARG B 206 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 removed outlier: 3.713A pdb=" N ALA B 231 " --> pdb=" O MET B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.508A pdb=" N ARG B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 257' Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.560A pdb=" N ILE B 267 " --> pdb=" O PRO B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 283 removed outlier: 3.726A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 294 Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.507A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 removed outlier: 3.712A pdb=" N GLN B 314 " --> pdb=" O ALA B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.503A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'D' and resid 1218 through 1230 Processing helix chain 'D' and resid 1231 through 1233 No H-bonds generated for 'chain 'D' and resid 1231 through 1233' Processing helix chain 'D' and resid 1256 through 1262 removed outlier: 4.117A pdb=" N VAL D1260 " --> pdb=" O GLY D1256 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN D1261 " --> pdb=" O PRO D1257 " (cutoff:3.500A) Processing helix chain 'D' and resid 1266 through 1271 removed outlier: 4.161A pdb=" N GLU D1270 " --> pdb=" O ARG D1266 " (cutoff:3.500A) Processing helix chain 'D' and resid 1274 through 1290 removed outlier: 4.223A pdb=" N ILE D1278 " --> pdb=" O HIS D1274 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA D1279 " --> pdb=" O LEU D1275 " (cutoff:3.500A) Processing helix chain 'D' and resid 1304 through 1319 Processing helix chain 'D' and resid 1321 through 1325 removed outlier: 4.353A pdb=" N ASP D1324 " --> pdb=" O GLN D1321 " (cutoff:3.500A) Processing helix chain 'D' and resid 1326 through 1334 removed outlier: 3.651A pdb=" N ILE D1331 " --> pdb=" O GLN D1327 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LEU D1332 " --> pdb=" O GLN D1328 " (cutoff:3.500A) Processing helix chain 'D' and resid 1335 through 1342 removed outlier: 3.713A pdb=" N GLU D1339 " --> pdb=" O THR D1335 " (cutoff:3.500A) Processing helix chain 'D' and resid 1380 through 1384 Processing helix chain 'D' and resid 1393 through 1403 removed outlier: 4.183A pdb=" N TYR D1397 " --> pdb=" O TYR D1393 " (cutoff:3.500A) Processing helix chain 'D' and resid 1404 through 1412 Processing helix chain 'D' and resid 1428 through 1433 removed outlier: 3.586A pdb=" N GLY D1432 " --> pdb=" O GLU D1429 " (cutoff:3.500A) Processing helix chain 'D' and resid 1434 through 1449 Processing helix chain 'D' and resid 1452 through 1470 removed outlier: 3.954A pdb=" N GLY D1470 " --> pdb=" O ILE D1466 " (cutoff:3.500A) Processing helix chain 'D' and resid 1490 through 1501 Processing helix chain 'D' and resid 1503 through 1512 Processing helix chain 'D' and resid 1528 through 1559 removed outlier: 3.642A pdb=" N ALA D1540 " --> pdb=" O ARG D1536 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL D1559 " --> pdb=" O VAL D1555 " (cutoff:3.500A) Processing helix chain 'D' and resid 1583 through 1616 Processing helix chain 'D' and resid 1617 through 1620 removed outlier: 3.993A pdb=" N ARG D1620 " --> pdb=" O MET D1617 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1617 through 1620' Processing helix chain 'D' and resid 1627 through 1636 removed outlier: 3.606A pdb=" N ILE D1631 " --> pdb=" O ASN D1627 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE D1634 " --> pdb=" O CYS D1630 " (cutoff:3.500A) Processing helix chain 'D' and resid 1640 through 1650 removed outlier: 4.011A pdb=" N CYS D1650 " --> pdb=" O ASP D1646 " (cutoff:3.500A) Processing helix chain 'D' and resid 1655 through 1668 removed outlier: 3.595A pdb=" N PHE D1659 " --> pdb=" O THR D1655 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D1660 " --> pdb=" O ASP D1656 " (cutoff:3.500A) Processing helix chain 'D' and resid 1698 through 1703 Processing helix chain 'D' and resid 1708 through 1716 removed outlier: 3.540A pdb=" N PHE D1715 " --> pdb=" O VAL D1711 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N VAL D1716 " --> pdb=" O LEU D1712 " (cutoff:3.500A) Processing helix chain 'D' and resid 1720 through 1734 Processing helix chain 'D' and resid 1753 through 1770 Processing helix chain 'D' and resid 1792 through 1804 Processing helix chain 'D' and resid 1805 through 1813 removed outlier: 4.287A pdb=" N VAL D1809 " --> pdb=" O VAL D1805 " (cutoff:3.500A) Processing helix chain 'D' and resid 1821 through 1829 removed outlier: 4.277A pdb=" N PHE D1825 " --> pdb=" O PRO D1821 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N TYR D1829 " --> pdb=" O PHE D1825 " (cutoff:3.500A) Processing helix chain 'D' and resid 1843 through 1855 removed outlier: 4.445A pdb=" N VAL D1847 " --> pdb=" O GLY D1843 " (cutoff:3.500A) Processing helix chain 'D' and resid 1857 through 1861 Processing helix chain 'D' and resid 1873 through 1887 removed outlier: 4.749A pdb=" N GLU D1879 " --> pdb=" O HIS D1875 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER D1880 " --> pdb=" O GLN D1876 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N ARG D1884 " --> pdb=" O SER D1880 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N VAL D1885 " --> pdb=" O MET D1881 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.946A pdb=" N SER A 60 " --> pdb=" O ASP A 56 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 61' Processing helix chain 'A' and resid 79 through 95 removed outlier: 3.587A pdb=" N LYS A 84 " --> pdb=" O ASP A 80 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.656A pdb=" N GLU A 100 " --> pdb=" O ALA A 97 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 97 through 101' Processing helix chain 'A' and resid 112 through 126 removed outlier: 3.857A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.652A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 194 removed outlier: 3.939A pdb=" N THR A 194 " --> pdb=" O MET A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.673A pdb=" N ARG A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 removed outlier: 3.713A pdb=" N ALA A 231 " --> pdb=" O MET A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.509A pdb=" N ARG A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 257' Processing helix chain 'A' and resid 258 through 262 Processing helix chain 'A' and resid 263 through 268 removed outlier: 3.560A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 283 removed outlier: 3.726A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 301 through 305 removed outlier: 3.508A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.713A pdb=" N GLN A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.504A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.947A pdb=" N SER C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 61' Processing helix chain 'C' and resid 79 through 95 removed outlier: 3.586A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLU C 93 " --> pdb=" O THR C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.657A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.857A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.652A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.939A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.672A pdb=" N ARG C 206 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 removed outlier: 3.712A pdb=" N ALA C 231 " --> pdb=" O MET C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.508A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 257' Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 removed outlier: 3.560A pdb=" N ILE C 267 " --> pdb=" O PRO C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 273 through 283 removed outlier: 3.726A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 294 Processing helix chain 'C' and resid 301 through 305 removed outlier: 3.508A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.712A pdb=" N GLN C 314 " --> pdb=" O ALA C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 350 through 356 removed outlier: 3.503A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing sheet with id=AA1, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.543A pdb=" N PHE B 31 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.505A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 removed outlier: 3.513A pdb=" N GLU B 72 " --> pdb=" O ILE B 75 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 176 through 178 removed outlier: 5.440A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 176 through 178 removed outlier: 4.089A pdb=" N GLN A 41 " --> pdb=" O ALA B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'D' and resid 1237 through 1238 removed outlier: 3.808A pdb=" N THR D1237 " --> pdb=" O VAL D1244 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N VAL D1244 " --> pdb=" O THR D1237 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU D1243 " --> pdb=" O ARG D1778 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N LEU D1780 " --> pdb=" O LEU D1243 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER D1245 " --> pdb=" O LEU D1780 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N CYS D1294 " --> pdb=" O LEU D1775 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL D1777 " --> pdb=" O CYS D1294 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE D1296 " --> pdb=" O VAL D1777 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N CYS D1779 " --> pdb=" O ILE D1296 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN D1293 " --> pdb=" O SER D1567 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE D1361 " --> pdb=" O ILE D1568 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N GLY D1356 " --> pdb=" O TYR D1376 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY D1370 " --> pdb=" O PHE D1362 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N GLU D1364 " --> pdb=" O ILE D1368 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ILE D1368 " --> pdb=" O GLU D1364 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 1343 through 1344 removed outlier: 3.611A pdb=" N SER D1352 " --> pdb=" O ALA D1344 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 1513 through 1517 Processing sheet with id=AB1, first strand: chain 'D' and resid 1673 through 1674 Processing sheet with id=AB2, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.544A pdb=" N PHE A 31 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.504A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 71 through 72 removed outlier: 3.513A pdb=" N GLU A 72 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AB6, first strand: chain 'A' and resid 169 through 170 removed outlier: 5.439A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AB8, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.544A pdb=" N PHE C 31 " --> pdb=" O VAL C 17 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.504A pdb=" N ARG C 37 " --> pdb=" O THR C 66 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 71 through 72 removed outlier: 3.513A pdb=" N GLU C 72 " --> pdb=" O ILE C 75 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AC3, first strand: chain 'C' and resid 169 through 170 removed outlier: 5.440A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 238 through 241 645 hydrogen bonds defined for protein. 1737 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: 5.15 Time building geometry restraints manager: 5.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 4664 1.35 - 1.46: 3246 1.46 - 1.58: 6417 1.58 - 1.70: 9 1.70 - 1.82: 153 Bond restraints: 14489 Sorted by residual: bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.404 -0.057 2.00e-02 2.50e+03 8.21e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.95e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.403 -0.056 2.00e-02 2.50e+03 7.92e+00 bond pdb=" CG HIC C 73 " pdb=" CD2 HIC C 73 " ideal model delta sigma weight residual 1.369 1.412 -0.043 2.00e-02 2.50e+03 4.64e+00 bond pdb=" CG HIC B 73 " pdb=" CD2 HIC B 73 " ideal model delta sigma weight residual 1.369 1.411 -0.042 2.00e-02 2.50e+03 4.46e+00 ... (remaining 14484 not shown) Histogram of bond angle deviations from ideal: 98.92 - 106.32: 453 106.32 - 113.71: 7947 113.71 - 121.11: 7300 121.11 - 128.51: 3849 128.51 - 135.91: 85 Bond angle restraints: 19634 Sorted by residual: angle pdb=" N ALA D1253 " pdb=" CA ALA D1253 " pdb=" C ALA D1253 " ideal model delta sigma weight residual 110.10 103.64 6.46 1.49e+00 4.50e-01 1.88e+01 angle pdb=" N LEU D1837 " pdb=" CA LEU D1837 " pdb=" C LEU D1837 " ideal model delta sigma weight residual 113.16 108.28 4.88 1.24e+00 6.50e-01 1.55e+01 angle pdb=" N TYR D1255 " pdb=" CA TYR D1255 " pdb=" C TYR D1255 " ideal model delta sigma weight residual 109.96 104.27 5.69 1.49e+00 4.50e-01 1.46e+01 angle pdb=" N LEU D1835 " pdb=" CA LEU D1835 " pdb=" C LEU D1835 " ideal model delta sigma weight residual 110.50 105.68 4.82 1.41e+00 5.03e-01 1.17e+01 angle pdb=" C ASN D1838 " pdb=" N VAL D1839 " pdb=" CA VAL D1839 " ideal model delta sigma weight residual 122.60 120.62 1.98 6.80e-01 2.16e+00 8.52e+00 ... (remaining 19629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.79: 8514 30.79 - 61.58: 205 61.58 - 92.37: 20 92.37 - 123.17: 0 123.17 - 153.96: 9 Dihedral angle restraints: 8748 sinusoidal: 3550 harmonic: 5198 Sorted by residual: dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 93.96 -153.96 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 93.90 -153.90 1 2.00e+01 2.50e-03 4.56e+01 dihedral pdb=" O2A ADP A 401 " pdb=" O3A ADP A 401 " pdb=" PA ADP A 401 " pdb=" PB ADP A 401 " ideal model delta sinusoidal sigma weight residual -60.00 93.88 -153.88 1 2.00e+01 2.50e-03 4.55e+01 ... (remaining 8745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1998 0.080 - 0.159: 188 0.159 - 0.238: 2 0.238 - 0.318: 0 0.318 - 0.397: 1 Chirality restraints: 2189 Sorted by residual: chirality pdb=" CG LEU D1837 " pdb=" CB LEU D1837 " pdb=" CD1 LEU D1837 " pdb=" CD2 LEU D1837 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" CA ALA D1834 " pdb=" N ALA D1834 " pdb=" C ALA D1834 " pdb=" CB ALA D1834 " both_signs ideal model delta sigma weight residual False 2.48 2.28 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA TYR D1255 " pdb=" N TYR D1255 " pdb=" C TYR D1255 " pdb=" CB TYR D1255 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.88e-01 ... (remaining 2186 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR D1857 " 0.041 5.00e-02 4.00e+02 6.32e-02 6.40e+00 pdb=" N PRO D1858 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO D1858 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D1858 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL D1833 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C VAL D1833 " -0.027 2.00e-02 2.50e+03 pdb=" O VAL D1833 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA D1834 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN D1271 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO D1272 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO D1272 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO D1272 " 0.020 5.00e-02 4.00e+02 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 2315 2.76 - 3.30: 13618 3.30 - 3.83: 22778 3.83 - 4.37: 26698 4.37 - 4.90: 46113 Nonbonded interactions: 111522 Sorted by model distance: nonbonded pdb=" OE1 GLN B 137 " pdb="MG MG B 402 " model vdw 2.228 2.170 nonbonded pdb=" O2B ADP A 401 " pdb="MG MG A 402 " model vdw 2.230 2.170 nonbonded pdb=" OE1 GLN B 354 " pdb=" OH TYR D1639 " model vdw 2.254 3.040 nonbonded pdb=" OD1 ASN A 111 " pdb=" NH1 ARG A 177 " model vdw 2.279 3.120 nonbonded pdb=" OD1 ASN C 111 " pdb=" NH1 ARG C 177 " model vdw 2.279 3.120 ... (remaining 111517 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.520 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 40.480 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 0.057 14489 Z= 0.162 Angle : 0.574 8.220 19634 Z= 0.306 Chirality : 0.044 0.397 2189 Planarity : 0.003 0.063 2525 Dihedral : 14.694 153.957 5404 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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 (0.22), residues: 1765 helix: 1.06 (0.21), residues: 705 sheet: -0.03 (0.31), residues: 304 loop : 0.11 (0.25), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D1550 HIS 0.002 0.000 HIS D1666 PHE 0.013 0.001 PHE D1230 TYR 0.015 0.001 TYR D1473 ARG 0.003 0.000 ARG D1620 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 1211 MET cc_start: 0.8593 (mmp) cc_final: 0.8329 (mmp) REVERT: D 1286 MET cc_start: 0.9012 (mmp) cc_final: 0.8518 (mmp) REVERT: D 1446 MET cc_start: 0.8921 (ppp) cc_final: 0.8369 (ppp) REVERT: D 1514 LYS cc_start: 0.9105 (tttt) cc_final: 0.8358 (tttm) REVERT: D 1596 LEU cc_start: 0.9631 (mm) cc_final: 0.9165 (pp) REVERT: D 1776 PHE cc_start: 0.8216 (m-10) cc_final: 0.7617 (m-10) REVERT: D 1796 MET cc_start: 0.8964 (mmp) cc_final: 0.8749 (mmp) REVERT: D 1881 MET cc_start: 0.8381 (ppp) cc_final: 0.8096 (ttt) REVERT: A 325 MET cc_start: 0.8189 (mtp) cc_final: 0.7388 (mtt) REVERT: A 334 GLU cc_start: 0.8087 (pm20) cc_final: 0.7771 (pm20) REVERT: C 61 LYS cc_start: 0.8851 (mtpt) cc_final: 0.8535 (ttmm) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2734 time to fit residues: 90.9497 Evaluate side-chains 111 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 111 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 8.9990 chunk 134 optimal weight: 0.9990 chunk 74 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 71 optimal weight: 9.9990 chunk 138 optimal weight: 0.6980 chunk 53 optimal weight: 30.0000 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 160 optimal weight: 0.9980 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 49 GLN B 360 GLN D1225 ASN ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1590 ASN D1597 GLN D1697 HIS D1784 HIS D1823 GLN D1873 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 14489 Z= 0.347 Angle : 0.657 7.039 19634 Z= 0.330 Chirality : 0.046 0.158 2189 Planarity : 0.005 0.047 2525 Dihedral : 10.471 169.065 1985 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.24 % Allowed : 7.26 % Favored : 91.49 % 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: 0.48 (0.21), residues: 1765 helix: 0.96 (0.20), residues: 728 sheet: 0.08 (0.33), residues: 284 loop : -0.08 (0.25), residues: 753 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 340 HIS 0.009 0.001 HIS D1784 PHE 0.014 0.001 PHE D1699 TYR 0.016 0.002 TYR D1665 ARG 0.006 0.001 ARG C 335 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 114 time to evaluate : 1.712 Fit side-chains revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8350 (tm-30) cc_final: 0.8030 (tm-30) REVERT: B 325 MET cc_start: 0.8237 (mtp) cc_final: 0.7970 (ttm) REVERT: D 1211 MET cc_start: 0.8645 (mmp) cc_final: 0.8385 (mmp) REVERT: D 1326 MET cc_start: 0.9261 (tpp) cc_final: 0.8958 (tmm) REVERT: D 1446 MET cc_start: 0.8928 (ppp) cc_final: 0.8494 (ppp) REVERT: D 1617 MET cc_start: 0.8006 (mpp) cc_final: 0.7739 (mmp) REVERT: D 1796 MET cc_start: 0.8942 (mmp) cc_final: 0.8625 (mmp) REVERT: A 283 MET cc_start: 0.7421 (mtt) cc_final: 0.7098 (mtt) REVERT: A 325 MET cc_start: 0.8307 (mtp) cc_final: 0.7483 (mtt) REVERT: A 334 GLU cc_start: 0.8048 (pm20) cc_final: 0.7810 (pm20) REVERT: C 184 ASP cc_start: 0.8303 (m-30) cc_final: 0.8059 (m-30) outliers start: 19 outliers final: 14 residues processed: 126 average time/residue: 0.2536 time to fit residues: 48.9089 Evaluate side-chains 114 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 1.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain D residue 1657 HIS Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 20.0000 chunk 133 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 173 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 159 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN B 297 ASN D1225 ASN ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1501 GLN D1648 GLN C 225 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 14489 Z= 0.255 Angle : 0.580 7.461 19634 Z= 0.288 Chirality : 0.044 0.144 2189 Planarity : 0.004 0.044 2525 Dihedral : 10.189 173.612 1985 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.18 % Allowed : 9.10 % Favored : 89.73 % 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: 0.51 (0.22), residues: 1765 helix: 1.01 (0.20), residues: 735 sheet: 0.03 (0.33), residues: 284 loop : -0.08 (0.25), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1619 HIS 0.004 0.001 HIS D1687 PHE 0.012 0.001 PHE D1230 TYR 0.015 0.001 TYR D1665 ARG 0.005 0.000 ARG D1266 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 105 time to evaluate : 1.716 Fit side-chains revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8363 (tm-30) cc_final: 0.8034 (tm-30) REVERT: B 294 TYR cc_start: 0.9157 (m-10) cc_final: 0.8823 (m-80) REVERT: B 325 MET cc_start: 0.8311 (mtp) cc_final: 0.7995 (ttm) REVERT: D 1211 MET cc_start: 0.8617 (mmp) cc_final: 0.8376 (mmp) REVERT: D 1319 MET cc_start: 0.7931 (ptp) cc_final: 0.7174 (ppp) REVERT: D 1326 MET cc_start: 0.9267 (tpp) cc_final: 0.8961 (tmm) REVERT: D 1446 MET cc_start: 0.9068 (ppp) cc_final: 0.8601 (ppp) REVERT: D 1596 LEU cc_start: 0.9469 (mt) cc_final: 0.9047 (pp) REVERT: D 1617 MET cc_start: 0.8138 (mpp) cc_final: 0.7927 (mmp) REVERT: D 1796 MET cc_start: 0.9003 (mmp) cc_final: 0.8753 (mmp) REVERT: D 1860 MET cc_start: 0.6643 (tpt) cc_final: 0.6297 (tpt) REVERT: A 283 MET cc_start: 0.7270 (mtt) cc_final: 0.7027 (mtt) REVERT: A 325 MET cc_start: 0.8288 (mtp) cc_final: 0.7500 (mtt) outliers start: 18 outliers final: 15 residues processed: 117 average time/residue: 0.2341 time to fit residues: 42.9613 Evaluate side-chains 116 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 101 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1359 VAL Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain D residue 1657 HIS Chi-restraints excluded: chain A residue 6 THR Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 171 optimal weight: 0.5980 chunk 84 optimal weight: 0.0970 chunk 153 optimal weight: 0.9990 chunk 46 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 12 ASN ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1343 ASN A 92 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14489 Z= 0.209 Angle : 0.558 7.967 19634 Z= 0.275 Chirality : 0.043 0.142 2189 Planarity : 0.004 0.042 2525 Dihedral : 9.908 175.791 1985 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.44 % Allowed : 11.32 % Favored : 87.24 % 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: 0.61 (0.22), residues: 1765 helix: 1.09 (0.20), residues: 735 sheet: 0.18 (0.33), residues: 281 loop : -0.06 (0.25), residues: 749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D1619 HIS 0.003 0.001 HIS D1667 PHE 0.011 0.001 PHE D1230 TYR 0.014 0.001 TYR D1665 ARG 0.004 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 104 time to evaluate : 1.555 Fit side-chains revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8459 (tm-30) cc_final: 0.8085 (tm-30) REVERT: B 294 TYR cc_start: 0.9103 (m-10) cc_final: 0.8741 (m-80) REVERT: B 325 MET cc_start: 0.8343 (mtp) cc_final: 0.8012 (ttm) REVERT: D 1211 MET cc_start: 0.8642 (mmp) cc_final: 0.8395 (mmp) REVERT: D 1326 MET cc_start: 0.9353 (tpp) cc_final: 0.9072 (tmm) REVERT: D 1446 MET cc_start: 0.9142 (ppp) cc_final: 0.8684 (ppp) REVERT: D 1596 LEU cc_start: 0.9511 (mt) cc_final: 0.9067 (pp) REVERT: D 1796 MET cc_start: 0.9017 (mmp) cc_final: 0.8788 (mmp) REVERT: D 1860 MET cc_start: 0.6585 (tpt) cc_final: 0.6254 (tpt) REVERT: A 325 MET cc_start: 0.8308 (mtp) cc_final: 0.7543 (mtt) outliers start: 22 outliers final: 15 residues processed: 117 average time/residue: 0.2215 time to fit residues: 41.2138 Evaluate side-chains 114 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 0.3980 chunk 97 optimal weight: 30.0000 chunk 2 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 70 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 118 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 153 optimal weight: 0.6980 chunk 43 optimal weight: 20.0000 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1760 GLN A 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14489 Z= 0.211 Angle : 0.547 8.516 19634 Z= 0.269 Chirality : 0.043 0.137 2189 Planarity : 0.004 0.042 2525 Dihedral : 9.689 177.062 1985 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.51 % Allowed : 12.11 % Favored : 86.39 % 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: 0.73 (0.22), residues: 1765 helix: 1.22 (0.20), residues: 730 sheet: 0.17 (0.33), residues: 281 loop : 0.02 (0.25), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D1619 HIS 0.003 0.001 HIS B 371 PHE 0.010 0.001 PHE D1699 TYR 0.014 0.001 TYR B 279 ARG 0.003 0.000 ARG A 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 109 time to evaluate : 1.531 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8554 (tm-30) cc_final: 0.8089 (tm-30) REVERT: B 325 MET cc_start: 0.8369 (mtp) cc_final: 0.8143 (ttm) REVERT: B 360 GLN cc_start: 0.8125 (tm130) cc_final: 0.7709 (tm130) REVERT: D 1211 MET cc_start: 0.8609 (mmp) cc_final: 0.8386 (mmp) REVERT: D 1286 MET cc_start: 0.9113 (mmp) cc_final: 0.8910 (mmp) REVERT: D 1326 MET cc_start: 0.9358 (tpp) cc_final: 0.9117 (tmm) REVERT: D 1446 MET cc_start: 0.9226 (ppp) cc_final: 0.8851 (ppp) REVERT: D 1596 LEU cc_start: 0.9534 (mt) cc_final: 0.9070 (pp) REVERT: D 1796 MET cc_start: 0.9065 (mmp) cc_final: 0.8852 (mmp) REVERT: D 1860 MET cc_start: 0.6599 (tpt) cc_final: 0.6321 (tpt) REVERT: A 325 MET cc_start: 0.8398 (mtp) cc_final: 0.7605 (mtt) outliers start: 23 outliers final: 19 residues processed: 123 average time/residue: 0.2154 time to fit residues: 42.7169 Evaluate side-chains 120 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 101 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 10.0000 chunk 154 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 100 optimal weight: 30.0000 chunk 42 optimal weight: 10.0000 chunk 171 optimal weight: 1.9990 chunk 142 optimal weight: 5.9990 chunk 79 optimal weight: 7.9990 chunk 14 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1468 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 14489 Z= 0.418 Angle : 0.657 8.121 19634 Z= 0.327 Chirality : 0.047 0.222 2189 Planarity : 0.004 0.041 2525 Dihedral : 9.930 176.571 1985 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.83 % Allowed : 13.29 % Favored : 84.88 % 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: 0.51 (0.22), residues: 1765 helix: 1.16 (0.21), residues: 724 sheet: -0.01 (0.33), residues: 281 loop : -0.21 (0.25), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D1619 HIS 0.006 0.001 HIS D1725 PHE 0.017 0.001 PHE D1699 TYR 0.019 0.002 TYR A 279 ARG 0.004 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 98 time to evaluate : 1.698 Fit side-chains revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8222 (tm-30) REVERT: B 325 MET cc_start: 0.8432 (mtp) cc_final: 0.8178 (ttm) REVERT: B 360 GLN cc_start: 0.8116 (tm130) cc_final: 0.7723 (tm130) REVERT: D 1211 MET cc_start: 0.8656 (mmp) cc_final: 0.8409 (mmp) REVERT: D 1286 MET cc_start: 0.9147 (mmp) cc_final: 0.8900 (mmp) REVERT: D 1326 MET cc_start: 0.9395 (tpp) cc_final: 0.9158 (tmm) REVERT: D 1446 MET cc_start: 0.9281 (ppp) cc_final: 0.8909 (ppp) REVERT: D 1796 MET cc_start: 0.9113 (mmp) cc_final: 0.8902 (mmp) REVERT: D 1860 MET cc_start: 0.6624 (tpt) cc_final: 0.6396 (tpt) REVERT: A 325 MET cc_start: 0.8480 (mtp) cc_final: 0.7725 (mtt) outliers start: 28 outliers final: 23 residues processed: 116 average time/residue: 0.2682 time to fit residues: 48.7580 Evaluate side-chains 118 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 95 time to evaluate : 1.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 194 THR Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain D residue 1770 GLU Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 30.0000 chunk 125 optimal weight: 0.7980 chunk 96 optimal weight: 20.0000 chunk 144 optimal weight: 6.9990 chunk 95 optimal weight: 6.9990 chunk 170 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 78 optimal weight: 20.0000 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D1262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 14489 Z= 0.159 Angle : 0.554 9.051 19634 Z= 0.274 Chirality : 0.043 0.211 2189 Planarity : 0.004 0.042 2525 Dihedral : 9.627 175.848 1985 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.24 % Allowed : 14.99 % Favored : 83.77 % 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: 0.76 (0.22), residues: 1765 helix: 1.27 (0.21), residues: 718 sheet: 0.11 (0.33), residues: 281 loop : 0.06 (0.25), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP D1619 HIS 0.002 0.001 HIS D1667 PHE 0.011 0.001 PHE D1727 TYR 0.016 0.001 TYR B 279 ARG 0.009 0.000 ARG D1721 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3530 Ramachandran restraints generated. 1765 Oldfield, 0 Emsley, 1765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 1.499 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 121 GLN cc_start: 0.8595 (tm-30) cc_final: 0.8168 (tm-30) REVERT: B 325 MET cc_start: 0.8460 (mtp) cc_final: 0.8255 (ttm) REVERT: D 1211 MET cc_start: 0.8634 (mmp) cc_final: 0.8383 (mmp) REVERT: D 1326 MET cc_start: 0.9383 (tpp) cc_final: 0.9143 (tmm) REVERT: D 1446 MET cc_start: 0.9277 (ppp) cc_final: 0.8884 (ppp) REVERT: D 1860 MET cc_start: 0.6531 (tpt) cc_final: 0.6299 (tpt) REVERT: A 325 MET cc_start: 0.8489 (mtp) cc_final: 0.7687 (mtt) outliers start: 19 outliers final: 16 residues processed: 118 average time/residue: 0.2179 time to fit residues: 40.7156 Evaluate side-chains 118 residues out of total 1528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 123 MET Chi-restraints excluded: chain B residue 345 ILE Chi-restraints excluded: chain B residue 374 CYS Chi-restraints excluded: chain D residue 1288 ASP Chi-restraints excluded: chain D residue 1516 THR Chi-restraints excluded: chain D residue 1560 SER Chi-restraints excluded: chain D residue 1770 GLU Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 115 ASN Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 374 CYS Chi-restraints excluded: chain C residue 5 THR Chi-restraints excluded: chain C residue 123 MET Chi-restraints excluded: chain C residue 345 ILE Chi-restraints excluded: chain C residue 374 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/programs/real_space_refine.py", line 200, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 766, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.8213 > 50: distance: 16 - 26: 16.150 distance: 26 - 27: 21.510 distance: 26 - 110: 18.013 distance: 27 - 28: 16.027 distance: 27 - 30: 5.356 distance: 28 - 29: 11.526 distance: 28 - 32: 10.595 distance: 29 - 107: 31.423 distance: 30 - 31: 13.062 distance: 32 - 33: 6.445 distance: 33 - 34: 8.180 distance: 33 - 36: 7.120 distance: 34 - 35: 11.361 distance: 34 - 41: 26.238 distance: 36 - 37: 10.192 distance: 37 - 38: 16.328 distance: 38 - 39: 12.293 distance: 39 - 40: 4.415 distance: 41 - 42: 5.496 distance: 41 - 47: 32.532 distance: 42 - 43: 20.405 distance: 42 - 45: 31.578 distance: 43 - 44: 33.449 distance: 43 - 48: 7.326 distance: 45 - 46: 23.174 distance: 46 - 47: 9.102 distance: 48 - 49: 18.969 distance: 49 - 50: 22.718 distance: 49 - 52: 16.350 distance: 50 - 51: 22.108 distance: 50 - 57: 39.505 distance: 52 - 53: 28.162 distance: 54 - 55: 21.521 distance: 55 - 56: 22.236 distance: 57 - 58: 19.324 distance: 58 - 59: 16.900 distance: 58 - 61: 30.108 distance: 59 - 60: 11.090 distance: 59 - 65: 7.903 distance: 61 - 62: 25.567 distance: 62 - 63: 28.146 distance: 63 - 64: 26.240 distance: 65 - 66: 35.582 distance: 65 - 71: 34.233 distance: 66 - 67: 8.164 distance: 66 - 69: 27.305 distance: 67 - 68: 8.997 distance: 67 - 72: 39.623 distance: 69 - 70: 37.192 distance: 70 - 71: 15.244 distance: 72 - 73: 31.508 distance: 73 - 74: 13.617 distance: 73 - 76: 21.663 distance: 74 - 75: 5.613 distance: 74 - 80: 13.821 distance: 76 - 77: 25.223 distance: 77 - 78: 8.492 distance: 77 - 79: 14.261 distance: 80 - 81: 44.446 distance: 80 - 86: 31.365 distance: 81 - 82: 31.838 distance: 81 - 84: 21.095 distance: 82 - 83: 10.386 distance: 82 - 87: 14.220 distance: 85 - 86: 26.210 distance: 87 - 88: 19.760 distance: 88 - 89: 11.676 distance: 88 - 91: 8.185 distance: 89 - 90: 19.056 distance: 89 - 96: 6.557 distance: 91 - 92: 10.385 distance: 92 - 93: 9.713 distance: 93 - 95: 5.489 distance: 96 - 97: 10.086 distance: 96 - 129: 15.901 distance: 97 - 98: 18.868 distance: 97 - 100: 9.216 distance: 98 - 99: 6.731 distance: 98 - 107: 14.354 distance: 99 - 126: 10.531 distance: 101 - 102: 3.522 distance: 101 - 103: 5.132 distance: 102 - 104: 6.763 distance: 103 - 105: 6.881 distance: 104 - 106: 4.427 distance: 105 - 106: 4.820