Starting phenix.real_space_refine on Thu Feb 15 15:04:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmf_33295/02_2024/7xmf_33295_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmf_33295/02_2024/7xmf_33295.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmf_33295/02_2024/7xmf_33295.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmf_33295/02_2024/7xmf_33295.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmf_33295/02_2024/7xmf_33295_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmf_33295/02_2024/7xmf_33295_updated.pdb" } resolution = 3.07 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= 0.026 sd= 0.105 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 924 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 96 5.16 5 C 7690 2.51 5 N 1851 2.21 5 O 2071 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 185": "NH1" <-> "NH2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" Residue "A ASP 247": "OD1" <-> "OD2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 287": "OE1" <-> "OE2" Residue "A GLU 294": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "A PHE 299": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 311": "OD1" <-> "OD2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 364": "OE1" <-> "OE2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 745": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 747": "OD1" <-> "OD2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A GLU 770": "OE1" <-> "OE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A GLU 790": "OE1" <-> "OE2" Residue "A ASP 812": "OD1" <-> "OD2" Residue "A PHE 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 838": "NH1" <-> "NH2" Residue "A GLU 894": "OE1" <-> "OE2" Residue "A ARG 922": "NH1" <-> "NH2" Residue "A PHE 971": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1182": "NH1" <-> "NH2" Residue "A GLU 1195": "OE1" <-> "OE2" Residue "A GLU 1212": "OE1" <-> "OE2" Residue "A GLU 1217": "OE1" <-> "OE2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A ASP 1267": "OD1" <-> "OD2" Residue "A ARG 1293": "NH1" <-> "NH2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "A TYR 1348": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1369": "OE1" <-> "OE2" Residue "A ASP 1422": "OD1" <-> "OD2" Residue "A PHE 1443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1471": "OD1" <-> "OD2" Residue "A GLU 1476": "OE1" <-> "OE2" Residue "A GLU 1477": "OE1" <-> "OE2" Residue "A TYR 1482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1499": "NH1" <-> "NH2" Residue "A ASP 1582": "OD1" <-> "OD2" Residue "A PHE 1583": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1610": "NH1" <-> "NH2" Residue "A ARG 1613": "NH1" <-> "NH2" Residue "A ARG 1619": "NH1" <-> "NH2" Residue "A ARG 1622": "NH1" <-> "NH2" Residue "A TYR 1658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1729": "OD1" <-> "OD2" Residue "A TYR 1739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1755": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1761": "OE1" <-> "OE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 84": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 190": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C GLU 120": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11709 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1140, 9185 Classifications: {'peptide': 1140} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 1108} Chain breaks: 3 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1416 Classifications: {'peptide': 173} Link IDs: {'TRANS': 172} Chain: "C" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 24 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {'G2W': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 6.75, per 1000 atoms: 0.58 Number of scatterers: 11709 At special positions: 0 Unit cell: (130, 139.36, 114.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 F 1 9.00 O 2071 8.00 N 1851 7.00 C 7690 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 275 " - pdb=" SG CYS A 315 " distance=2.03 Simple disulfide: pdb=" SG CYS A 897 " - pdb=" SG CYS A 903 " distance=2.03 Simple disulfide: pdb=" SG CYS A 935 " - pdb=" SG CYS A 944 " distance=2.02 Simple disulfide: pdb=" SG CYS A1350 " - pdb=" SG CYS A1370 " distance=2.02 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.03 Simple disulfide: pdb=" SG CYS B 21 " - pdb=" SG CYS B 43 " distance=2.03 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.57 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.04 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 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " NAG-ASN " NAG A2301 " - " ASN A1375 " " NAG A2302 " - " ASN A 283 " " NAG B 501 " - " ASN B 93 " " NAG B 502 " - " ASN B 110 " " NAG B 503 " - " ASN B 114 " " NAG B 504 " - " ASN B 135 " " NAG D 1 " - " ASN A1352 " " NAG E 1 " - " ASN A1366 " Time building additional restraints: 4.98 Conformation dependent library (CDL) restraints added in 2.5 seconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2714 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 7 sheets defined 60.8% alpha, 6.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.11 Creating SS restraints... Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 126 through 145 removed outlier: 3.848A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N MET A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 174 removed outlier: 3.698A pdb=" N ASN A 154 " --> pdb=" O TRP A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 184 No H-bonds generated for 'chain 'A' and resid 181 through 184' Processing helix chain 'A' and resid 189 through 203 Processing helix chain 'A' and resid 210 through 227 removed outlier: 4.309A pdb=" N PHE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N VAL A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ARG A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N ALA A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N THR A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 267 removed outlier: 3.666A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N ASP A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N VAL A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 296 through 300 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 347 through 358 Processing helix chain 'A' and resid 363 through 374 Processing helix chain 'A' and resid 376 through 416 removed outlier: 3.664A pdb=" N PHE A 387 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU A 388 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY A 389 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N SER A 390 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N PHE A 391 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N TYR A 392 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU A 393 " --> pdb=" O SER A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 746 through 761 Processing helix chain 'A' and resid 770 through 798 Processing helix chain 'A' and resid 801 through 804 No H-bonds generated for 'chain 'A' and resid 801 through 804' Processing helix chain 'A' and resid 807 through 822 removed outlier: 4.622A pdb=" N GLU A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 846 removed outlier: 4.042A pdb=" N ARG A 838 " --> pdb=" O ARG A 835 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 839 " --> pdb=" O SER A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 862 Processing helix chain 'A' and resid 867 through 898 removed outlier: 5.101A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.024A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N CYS A 897 " --> pdb=" O LYS A 893 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N LYS A 898 " --> pdb=" O GLU A 894 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 924 Processing helix chain 'A' and resid 929 through 939 removed outlier: 3.958A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 971 Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1192 through 1209 removed outlier: 4.024A pdb=" N LEU A1209 " --> pdb=" O SER A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1216 No H-bonds generated for 'chain 'A' and resid 1214 through 1216' Processing helix chain 'A' and resid 1220 through 1248 removed outlier: 4.040A pdb=" N LYS A1231 " --> pdb=" O GLU A1227 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1254 Processing helix chain 'A' and resid 1257 through 1278 Processing helix chain 'A' and resid 1285 through 1300 removed outlier: 3.941A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ARG A1293 " --> pdb=" O LEU A1289 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ALA A1294 " --> pdb=" O ARG A1290 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LEU A1295 " --> pdb=" O THR A1291 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ARG A1296 " --> pdb=" O LEU A1292 " (cutoff:3.500A) Proline residue: A1297 - end of helix removed outlier: 4.986A pdb=" N ALA A1300 " --> pdb=" O ARG A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1343 removed outlier: 3.613A pdb=" N VAL A1310 " --> pdb=" O GLY A1306 " (cutoff:3.500A) Proline residue: A1319 - end of helix Processing helix chain 'A' and resid 1367 through 1376 Processing helix chain 'A' and resid 1392 through 1404 Processing helix chain 'A' and resid 1408 through 1417 removed outlier: 3.677A pdb=" N ALA A1414 " --> pdb=" O ILE A1410 " (cutoff:3.500A) Processing helix chain 'A' and resid 1433 through 1466 removed outlier: 3.751A pdb=" N PHE A1446 " --> pdb=" O ILE A1442 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1489 removed outlier: 4.262A pdb=" N LEU A1488 " --> pdb=" O ALA A1484 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLY A1489 " --> pdb=" O MET A1485 " (cutoff:3.500A) Processing helix chain 'A' and resid 1503 through 1513 Processing helix chain 'A' and resid 1515 through 1533 Processing helix chain 'A' and resid 1541 through 1568 Processing helix chain 'A' and resid 1573 through 1575 No H-bonds generated for 'chain 'A' and resid 1573 through 1575' Processing helix chain 'A' and resid 1577 through 1602 Processing helix chain 'A' and resid 1606 through 1625 removed outlier: 4.474A pdb=" N ALA A1615 " --> pdb=" O VAL A1611 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ARG A1616 " --> pdb=" O ILE A1612 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ILE A1617 " --> pdb=" O ARG A1613 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N GLY A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ARG A1619 " --> pdb=" O ALA A1615 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N LEU A1623 " --> pdb=" O ARG A1619 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N VAL A1624 " --> pdb=" O ILE A1620 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LYS A1625 " --> pdb=" O LEU A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1665 removed outlier: 3.550A pdb=" N LEU A1633 " --> pdb=" O GLY A1629 " (cutoff:3.500A) Proline residue: A1642 - end of helix Processing helix chain 'A' and resid 1684 through 1696 removed outlier: 4.109A pdb=" N THR A1696 " --> pdb=" O PHE A1692 " (cutoff:3.500A) Processing helix chain 'A' and resid 1700 through 1705 Processing helix chain 'A' and resid 1733 through 1767 Processing helix chain 'B' and resid 154 through 190 Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing sheet with id= A, first strand: chain 'A' and resid 273 through 277 Processing sheet with id= B, first strand: chain 'A' and resid 1349 through 1352 Processing sheet with id= C, first strand: chain 'B' and resid 36 through 38 Processing sheet with id= D, first strand: chain 'B' and resid 138 through 144 removed outlier: 3.618A pdb=" N PHE B 54 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU B 71 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N PHE B 59 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N LYS B 69 " --> pdb=" O PHE B 59 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 31 through 34 removed outlier: 4.115A pdb=" N GLU C 31 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 37 through 40 removed outlier: 7.687A pdb=" N LEU C 38 " --> pdb=" O LYS C 141 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N HIS C 143 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL C 40 " --> pdb=" O HIS C 143 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N GLN C 145 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 46 through 48 672 hydrogen bonds defined for protein. 1815 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: 3.65 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.35: 3549 1.35 - 1.51: 4364 1.51 - 1.68: 3915 1.68 - 1.84: 153 1.84 - 2.01: 1 Bond restraints: 11982 Sorted by residual: bond pdb=" C17 G2W A2303 " pdb=" N05 G2W A2303 " ideal model delta sigma weight residual 1.322 1.472 -0.150 2.00e-02 2.50e+03 5.65e+01 bond pdb=" C17 G2W A2303 " pdb=" N06 G2W A2303 " ideal model delta sigma weight residual 1.334 1.480 -0.146 2.00e-02 2.50e+03 5.29e+01 bond pdb=" C24 G2W A2303 " pdb=" C26 G2W A2303 " ideal model delta sigma weight residual 1.391 1.534 -0.143 2.00e-02 2.50e+03 5.11e+01 bond pdb=" C21 G2W A2303 " pdb=" C22 G2W A2303 " ideal model delta sigma weight residual 1.379 1.520 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C25 G2W A2303 " pdb=" C27 G2W A2303 " ideal model delta sigma weight residual 1.383 1.523 -0.140 2.00e-02 2.50e+03 4.88e+01 ... (remaining 11977 not shown) Histogram of bond angle deviations from ideal: 81.13 - 92.64: 5 92.64 - 104.15: 147 104.15 - 115.66: 7516 115.66 - 127.17: 8455 127.17 - 138.68: 113 Bond angle restraints: 16236 Sorted by residual: angle pdb=" C ASP A 799 " pdb=" CA ASP A 799 " pdb=" CB ASP A 799 " ideal model delta sigma weight residual 110.17 136.07 -25.90 1.97e+00 2.58e-01 1.73e+02 angle pdb=" N ASP A 799 " pdb=" CA ASP A 799 " pdb=" C ASP A 799 " ideal model delta sigma weight residual 109.81 81.13 28.68 2.21e+00 2.05e-01 1.68e+02 angle pdb=" C MET C 85 " pdb=" CA MET C 85 " pdb=" CB MET C 85 " ideal model delta sigma weight residual 111.23 94.71 16.52 1.63e+00 3.76e-01 1.03e+02 angle pdb=" C ASN C 131 " pdb=" N PRO C 132 " pdb=" CA PRO C 132 " ideal model delta sigma weight residual 119.66 114.07 5.59 7.20e-01 1.93e+00 6.03e+01 angle pdb=" CA CYS C 127 " pdb=" CB CYS C 127 " pdb=" SG CYS C 127 " ideal model delta sigma weight residual 114.40 128.18 -13.78 2.30e+00 1.89e-01 3.59e+01 ... (remaining 16231 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.88: 6600 23.88 - 47.76: 500 47.76 - 71.64: 79 71.64 - 95.52: 17 95.52 - 119.40: 3 Dihedral angle restraints: 7199 sinusoidal: 2999 harmonic: 4200 Sorted by residual: dihedral pdb=" CB CYS A 935 " pdb=" SG CYS A 935 " pdb=" SG CYS A 944 " pdb=" CB CYS A 944 " ideal model delta sinusoidal sigma weight residual -86.00 -162.02 76.02 1 1.00e+01 1.00e-02 7.28e+01 dihedral pdb=" C MET C 85 " pdb=" N MET C 85 " pdb=" CA MET C 85 " pdb=" CB MET C 85 " ideal model delta harmonic sigma weight residual -122.60 -106.78 -15.82 0 2.50e+00 1.60e-01 4.00e+01 dihedral pdb=" CB CYS A 275 " pdb=" SG CYS A 275 " pdb=" SG CYS A 315 " pdb=" CB CYS A 315 " ideal model delta sinusoidal sigma weight residual -86.00 -136.23 50.23 1 1.00e+01 1.00e-02 3.46e+01 ... (remaining 7196 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1735 0.084 - 0.168: 143 0.168 - 0.253: 8 0.253 - 0.337: 5 0.337 - 0.421: 1 Chirality restraints: 1892 Sorted by residual: chirality pdb=" C1 NAG B 504 " pdb=" ND2 ASN B 135 " pdb=" C2 NAG B 504 " pdb=" O5 NAG B 504 " both_signs ideal model delta sigma weight residual False -2.40 -1.98 -0.42 2.00e-01 2.50e+01 4.43e+00 chirality pdb=" CA ASP A 799 " pdb=" N ASP A 799 " pdb=" C ASP A 799 " pdb=" CB ASP A 799 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.37 -0.03 2.00e-02 2.50e+03 2.51e+00 ... (remaining 1889 not shown) Planarity restraints: 1989 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 799 " 0.030 2.00e-02 2.50e+03 6.05e-02 3.66e+01 pdb=" C ASP A 799 " -0.105 2.00e-02 2.50e+03 pdb=" O ASP A 799 " 0.040 2.00e-02 2.50e+03 pdb=" N PRO A 800 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN C 104 " 0.061 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO C 105 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 105 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 105 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO C 132 " 0.053 5.00e-02 4.00e+02 8.07e-02 1.04e+01 pdb=" N PRO C 133 " -0.140 5.00e-02 4.00e+02 pdb=" CA PRO C 133 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 133 " 0.042 5.00e-02 4.00e+02 ... (remaining 1986 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 88 2.54 - 3.13: 9711 3.13 - 3.72: 18473 3.72 - 4.31: 26045 4.31 - 4.90: 42469 Nonbonded interactions: 96786 Sorted by model distance: nonbonded pdb=" N ASP A 799 " pdb=" O ASP A 799 " model vdw 1.953 2.496 nonbonded pdb=" O GLY A1444 " pdb=" OG1 THR A1448 " model vdw 2.045 2.440 nonbonded pdb=" O PHE A1738 " pdb=" OG SER A1742 " model vdw 2.069 2.440 nonbonded pdb=" CD2 TYR C 128 " pdb=" NH2 ARG C 137 " model vdw 2.087 3.420 nonbonded pdb=" O GLN C 62 " pdb=" CD PRO C 132 " model vdw 2.107 3.440 ... (remaining 96781 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 'D' selection = chain 'E' } 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=0.41 max=1.00 mean=1.00 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 4.140 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 35.560 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.008 0.199 11982 Z= 0.492 Angle : 0.868 28.675 16236 Z= 0.485 Chirality : 0.051 0.421 1892 Planarity : 0.005 0.093 1981 Dihedral : 16.545 119.403 4458 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 16.26 Ramachandran Plot: Outliers : 0.35 % Allowed : 5.56 % Favored : 94.09 % Rotamer: Outliers : 3.37 % Allowed : 19.03 % Favored : 77.60 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.20), residues: 1421 helix: -1.18 (0.15), residues: 873 sheet: -1.36 (0.45), residues: 137 loop : -2.23 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 67 HIS 0.004 0.001 HIS A 766 PHE 0.018 0.002 PHE C 80 TYR 0.018 0.002 TYR C 125 ARG 0.003 0.001 ARG A1622 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 227 time to evaluate : 1.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.6706 (tt) cc_final: 0.6244 (mt) REVERT: A 254 PHE cc_start: 0.8027 (t80) cc_final: 0.7803 (t80) REVERT: A 279 SER cc_start: 0.8583 (t) cc_final: 0.8304 (p) REVERT: A 405 TYR cc_start: 0.7166 (t80) cc_final: 0.6960 (t80) REVERT: A 794 LYS cc_start: 0.6091 (mmmt) cc_final: 0.4868 (tttm) REVERT: A 796 ILE cc_start: 0.7027 (pp) cc_final: 0.6760 (pt) REVERT: A 1251 LYS cc_start: 0.7693 (tttt) cc_final: 0.7412 (mptt) REVERT: A 1252 THR cc_start: 0.8608 (p) cc_final: 0.8245 (t) REVERT: A 1424 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7495 (tp-100) REVERT: A 1519 ILE cc_start: 0.8581 (pt) cc_final: 0.8337 (tp) REVERT: A 1541 GLN cc_start: 0.7787 (tp40) cc_final: 0.7494 (mm-40) REVERT: A 1579 ASN cc_start: 0.7970 (m-40) cc_final: 0.7735 (m-40) REVERT: A 1720 VAL cc_start: 0.7918 (OUTLIER) cc_final: 0.7716 (t) REVERT: B 118 ASP cc_start: 0.7125 (m-30) cc_final: 0.6720 (m-30) outliers start: 43 outliers final: 23 residues processed: 264 average time/residue: 0.2337 time to fit residues: 89.3103 Evaluate side-chains 202 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 177 time to evaluate : 1.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 851 THR Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 1188 ILE Chi-restraints excluded: chain A residue 1272 THR Chi-restraints excluded: chain A residue 1330 ILE Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1424 GLN Chi-restraints excluded: chain A residue 1675 ILE Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 190 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 83 optimal weight: 0.0970 chunk 129 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 146 ASN A 265 GLN A 282 ASN A 365 ASN A 395 ASN A 409 ASN A 765 HIS A 861 ASN A 941 GLN A 956 ASN A1459 ASN A1463 GLN A1528 ASN B 61 GLN B 102 GLN B 115 HIS C 118 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11982 Z= 0.185 Angle : 0.630 10.490 16236 Z= 0.327 Chirality : 0.042 0.295 1892 Planarity : 0.005 0.070 1981 Dihedral : 9.936 110.207 1810 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 3.84 % Allowed : 20.44 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: -1.00 (0.21), residues: 1421 helix: -0.02 (0.16), residues: 866 sheet: -1.22 (0.45), residues: 131 loop : -1.60 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1382 HIS 0.002 0.001 HIS A 909 PHE 0.015 0.001 PHE A1440 TYR 0.015 0.001 TYR A1739 ARG 0.007 0.000 ARG C 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 187 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.6678 (tt) cc_final: 0.6244 (mt) REVERT: A 130 MET cc_start: 0.6222 (OUTLIER) cc_final: 0.5865 (tpp) REVERT: A 243 LYS cc_start: 0.7908 (mtpt) cc_final: 0.7271 (tppt) REVERT: A 254 PHE cc_start: 0.7950 (t80) cc_final: 0.7625 (t80) REVERT: A 279 SER cc_start: 0.8539 (t) cc_final: 0.8235 (p) REVERT: A 742 MET cc_start: 0.6237 (ttm) cc_final: 0.6002 (ttm) REVERT: A 794 LYS cc_start: 0.6316 (mmmt) cc_final: 0.5229 (mmmt) REVERT: A 796 ILE cc_start: 0.7103 (pp) cc_final: 0.6765 (pt) REVERT: A 837 PHE cc_start: 0.7429 (m-10) cc_final: 0.6936 (m-10) REVERT: A 1251 LYS cc_start: 0.7738 (tttt) cc_final: 0.7430 (mptt) REVERT: A 1252 THR cc_start: 0.8518 (p) cc_final: 0.8168 (t) REVERT: A 1424 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7383 (tp-100) REVERT: B 154 MET cc_start: 0.6650 (tmm) cc_final: 0.6427 (tmm) REVERT: C 79 MET cc_start: 0.0071 (ppp) cc_final: -0.1826 (mmm) outliers start: 49 outliers final: 27 residues processed: 228 average time/residue: 0.2150 time to fit residues: 72.8187 Evaluate side-chains 193 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 298 ASP Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1424 GLN Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1718 LYS Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain C residue 148 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 72 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 108 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 130 optimal weight: 9.9990 chunk 140 optimal weight: 8.9990 chunk 115 optimal weight: 0.0050 chunk 129 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 overall best weight: 2.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 765 HIS A 909 HIS A1463 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7106 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 11982 Z= 0.355 Angle : 0.676 11.544 16236 Z= 0.349 Chirality : 0.045 0.355 1892 Planarity : 0.005 0.051 1981 Dihedral : 10.545 121.688 1789 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 5.17 % Allowed : 20.67 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: -0.77 (0.22), residues: 1421 helix: 0.17 (0.17), residues: 857 sheet: -1.03 (0.47), residues: 128 loop : -1.54 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A1408 HIS 0.003 0.001 HIS A 766 PHE 0.021 0.002 PHE A1343 TYR 0.022 0.002 TYR A1548 ARG 0.004 0.001 ARG A 907 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 171 time to evaluate : 1.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7268 (tppt) REVERT: A 742 MET cc_start: 0.6241 (ttm) cc_final: 0.5902 (ttm) REVERT: A 796 ILE cc_start: 0.7079 (pp) cc_final: 0.6849 (pt) REVERT: A 1251 LYS cc_start: 0.7885 (tttt) cc_final: 0.7482 (mptt) REVERT: A 1431 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8216 (tp) REVERT: A 1477 GLU cc_start: 0.7366 (tp30) cc_final: 0.7132 (tp30) REVERT: A 1519 ILE cc_start: 0.8488 (pt) cc_final: 0.8281 (tp) REVERT: A 1556 ILE cc_start: 0.8025 (tp) cc_final: 0.7774 (tp) REVERT: A 1668 TYR cc_start: 0.8089 (m-80) cc_final: 0.7795 (m-80) REVERT: A 1691 LEU cc_start: 0.8258 (OUTLIER) cc_final: 0.8049 (mp) REVERT: B 68 VAL cc_start: 0.8315 (OUTLIER) cc_final: 0.7853 (p) REVERT: B 154 MET cc_start: 0.6833 (tmm) cc_final: 0.6565 (tmm) REVERT: C 79 MET cc_start: -0.0134 (ppp) cc_final: -0.2076 (mmm) outliers start: 66 outliers final: 40 residues processed: 223 average time/residue: 0.2057 time to fit residues: 69.0114 Evaluate side-chains 203 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 160 time to evaluate : 1.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1277 THR Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1424 GLN Chi-restraints excluded: chain A residue 1431 LEU Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1523 VAL Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1724 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain C residue 55 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 128 optimal weight: 5.9990 chunk 97 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 138 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 123 optimal weight: 9.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 765 HIS A 766 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11982 Z= 0.228 Angle : 0.615 10.918 16236 Z= 0.314 Chirality : 0.042 0.314 1892 Planarity : 0.004 0.040 1981 Dihedral : 10.236 120.011 1785 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.76 % Allowed : 22.79 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: -0.35 (0.22), residues: 1421 helix: 0.50 (0.17), residues: 846 sheet: -1.04 (0.46), residues: 129 loop : -1.23 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1382 HIS 0.013 0.001 HIS A 765 PHE 0.015 0.001 PHE A 963 TYR 0.021 0.001 TYR A1548 ARG 0.003 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 167 time to evaluate : 1.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.7955 (mtpt) cc_final: 0.7256 (tppt) REVERT: A 742 MET cc_start: 0.6199 (ttm) cc_final: 0.5787 (ttm) REVERT: A 794 LYS cc_start: 0.6274 (OUTLIER) cc_final: 0.5186 (mmmt) REVERT: A 796 ILE cc_start: 0.7207 (pp) cc_final: 0.6902 (pt) REVERT: A 837 PHE cc_start: 0.7589 (m-10) cc_final: 0.7180 (m-10) REVERT: A 1251 LYS cc_start: 0.7862 (tttt) cc_final: 0.7460 (mptt) REVERT: A 1424 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7413 (tp-100) REVERT: A 1519 ILE cc_start: 0.8490 (pt) cc_final: 0.8263 (tp) REVERT: A 1556 ILE cc_start: 0.7907 (tp) cc_final: 0.7666 (tp) REVERT: A 1720 VAL cc_start: 0.8042 (m) cc_final: 0.7834 (t) REVERT: C 79 MET cc_start: -0.0163 (ppp) cc_final: -0.2122 (mmm) outliers start: 48 outliers final: 34 residues processed: 207 average time/residue: 0.2167 time to fit residues: 66.1056 Evaluate side-chains 198 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 162 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 895 CYS Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1424 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1724 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 153 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 115 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 117 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 70 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN B 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11982 Z= 0.210 Angle : 0.601 9.751 16236 Z= 0.305 Chirality : 0.041 0.291 1892 Planarity : 0.004 0.042 1981 Dihedral : 10.014 119.451 1784 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.15 % Allowed : 22.63 % Favored : 73.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: -0.15 (0.23), residues: 1421 helix: 0.66 (0.18), residues: 844 sheet: -0.97 (0.46), residues: 129 loop : -1.15 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1382 HIS 0.002 0.000 HIS A 766 PHE 0.014 0.001 PHE A 963 TYR 0.022 0.001 TYR A1548 ARG 0.003 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 165 time to evaluate : 1.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.7943 (mtpt) cc_final: 0.7245 (tppt) REVERT: A 364 GLU cc_start: 0.8163 (OUTLIER) cc_final: 0.7075 (pm20) REVERT: A 742 MET cc_start: 0.6054 (ttm) cc_final: 0.5596 (ttm) REVERT: A 794 LYS cc_start: 0.6383 (OUTLIER) cc_final: 0.5447 (mmmt) REVERT: A 796 ILE cc_start: 0.7171 (pp) cc_final: 0.6859 (pt) REVERT: A 837 PHE cc_start: 0.7560 (m-10) cc_final: 0.7132 (m-10) REVERT: A 1251 LYS cc_start: 0.7818 (tttt) cc_final: 0.7475 (mptt) REVERT: A 1276 ASN cc_start: 0.7944 (t0) cc_final: 0.7477 (m-40) REVERT: A 1470 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.6743 (mp10) REVERT: A 1519 ILE cc_start: 0.8497 (pt) cc_final: 0.8276 (tp) REVERT: A 1556 ILE cc_start: 0.7915 (tp) cc_final: 0.7683 (tp) REVERT: A 1720 VAL cc_start: 0.8015 (OUTLIER) cc_final: 0.7785 (t) REVERT: C 79 MET cc_start: 0.0022 (ppp) cc_final: -0.2068 (mmm) outliers start: 53 outliers final: 39 residues processed: 206 average time/residue: 0.2096 time to fit residues: 64.0863 Evaluate side-chains 203 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 160 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1523 VAL Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1724 SER Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 144 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 46 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 138 optimal weight: 40.0000 chunk 114 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 72 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 956 ASN A1505 GLN A1709 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.2483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11982 Z= 0.191 Angle : 0.590 9.745 16236 Z= 0.298 Chirality : 0.041 0.271 1892 Planarity : 0.004 0.041 1981 Dihedral : 9.694 118.579 1781 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.62 % Allowed : 21.93 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: -0.05 (0.23), residues: 1421 helix: 0.74 (0.18), residues: 844 sheet: -0.92 (0.46), residues: 129 loop : -1.10 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1382 HIS 0.002 0.000 HIS A 766 PHE 0.013 0.001 PHE A 963 TYR 0.023 0.001 TYR A1548 ARG 0.002 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 168 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.7889 (mtpt) cc_final: 0.7214 (tppt) REVERT: A 364 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7160 (pm20) REVERT: A 742 MET cc_start: 0.6008 (ttm) cc_final: 0.5561 (ttm) REVERT: A 794 LYS cc_start: 0.6483 (OUTLIER) cc_final: 0.5346 (mmtp) REVERT: A 796 ILE cc_start: 0.7329 (pp) cc_final: 0.7038 (pt) REVERT: A 837 PHE cc_start: 0.7534 (m-10) cc_final: 0.7121 (m-10) REVERT: A 861 ASN cc_start: 0.6209 (m-40) cc_final: 0.5565 (m-40) REVERT: A 1230 ASP cc_start: 0.7838 (t0) cc_final: 0.7358 (m-30) REVERT: A 1251 LYS cc_start: 0.7843 (tttt) cc_final: 0.7482 (mptt) REVERT: A 1276 ASN cc_start: 0.7850 (t0) cc_final: 0.7478 (m-40) REVERT: A 1470 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.6756 (mp10) REVERT: A 1519 ILE cc_start: 0.8498 (pt) cc_final: 0.8272 (tp) REVERT: A 1556 ILE cc_start: 0.7849 (tp) cc_final: 0.7617 (tp) REVERT: A 1720 VAL cc_start: 0.7974 (OUTLIER) cc_final: 0.7761 (t) REVERT: C 79 MET cc_start: 0.0094 (ppp) cc_final: -0.2094 (mmm) outliers start: 59 outliers final: 47 residues processed: 210 average time/residue: 0.2243 time to fit residues: 70.2484 Evaluate side-chains 213 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 162 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 769 THR Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1505 GLN Chi-restraints excluded: chain A residue 1523 VAL Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 43 CYS Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 78 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 166 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 133 optimal weight: 9.9990 chunk 15 optimal weight: 3.9990 chunk 78 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 116 optimal weight: 0.0770 chunk 77 optimal weight: 0.9990 chunk 137 optimal weight: 0.0040 chunk 86 optimal weight: 20.0000 chunk 84 optimal weight: 0.0870 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 2.9990 overall best weight: 0.4328 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 765 HIS A 911 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7016 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11982 Z= 0.149 Angle : 0.573 12.055 16236 Z= 0.288 Chirality : 0.040 0.246 1892 Planarity : 0.004 0.042 1981 Dihedral : 9.519 117.675 1781 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.68 % Allowed : 23.26 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.07 (0.23), residues: 1421 helix: 0.85 (0.18), residues: 848 sheet: -0.97 (0.46), residues: 132 loop : -1.09 (0.31), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1382 HIS 0.002 0.000 HIS C 139 PHE 0.024 0.001 PHE A 183 TYR 0.023 0.001 TYR A1548 ARG 0.002 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 176 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 LYS cc_start: 0.7843 (mtpt) cc_final: 0.7116 (tppt) REVERT: A 354 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7744 (tt) REVERT: A 364 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7666 (pm20) REVERT: A 742 MET cc_start: 0.6050 (ttm) cc_final: 0.5838 (ttm) REVERT: A 794 LYS cc_start: 0.6241 (OUTLIER) cc_final: 0.5587 (mmtp) REVERT: A 796 ILE cc_start: 0.7331 (pp) cc_final: 0.7045 (pt) REVERT: A 837 PHE cc_start: 0.7509 (m-10) cc_final: 0.7066 (m-10) REVERT: A 861 ASN cc_start: 0.6204 (m-40) cc_final: 0.5575 (m-40) REVERT: A 1230 ASP cc_start: 0.7739 (t0) cc_final: 0.7307 (m-30) REVERT: A 1251 LYS cc_start: 0.7769 (tttt) cc_final: 0.7447 (mptt) REVERT: A 1276 ASN cc_start: 0.7852 (t0) cc_final: 0.7523 (m-40) REVERT: A 1470 GLN cc_start: 0.7715 (OUTLIER) cc_final: 0.6757 (mp10) REVERT: A 1519 ILE cc_start: 0.8494 (pt) cc_final: 0.8269 (tp) REVERT: A 1556 ILE cc_start: 0.7880 (tp) cc_final: 0.7637 (tp) REVERT: A 1691 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7895 (mp) REVERT: A 1720 VAL cc_start: 0.7970 (OUTLIER) cc_final: 0.7761 (t) REVERT: C 79 MET cc_start: 0.0123 (ppp) cc_final: -0.1939 (mmm) REVERT: C 130 MET cc_start: 0.0756 (ppp) cc_final: 0.0342 (pmm) outliers start: 47 outliers final: 33 residues processed: 212 average time/residue: 0.2184 time to fit residues: 68.8969 Evaluate side-chains 204 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 165 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1380 VAL Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 166 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 55 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 27 optimal weight: 0.0060 chunk 26 optimal weight: 0.8980 chunk 87 optimal weight: 8.9990 chunk 93 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 125 optimal weight: 0.9980 overall best weight: 0.7596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 410 GLN A 765 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11982 Z= 0.166 Angle : 0.583 11.070 16236 Z= 0.292 Chirality : 0.040 0.250 1892 Planarity : 0.004 0.041 1981 Dihedral : 9.404 116.420 1780 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.92 % Allowed : 23.02 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.11 (0.23), residues: 1421 helix: 0.91 (0.18), residues: 848 sheet: -0.94 (0.44), residues: 138 loop : -1.12 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A1382 HIS 0.002 0.000 HIS C 139 PHE 0.013 0.001 PHE A 963 TYR 0.023 0.001 TYR A1548 ARG 0.002 0.000 ARG B 85 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 167 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.6504 (tt) cc_final: 0.6057 (mt) REVERT: A 153 LYS cc_start: 0.8924 (mmtp) cc_final: 0.8297 (ttpp) REVERT: A 243 LYS cc_start: 0.7786 (mtpt) cc_final: 0.7124 (tppt) REVERT: A 364 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7555 (pm20) REVERT: A 742 MET cc_start: 0.6030 (ttm) cc_final: 0.5809 (ttm) REVERT: A 794 LYS cc_start: 0.6541 (OUTLIER) cc_final: 0.5636 (mmtp) REVERT: A 796 ILE cc_start: 0.7409 (pp) cc_final: 0.7146 (pt) REVERT: A 841 ARG cc_start: 0.7159 (mmm-85) cc_final: 0.6789 (mmm-85) REVERT: A 861 ASN cc_start: 0.6271 (m-40) cc_final: 0.5662 (m-40) REVERT: A 1230 ASP cc_start: 0.7696 (t0) cc_final: 0.7311 (m-30) REVERT: A 1251 LYS cc_start: 0.7794 (tttt) cc_final: 0.7475 (mptt) REVERT: A 1276 ASN cc_start: 0.7848 (t0) cc_final: 0.7467 (m-40) REVERT: A 1470 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.6766 (mp10) REVERT: A 1519 ILE cc_start: 0.8496 (pt) cc_final: 0.8280 (tp) REVERT: A 1556 ILE cc_start: 0.7885 (tp) cc_final: 0.7618 (tp) REVERT: A 1691 LEU cc_start: 0.8126 (OUTLIER) cc_final: 0.7911 (mp) REVERT: A 1720 VAL cc_start: 0.7991 (OUTLIER) cc_final: 0.7766 (t) REVERT: C 79 MET cc_start: 0.0114 (ppp) cc_final: -0.1981 (mmm) outliers start: 50 outliers final: 43 residues processed: 204 average time/residue: 0.2218 time to fit residues: 66.4861 Evaluate side-chains 213 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 165 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 945 LEU Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 961 ASN Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1221 THR Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 34 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 166 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 132 optimal weight: 3.9990 chunk 120 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 116 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 127 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11982 Z= 0.244 Angle : 0.611 10.935 16236 Z= 0.306 Chirality : 0.041 0.283 1892 Planarity : 0.004 0.041 1981 Dihedral : 9.434 115.213 1779 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.21 % Favored : 94.72 % Rotamer: Outliers : 3.60 % Allowed : 23.57 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.00 (0.23), residues: 1421 helix: 0.81 (0.18), residues: 849 sheet: -0.96 (0.44), residues: 138 loop : -1.14 (0.31), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A1382 HIS 0.002 0.000 HIS A 766 PHE 0.028 0.001 PHE A 183 TYR 0.023 0.001 TYR A1548 ARG 0.003 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 166 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.6592 (OUTLIER) cc_final: 0.6127 (mt) REVERT: A 153 LYS cc_start: 0.8929 (mmtp) cc_final: 0.8318 (ttpp) REVERT: A 243 LYS cc_start: 0.7768 (mtpt) cc_final: 0.7149 (tppt) REVERT: A 279 SER cc_start: 0.8427 (t) cc_final: 0.8050 (p) REVERT: A 364 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7948 (pm20) REVERT: A 742 MET cc_start: 0.5952 (ttm) cc_final: 0.5715 (ttm) REVERT: A 794 LYS cc_start: 0.6278 (OUTLIER) cc_final: 0.5662 (mmtp) REVERT: A 796 ILE cc_start: 0.7436 (pp) cc_final: 0.7107 (pt) REVERT: A 837 PHE cc_start: 0.7358 (m-10) cc_final: 0.6999 (m-10) REVERT: A 841 ARG cc_start: 0.7238 (mmm-85) cc_final: 0.6937 (mmm-85) REVERT: A 861 ASN cc_start: 0.6232 (m-40) cc_final: 0.5578 (m-40) REVERT: A 1230 ASP cc_start: 0.7777 (t0) cc_final: 0.7320 (m-30) REVERT: A 1251 LYS cc_start: 0.7803 (tttt) cc_final: 0.7480 (mptt) REVERT: A 1276 ASN cc_start: 0.7887 (t0) cc_final: 0.7481 (m-40) REVERT: A 1470 GLN cc_start: 0.7762 (OUTLIER) cc_final: 0.6771 (mp10) REVERT: A 1556 ILE cc_start: 0.7878 (tp) cc_final: 0.7624 (tp) REVERT: A 1668 TYR cc_start: 0.7904 (m-80) cc_final: 0.7584 (m-80) REVERT: A 1691 LEU cc_start: 0.8178 (OUTLIER) cc_final: 0.7946 (mp) REVERT: A 1754 MET cc_start: 0.8125 (mtt) cc_final: 0.7887 (mtt) REVERT: C 79 MET cc_start: 0.0141 (ppp) cc_final: -0.1985 (mmm) REVERT: C 130 MET cc_start: 0.0668 (ppp) cc_final: 0.0244 (pmm) outliers start: 46 outliers final: 36 residues processed: 202 average time/residue: 0.2585 time to fit residues: 75.8586 Evaluate side-chains 204 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 163 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 794 LYS Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 144 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 135 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 131 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 69 optimal weight: 1.9990 chunk 90 optimal weight: 0.0980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 765 HIS ** B 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11982 Z= 0.195 Angle : 0.605 10.676 16236 Z= 0.301 Chirality : 0.041 0.263 1892 Planarity : 0.004 0.041 1981 Dihedral : 9.348 114.821 1779 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.79 % Rotamer: Outliers : 3.37 % Allowed : 23.73 % Favored : 72.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.11 (0.23), residues: 1421 helix: 0.90 (0.18), residues: 848 sheet: -0.92 (0.44), residues: 138 loop : -1.11 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1382 HIS 0.002 0.000 HIS A 766 PHE 0.021 0.001 PHE A1233 TYR 0.024 0.001 TYR A1548 ARG 0.006 0.000 ARG A 838 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 171 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 LEU cc_start: 0.6503 (tt) cc_final: 0.6062 (mt) REVERT: A 153 LYS cc_start: 0.8909 (mmtp) cc_final: 0.8320 (ttpp) REVERT: A 243 LYS cc_start: 0.7773 (mtpt) cc_final: 0.7155 (tppt) REVERT: A 279 SER cc_start: 0.8369 (t) cc_final: 0.8004 (p) REVERT: A 364 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7966 (pm20) REVERT: A 796 ILE cc_start: 0.7473 (pp) cc_final: 0.7209 (pt) REVERT: A 837 PHE cc_start: 0.7334 (m-10) cc_final: 0.7078 (m-10) REVERT: A 841 ARG cc_start: 0.7261 (mmm-85) cc_final: 0.6888 (mmm-85) REVERT: A 861 ASN cc_start: 0.6297 (m-40) cc_final: 0.5688 (m-40) REVERT: A 1230 ASP cc_start: 0.7760 (t0) cc_final: 0.7342 (m-30) REVERT: A 1251 LYS cc_start: 0.7748 (tttt) cc_final: 0.7446 (mptt) REVERT: A 1276 ASN cc_start: 0.7865 (t0) cc_final: 0.7484 (m-40) REVERT: A 1470 GLN cc_start: 0.7744 (OUTLIER) cc_final: 0.6755 (mp10) REVERT: A 1556 ILE cc_start: 0.7857 (tp) cc_final: 0.7603 (tp) REVERT: A 1668 TYR cc_start: 0.7792 (m-80) cc_final: 0.7478 (m-80) REVERT: A 1691 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7938 (mp) REVERT: A 1754 MET cc_start: 0.8155 (mtt) cc_final: 0.7920 (mtt) REVERT: B 159 SER cc_start: 0.8741 (t) cc_final: 0.8329 (m) REVERT: C 79 MET cc_start: 0.0124 (ppp) cc_final: -0.2018 (mmm) REVERT: C 130 MET cc_start: 0.0691 (ppp) cc_final: 0.0249 (pmm) outliers start: 43 outliers final: 37 residues processed: 204 average time/residue: 0.2366 time to fit residues: 70.9208 Evaluate side-chains 207 residues out of total 1288 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 167 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 285 THR Chi-restraints excluded: chain A residue 299 PHE Chi-restraints excluded: chain A residue 315 CYS Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 362 TYR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 781 LEU Chi-restraints excluded: chain A residue 844 LYS Chi-restraints excluded: chain A residue 870 THR Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 935 CYS Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 950 MET Chi-restraints excluded: chain A residue 959 VAL Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1318 ILE Chi-restraints excluded: chain A residue 1324 VAL Chi-restraints excluded: chain A residue 1362 SER Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1470 GLN Chi-restraints excluded: chain A residue 1497 ILE Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1683 THR Chi-restraints excluded: chain A residue 1691 LEU Chi-restraints excluded: chain A residue 1726 VAL Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 166 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 143 random chunks: chunk 120 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 116 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 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 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.179937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.138730 restraints weight = 14701.865| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 3.08 r_work: 0.3323 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3330 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3330 r_free = 0.3330 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3330 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 11982 Z= 0.225 Angle : 0.871 57.291 16236 Z= 0.547 Chirality : 0.041 0.376 1892 Planarity : 0.004 0.084 1981 Dihedral : 9.329 114.756 1779 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.79 % Rotamer: Outliers : 3.05 % Allowed : 23.96 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.07 % 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: 0.12 (0.23), residues: 1421 helix: 0.91 (0.18), residues: 848 sheet: -0.92 (0.44), residues: 138 loop : -1.11 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1382 HIS 0.117 0.005 HIS A 765 PHE 0.029 0.001 PHE A 745 TYR 0.022 0.001 TYR A1548 ARG 0.006 0.000 ARG A 838 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2718.31 seconds wall clock time: 49 minutes 58.98 seconds (2998.98 seconds total)