Starting phenix.real_space_refine on Thu Feb 15 14:52:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmg_33296/02_2024/7xmg_33296_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmg_33296/02_2024/7xmg_33296.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmg_33296/02_2024/7xmg_33296.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmg_33296/02_2024/7xmg_33296.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmg_33296/02_2024/7xmg_33296_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xmg_33296/02_2024/7xmg_33296_updated.pdb" } resolution = 3.09 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= 0.005 sd= 0.094 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 7679 2.51 5 N 1847 2.21 5 O 2067 1.98 5 F 3 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 ASP 186": "OD1" <-> "OD2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 214": "NH1" <-> "NH2" 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 GLU 307": "OE1" <-> "OE2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 414": "OE1" <-> "OE2" Residue "A ASP 747": "OD1" <-> "OD2" Residue "A PHE 760": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 764": "OE1" <-> "OE2" Residue "A GLU 771": "OE1" <-> "OE2" Residue "A GLU 802": "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 ASP 902": "OD1" <-> "OD2" Residue "A ARG 922": "NH1" <-> "NH2" Residue "A ASP 934": "OD1" <-> "OD2" Residue "A PHE 963": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1182": "NH1" <-> "NH2" Residue "A PHE 1194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1195": "OE1" <-> "OE2" Residue "A GLU 1212": "OE1" <-> "OE2" Residue "A ARG 1218": "NH1" <-> "NH2" Residue "A ASP 1230": "OD1" <-> "OD2" Residue "A PHE 1254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1293": "NH1" <-> "NH2" Residue "A ARG 1308": "NH1" <-> "NH2" Residue "A PHE 1359": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1369": "OE1" <-> "OE2" Residue "A PHE 1443": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1476": "OE1" <-> "OE2" Residue "A TYR 1482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1499": "NH1" <-> "NH2" Residue "A GLU 1535": "OE1" <-> "OE2" Residue "A GLU 1537": "OE1" <-> "OE2" Residue "A GLU 1561": "OE1" <-> "OE2" Residue "A ASP 1582": "OD1" <-> "OD2" Residue "A PHE 1603": "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 ASP 1673": "OD1" <-> "OD2" Residue "A PHE 1679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1681": "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 GLU 1761": "OE1" <-> "OE2" Residue "B GLU 27": "OE1" <-> "OE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B GLU 65": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B GLU 81": "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 PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 148": "OD1" <-> "OD2" Residue "B ARG 152": "NH1" <-> "NH2" Residue "B TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 120": "OE1" <-> "OE2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "F ARG 135": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11692 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 9175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1138, 9175 Classifications: {'peptide': 1138} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 29, 'TRANS': 1106} Chain breaks: 3 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: "F" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 938 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'TYR:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 30 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: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 51 Unusual residues: {'G4I': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 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: 5.95, per 1000 atoms: 0.51 Number of scatterers: 11692 At special positions: 0 Unit cell: (128.96, 138.32, 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 3 9.00 O 2067 8.00 N 1847 7.00 C 7679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 315 " - pdb=" SG CYS A 330 " distance=2.05 Simple disulfide: pdb=" SG CYS A 895 " - pdb=" SG CYS F 55 " distance=2.27 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=2.03 Simple disulfide: pdb=" SG CYS A1715 " - pdb=" SG CYS A1730 " distance=2.70 Simple disulfide: pdb=" SG CYS B 40 " - pdb=" SG CYS B 121 " distance=2.03 Simple disulfide: pdb=" SG CYS F 50 " - pdb=" SG CYS F 127 " distance=2.57 Simple disulfide: pdb=" SG CYS F 72 " - pdb=" SG CYS F 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 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: 4.96 Conformation dependent library (CDL) restraints added in 2.2 seconds 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2710 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 53 helices and 7 sheets defined 60.7% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.87 Creating SS restraints... Processing helix chain 'A' and resid 115 through 123 Processing helix chain 'A' and resid 126 through 144 removed outlier: 4.067A pdb=" N THR A 144 " --> pdb=" O CYS A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 174 removed outlier: 3.782A pdb=" N LYS A 153 " --> pdb=" O ASP A 150 " (cutoff:3.500A) removed outlier: 4.354A 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 187 through 203 removed outlier: 3.991A pdb=" N LEU A 191 " --> pdb=" O TRP A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 227 removed outlier: 4.706A pdb=" N PHE A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ARG A 217 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 4.864A pdb=" N VAL A 218 " --> pdb=" O ARG A 214 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N LEU A 219 " --> pdb=" O THR A 215 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ARG A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N ALA A 221 " --> pdb=" O ARG A 217 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N THR A 224 " --> pdb=" O ARG A 220 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 226 " --> pdb=" O LEU A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 267 removed outlier: 3.604A pdb=" N LYS A 243 " --> pdb=" O ILE A 239 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N LYS A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N ASP A 247 " --> pdb=" O LYS A 243 " (cutoff:3.500A) removed outlier: 4.461A 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 302 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 413 removed outlier: 3.879A pdb=" N ILE A 380 " --> pdb=" O THR A 377 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE A 387 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU A 388 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLY A 389 " --> pdb=" O ILE A 386 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER A 390 " --> pdb=" O PHE A 387 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 391 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N TYR A 392 " --> pdb=" O GLY A 389 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASN A 395 " --> pdb=" O TYR A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 743 through 761 removed outlier: 3.693A pdb=" N ASP A 747 " --> pdb=" O ASP A 743 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N LEU A 748 " --> pdb=" O PRO A 744 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 797 Processing helix chain 'A' and resid 800 through 804 Processing helix chain 'A' and resid 807 through 822 removed outlier: 4.276A pdb=" N GLU A 822 " --> pdb=" O LEU A 818 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 847 removed outlier: 3.601A pdb=" N LYS A 847 " --> pdb=" O LYS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 863 removed outlier: 3.786A pdb=" N VAL A 863 " --> pdb=" O ILE A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 898 removed outlier: 5.514A pdb=" N LYS A 890 " --> pdb=" O GLN A 886 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N SER A 891 " --> pdb=" O LEU A 887 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N CYS A 897 " --> pdb=" O LYS A 893 " (cutoff:3.500A) removed outlier: 7.781A 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: 4.004A pdb=" N ASP A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 956 Processing helix chain 'A' and resid 959 through 972 removed outlier: 4.001A pdb=" N LEU A 964 " --> pdb=" O LEU A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1192 through 1209 removed outlier: 4.203A 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: 3.748A 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: 3.555A pdb=" N THR A1291 " --> pdb=" O LYS A1287 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU A1292 " --> pdb=" O SER A1288 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG A1293 " --> pdb=" O LEU A1289 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ALA A1294 " --> pdb=" O ARG A1290 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LEU A1295 " --> pdb=" O THR A1291 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG A1296 " --> pdb=" O LEU A1292 " (cutoff:3.500A) Proline residue: A1297 - end of helix removed outlier: 4.957A pdb=" N ALA A1300 " --> pdb=" O ARG A1296 " (cutoff:3.500A) Processing helix chain 'A' and resid 1305 through 1343 removed outlier: 3.624A 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 removed outlier: 3.668A pdb=" N ALA A1372 " --> pdb=" O SER A1368 " (cutoff:3.500A) Processing helix chain 'A' and resid 1392 through 1404 Processing helix chain 'A' and resid 1408 through 1417 Processing helix chain 'A' and resid 1433 through 1444 Processing helix chain 'A' and resid 1446 through 1466 Processing helix chain 'A' and resid 1476 through 1488 removed outlier: 4.266A pdb=" N LEU A1488 " --> pdb=" O ALA A1484 " (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: 4.401A pdb=" N ALA A1615 " --> pdb=" O VAL A1611 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N ARG A1616 " --> pdb=" O ILE A1612 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE A1617 " --> pdb=" O ARG A1613 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY A1618 " --> pdb=" O LEU A1614 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N ARG A1619 " --> pdb=" O ALA A1615 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE A1620 " --> pdb=" O ARG A1616 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU A1623 " --> pdb=" O ARG A1619 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N VAL A1624 " --> pdb=" O ILE A1620 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N LYS A1625 " --> pdb=" O LEU A1621 " (cutoff:3.500A) Processing helix chain 'A' and resid 1628 through 1665 removed outlier: 4.561A 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 1695 Processing helix chain 'A' and resid 1700 through 1707 Proline residue: A1706 - end of helix Processing helix chain 'A' and resid 1733 through 1767 Processing helix chain 'B' and resid 154 through 191 removed outlier: 3.656A pdb=" N THR B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 95 No H-bonds generated for 'chain 'F' and resid 93 through 95' Processing helix chain 'F' and resid 105 through 107 No H-bonds generated for 'chain 'F' and resid 105 through 107' Processing helix chain 'F' and resid 119 through 121 No H-bonds generated for 'chain 'F' 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 135 through 144 removed outlier: 3.811A pdb=" N PHE B 54 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 71 " --> pdb=" O TRP B 57 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N PHE B 59 " --> pdb=" O LYS B 69 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LYS B 69 " --> pdb=" O PHE B 59 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLN B 79 " --> pdb=" O ARG B 72 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'F' and resid 31 through 34 removed outlier: 4.127A pdb=" N GLU F 31 " --> pdb=" O ASN F 53 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 37 through 40 removed outlier: 7.686A pdb=" N LEU F 38 " --> pdb=" O LYS F 141 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N HIS F 143 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL F 40 " --> pdb=" O HIS F 143 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLN F 145 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU F 81 " --> pdb=" O TRP F 67 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N TYR F 69 " --> pdb=" O MET F 79 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N MET F 79 " --> pdb=" O TYR F 69 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 46 through 48 662 hydrogen bonds defined for protein. 1767 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: 3.72 Time building geometry restraints manager: 5.31 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: 3547 1.35 - 1.51: 3991 1.51 - 1.68: 4273 1.68 - 1.84: 152 1.84 - 2.01: 2 Bond restraints: 11965 Sorted by residual: bond pdb=" C21 G4I A2302 " pdb=" N10 G4I A2302 " ideal model delta sigma weight residual 1.279 1.467 -0.188 2.00e-02 2.50e+03 8.84e+01 bond pdb=" C36 G4I A2302 " pdb=" N12 G4I A2302 " ideal model delta sigma weight residual 1.264 1.440 -0.176 2.00e-02 2.50e+03 7.73e+01 bond pdb=" C36 G4I A2302 " pdb=" O06 G4I A2302 " ideal model delta sigma weight residual 1.340 1.184 0.156 2.00e-02 2.50e+03 6.12e+01 bond pdb=" C18 G4I A2302 " pdb=" N07 G4I A2302 " ideal model delta sigma weight residual 1.334 1.467 -0.133 2.00e-02 2.50e+03 4.45e+01 bond pdb=" CB CYS F 127 " pdb=" SG CYS F 127 " ideal model delta sigma weight residual 1.808 2.006 -0.198 3.30e-02 9.18e+02 3.60e+01 ... (remaining 11960 not shown) Histogram of bond angle deviations from ideal: 97.76 - 105.95: 207 105.95 - 114.14: 6995 114.14 - 122.33: 7660 122.33 - 130.51: 1304 130.51 - 138.70: 48 Bond angle restraints: 16214 Sorted by residual: angle pdb=" C ASN F 131 " pdb=" N PRO F 132 " pdb=" CA PRO F 132 " ideal model delta sigma weight residual 119.66 114.10 5.56 7.20e-01 1.93e+00 5.97e+01 angle pdb=" C MET F 85 " pdb=" CA MET F 85 " pdb=" CB MET F 85 " ideal model delta sigma weight residual 110.42 97.76 12.66 1.99e+00 2.53e-01 4.05e+01 angle pdb=" CA CYS F 127 " pdb=" CB CYS F 127 " pdb=" SG CYS F 127 " ideal model delta sigma weight residual 114.40 128.22 -13.82 2.30e+00 1.89e-01 3.61e+01 angle pdb=" O PRO F 132 " pdb=" C PRO F 132 " pdb=" N PRO F 133 " ideal model delta sigma weight residual 121.15 123.83 -2.68 4.70e-01 4.53e+00 3.24e+01 angle pdb=" N GLN F 62 " pdb=" CA GLN F 62 " pdb=" C GLN F 62 " ideal model delta sigma weight residual 111.36 116.94 -5.58 1.09e+00 8.42e-01 2.62e+01 ... (remaining 16209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.60: 6608 24.60 - 49.21: 485 49.21 - 73.81: 61 73.81 - 98.42: 17 98.42 - 123.02: 3 Dihedral angle restraints: 7174 sinusoidal: 2980 harmonic: 4194 Sorted by residual: dihedral pdb=" CB CYS A 895 " pdb=" SG CYS A 895 " pdb=" SG CYS F 55 " pdb=" CB CYS F 55 " ideal model delta sinusoidal sigma weight residual -86.00 -2.24 -83.76 1 1.00e+01 1.00e-02 8.56e+01 dihedral pdb=" CB CYS A 315 " pdb=" SG CYS A 315 " pdb=" SG CYS A 330 " pdb=" CB CYS A 330 " ideal model delta sinusoidal sigma weight residual -86.00 -166.79 80.79 1 1.00e+01 1.00e-02 8.06e+01 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 -165.63 79.63 1 1.00e+01 1.00e-02 7.87e+01 ... (remaining 7171 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 1535 0.062 - 0.123: 308 0.123 - 0.185: 33 0.185 - 0.246: 7 0.246 - 0.308: 3 Chirality restraints: 1886 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 -2.09 -0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CA ASP A1673 " pdb=" N ASP A1673 " pdb=" C ASP A1673 " pdb=" CB ASP A1673 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CA PHE F 80 " pdb=" N PHE F 80 " pdb=" C PHE F 80 " pdb=" CB PHE F 80 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1883 not shown) Planarity restraints: 1985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 G4I A2302 " 0.246 2.00e-02 2.50e+03 2.16e-01 1.28e+03 pdb=" C17 G4I A2302 " -0.501 2.00e-02 2.50e+03 pdb=" C18 G4I A2302 " 0.096 2.00e-02 2.50e+03 pdb=" C21 G4I A2302 " -0.107 2.00e-02 2.50e+03 pdb=" C24 G4I A2302 " 0.153 2.00e-02 2.50e+03 pdb=" C27 G4I A2302 " 0.110 2.00e-02 2.50e+03 pdb=" N07 G4I A2302 " 0.146 2.00e-02 2.50e+03 pdb=" N08 G4I A2302 " -0.060 2.00e-02 2.50e+03 pdb=" N09 G4I A2302 " 0.201 2.00e-02 2.50e+03 pdb=" N10 G4I A2302 " -0.280 2.00e-02 2.50e+03 pdb=" N11 G4I A2302 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN F 104 " 0.061 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO F 105 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO F 105 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO F 105 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A1218 " 0.017 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ARG A1218 " -0.056 2.00e-02 2.50e+03 pdb=" O ARG A1218 " 0.021 2.00e-02 2.50e+03 pdb=" N LYS A1219 " 0.019 2.00e-02 2.50e+03 ... (remaining 1982 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 116 2.59 - 3.17: 10683 3.17 - 3.75: 18411 3.75 - 4.32: 25901 4.32 - 4.90: 41608 Nonbonded interactions: 96719 Sorted by model distance: nonbonded pdb=" O GLY A1444 " pdb=" OG1 THR A1448 " model vdw 2.017 2.440 nonbonded pdb=" O PHE A1738 " pdb=" OG SER A1742 " model vdw 2.101 2.440 nonbonded pdb=" O GLN F 62 " pdb=" CD PRO F 132 " model vdw 2.107 3.440 nonbonded pdb=" CE2 PHE F 101 " pdb=" O GLY F 103 " model vdw 2.108 3.340 nonbonded pdb=" O TRP A1332 " pdb=" OG SER A1336 " model vdw 2.137 2.440 ... (remaining 96714 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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 4.280 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 33.520 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 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 : 0.006 0.198 11965 Z= 0.397 Angle : 0.847 14.145 16214 Z= 0.474 Chirality : 0.050 0.308 1886 Planarity : 0.007 0.216 1978 Dihedral : 16.614 123.021 4437 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.33 % Favored : 92.39 % Rotamer: Outliers : 4.46 % Allowed : 19.47 % Favored : 76.08 % Cbeta Deviations : 0.07 % 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: -2.84 (0.19), residues: 1419 helix: -1.46 (0.15), residues: 865 sheet: -0.97 (0.49), residues: 126 loop : -2.76 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1382 HIS 0.004 0.001 HIS A 765 PHE 0.019 0.002 PHE F 80 TYR 0.022 0.002 TYR A1482 ARG 0.003 0.000 ARG F 115 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 264 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 291 ASN cc_start: 0.7443 (p0) cc_final: 0.7226 (p0) REVERT: A 294 GLU cc_start: 0.6392 (OUTLIER) cc_final: 0.5810 (tp30) REVERT: A 301 LYS cc_start: 0.7397 (mtmt) cc_final: 0.7135 (mmtt) REVERT: A 820 LEU cc_start: 0.7505 (OUTLIER) cc_final: 0.7249 (mm) REVERT: A 848 SER cc_start: 0.6508 (OUTLIER) cc_final: 0.6274 (p) REVERT: A 1201 MET cc_start: 0.7087 (tpp) cc_final: 0.6882 (tpp) REVERT: A 1309 VAL cc_start: 0.7554 (p) cc_final: 0.7343 (m) REVERT: A 1349 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6685 (pt0) REVERT: A 1435 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.7140 (pt) REVERT: A 1436 TYR cc_start: 0.7786 (t80) cc_final: 0.7484 (t80) REVERT: A 1465 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8081 (pptt) REVERT: A 1528 ASN cc_start: 0.7756 (t0) cc_final: 0.7454 (t0) REVERT: A 1532 MET cc_start: 0.8737 (mtt) cc_final: 0.8365 (mtt) REVERT: A 1537 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7305 (tm-30) REVERT: A 1541 GLN cc_start: 0.8372 (tp40) cc_final: 0.8091 (tp40) REVERT: A 1543 MET cc_start: 0.7112 (ttp) cc_final: 0.6714 (tpt) REVERT: A 1732 ASN cc_start: 0.7410 (t0) cc_final: 0.7095 (t0) REVERT: B 99 LYS cc_start: 0.7055 (tptm) cc_final: 0.6753 (tppt) REVERT: B 160 GLU cc_start: 0.7331 (tt0) cc_final: 0.7059 (tt0) REVERT: B 162 MET cc_start: 0.6182 (tpt) cc_final: 0.5888 (tpt) REVERT: B 166 LEU cc_start: 0.8293 (mt) cc_final: 0.8093 (mt) REVERT: B 182 TYR cc_start: 0.8083 (t80) cc_final: 0.7877 (t80) REVERT: F 85 MET cc_start: 0.2249 (mmm) cc_final: 0.1751 (mmm) outliers start: 57 outliers final: 31 residues processed: 309 average time/residue: 0.2219 time to fit residues: 99.0008 Evaluate side-chains 250 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 213 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 294 GLU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 413 ILE Chi-restraints excluded: chain A residue 765 HIS Chi-restraints excluded: chain A residue 817 THR Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 839 LEU Chi-restraints excluded: chain A residue 848 SER Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 876 ILE Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 929 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1243 LEU Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1302 SER Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1336 SER Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1545 GLU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1569 LEU Chi-restraints excluded: chain A residue 1589 SER Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain B residue 71 LEU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 109 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 59 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 chunk 111 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 128 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN A 240 GLN A 291 ASN A 365 ASN A 410 GLN A 941 GLN A 961 ASN A1276 ASN A1341 ASN A1502 ASN A1514 ASN ** A1528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1579 ASN ** A1665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1709 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 moved from start: 0.1367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11965 Z= 0.215 Angle : 0.679 14.312 16214 Z= 0.350 Chirality : 0.044 0.288 1886 Planarity : 0.005 0.056 1978 Dihedral : 9.339 107.721 1815 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.83 % Allowed : 23.38 % Favored : 72.79 % 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: -1.58 (0.21), residues: 1419 helix: -0.35 (0.17), residues: 849 sheet: -0.88 (0.48), residues: 120 loop : -2.29 (0.26), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 151 HIS 0.004 0.001 HIS B 134 PHE 0.017 0.001 PHE A 963 TYR 0.024 0.002 TYR A1739 ARG 0.007 0.000 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 237 time to evaluate : 1.370 Fit side-chains revert: symmetry clash REVERT: A 300 ARG cc_start: 0.7253 (ttm-80) cc_final: 0.6906 (mtt-85) REVERT: A 301 LYS cc_start: 0.7446 (mtmt) cc_final: 0.7162 (mmtt) REVERT: A 742 MET cc_start: 0.5405 (mmm) cc_final: 0.3547 (mtp) REVERT: A 798 MET cc_start: 0.4465 (ptm) cc_final: 0.4237 (ptp) REVERT: A 820 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7330 (mm) REVERT: A 1236 ILE cc_start: 0.8335 (mt) cc_final: 0.8034 (mp) REVERT: A 1305 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6614 (tt0) REVERT: A 1349 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.6485 (pm20) REVERT: A 1435 ILE cc_start: 0.7322 (OUTLIER) cc_final: 0.7045 (pt) REVERT: A 1436 TYR cc_start: 0.7742 (t80) cc_final: 0.7535 (t80) REVERT: A 1464 LYS cc_start: 0.7571 (tttm) cc_final: 0.7324 (ttmm) REVERT: A 1465 LYS cc_start: 0.8645 (mmmt) cc_final: 0.8096 (pptt) REVERT: A 1466 LYS cc_start: 0.8349 (mtpt) cc_final: 0.8061 (mtpt) REVERT: A 1541 GLN cc_start: 0.8380 (tp40) cc_final: 0.8130 (tp40) REVERT: A 1658 TYR cc_start: 0.8129 (m-80) cc_final: 0.7907 (m-80) REVERT: A 1732 ASN cc_start: 0.7395 (t0) cc_final: 0.7160 (t0) REVERT: B 69 LYS cc_start: 0.8104 (OUTLIER) cc_final: 0.7799 (ttpt) REVERT: B 99 LYS cc_start: 0.7033 (tptm) cc_final: 0.6718 (tppt) REVERT: B 160 GLU cc_start: 0.7363 (tt0) cc_final: 0.7058 (tt0) REVERT: B 162 MET cc_start: 0.6188 (tpt) cc_final: 0.5905 (tpt) REVERT: B 182 TYR cc_start: 0.7977 (t80) cc_final: 0.7475 (t80) outliers start: 49 outliers final: 25 residues processed: 276 average time/residue: 0.2289 time to fit residues: 90.6988 Evaluate side-chains 245 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 215 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 330 CYS Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 944 CYS Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1508 ILE Chi-restraints excluded: chain A residue 1524 LEU Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1564 LEU Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1664 SER Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 137 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 107 optimal weight: 0.0970 chunk 87 optimal weight: 0.5980 chunk 35 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 103 optimal weight: 0.0870 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 ASN A 189 ASN A 780 ASN ** A1528 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1579 ASN A1665 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 143 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11965 Z= 0.170 Angle : 0.619 13.490 16214 Z= 0.316 Chirality : 0.042 0.254 1886 Planarity : 0.004 0.041 1978 Dihedral : 8.046 97.024 1773 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 4.53 % Allowed : 23.38 % Favored : 72.09 % 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: -1.08 (0.21), residues: 1419 helix: 0.05 (0.17), residues: 853 sheet: -0.93 (0.46), residues: 120 loop : -2.02 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 151 HIS 0.004 0.001 HIS B 134 PHE 0.019 0.001 PHE A1197 TYR 0.024 0.001 TYR A1739 ARG 0.004 0.000 ARG F 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 222 time to evaluate : 1.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 ARG cc_start: 0.6424 (ttt-90) cc_final: 0.6167 (ttt90) REVERT: A 300 ARG cc_start: 0.7131 (ttm-80) cc_final: 0.6894 (mtt-85) REVERT: A 301 LYS cc_start: 0.7462 (mtmt) cc_final: 0.7062 (mmtt) REVERT: A 760 PHE cc_start: 0.7239 (t80) cc_final: 0.6954 (m-80) REVERT: A 927 GLU cc_start: 0.6457 (mt-10) cc_final: 0.6174 (mt-10) REVERT: A 961 ASN cc_start: 0.6325 (m110) cc_final: 0.6039 (m110) REVERT: A 1236 ILE cc_start: 0.8220 (mt) cc_final: 0.7954 (mp) REVERT: A 1287 LYS cc_start: 0.8355 (tppt) cc_final: 0.7717 (mtpt) REVERT: A 1305 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6446 (tt0) REVERT: A 1349 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.6378 (pt0) REVERT: A 1435 ILE cc_start: 0.7255 (OUTLIER) cc_final: 0.6971 (pt) REVERT: A 1464 LYS cc_start: 0.7480 (tttm) cc_final: 0.7249 (ttmm) REVERT: A 1465 LYS cc_start: 0.8605 (mmmt) cc_final: 0.8061 (pptt) REVERT: A 1466 LYS cc_start: 0.8308 (mtpt) cc_final: 0.8059 (mtpt) REVERT: A 1541 GLN cc_start: 0.8354 (tp40) cc_final: 0.8119 (tp40) REVERT: A 1658 TYR cc_start: 0.8091 (m-80) cc_final: 0.7860 (m-80) REVERT: A 1727 GLU cc_start: 0.7273 (OUTLIER) cc_final: 0.6722 (mt-10) REVERT: A 1741 VAL cc_start: 0.8462 (t) cc_final: 0.8210 (t) REVERT: B 69 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7690 (ttpt) REVERT: B 99 LYS cc_start: 0.7041 (tptm) cc_final: 0.6631 (tppt) REVERT: B 162 MET cc_start: 0.6205 (tpt) cc_final: 0.5939 (tpt) REVERT: B 182 TYR cc_start: 0.7902 (t80) cc_final: 0.7424 (t80) outliers start: 58 outliers final: 25 residues processed: 269 average time/residue: 0.2290 time to fit residues: 89.3195 Evaluate side-chains 243 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 213 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1368 SER Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1664 SER Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 86 optimal weight: 0.0070 chunk 129 optimal weight: 3.9990 chunk 137 optimal weight: 0.6980 chunk 122 optimal weight: 8.9990 chunk 36 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 1.5404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN ** A 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN A 911 ASN A1528 ASN A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6481 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11965 Z= 0.285 Angle : 0.658 13.779 16214 Z= 0.337 Chirality : 0.044 0.275 1886 Planarity : 0.004 0.039 1978 Dihedral : 7.468 79.744 1769 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.84 % Favored : 93.09 % Rotamer: Outliers : 5.32 % Allowed : 23.38 % Favored : 71.31 % 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 (0.22), residues: 1419 helix: 0.11 (0.17), residues: 846 sheet: -0.81 (0.47), residues: 117 loop : -1.99 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 151 HIS 0.004 0.001 HIS A 766 PHE 0.021 0.002 PHE A1740 TYR 0.022 0.002 TYR A1755 ARG 0.004 0.000 ARG A1290 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 217 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.8002 (mt) REVERT: A 300 ARG cc_start: 0.7394 (ttm-80) cc_final: 0.7084 (mtt-85) REVERT: A 301 LYS cc_start: 0.7510 (mtmt) cc_final: 0.7088 (mmtt) REVERT: A 742 MET cc_start: 0.4985 (mmm) cc_final: 0.3495 (mtp) REVERT: A 798 MET cc_start: 0.6085 (mtt) cc_final: 0.5706 (ptp) REVERT: A 820 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7009 (mm) REVERT: A 1251 LYS cc_start: 0.6316 (mtpt) cc_final: 0.6086 (mptt) REVERT: A 1287 LYS cc_start: 0.8401 (tppt) cc_final: 0.7700 (mtpt) REVERT: A 1305 GLU cc_start: 0.7132 (OUTLIER) cc_final: 0.6589 (tt0) REVERT: A 1349 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6486 (pm20) REVERT: A 1435 ILE cc_start: 0.7297 (OUTLIER) cc_final: 0.7006 (pt) REVERT: A 1464 LYS cc_start: 0.7520 (tttm) cc_final: 0.7273 (ttmm) REVERT: A 1465 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8038 (pptt) REVERT: A 1466 LYS cc_start: 0.8380 (mtpt) cc_final: 0.8112 (mtpt) REVERT: A 1470 GLN cc_start: 0.7316 (mm-40) cc_final: 0.7012 (mm110) REVERT: A 1541 GLN cc_start: 0.8344 (tp40) cc_final: 0.7811 (tp40) REVERT: A 1727 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6743 (mt-10) REVERT: B 69 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7742 (ttpt) REVERT: B 99 LYS cc_start: 0.7003 (tptm) cc_final: 0.6628 (tppt) REVERT: B 162 MET cc_start: 0.6205 (tpt) cc_final: 0.5961 (tpt) REVERT: B 182 TYR cc_start: 0.7903 (t80) cc_final: 0.7358 (t80) outliers start: 68 outliers final: 46 residues processed: 268 average time/residue: 0.2362 time to fit residues: 92.5189 Evaluate side-chains 261 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 208 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 963 PHE Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1292 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1368 SER Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1385 LEU Chi-restraints excluded: chain A residue 1390 ASP Chi-restraints excluded: chain A residue 1421 VAL Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1485 MET Chi-restraints excluded: chain A residue 1521 ILE Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1664 SER Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 106 ILE Chi-restraints excluded: chain B residue 137 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 117 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 70 optimal weight: 0.6980 chunk 123 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6437 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11965 Z= 0.186 Angle : 0.604 10.977 16214 Z= 0.311 Chirality : 0.042 0.289 1886 Planarity : 0.004 0.038 1978 Dihedral : 6.855 78.195 1769 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.64 % Favored : 94.29 % Rotamer: Outliers : 4.61 % Allowed : 24.78 % Favored : 70.60 % 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: 1419 helix: 0.31 (0.18), residues: 844 sheet: -0.63 (0.47), residues: 117 loop : -1.94 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 151 HIS 0.003 0.000 HIS B 134 PHE 0.014 0.001 PHE A1740 TYR 0.019 0.001 TYR A1739 ARG 0.004 0.000 ARG A1290 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 210 time to evaluate : 1.249 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.6659 (ttp) cc_final: 0.6407 (ttp) REVERT: A 222 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7736 (mt) REVERT: A 300 ARG cc_start: 0.7230 (ttm-80) cc_final: 0.6987 (mtt-85) REVERT: A 301 LYS cc_start: 0.7476 (mtmt) cc_final: 0.7100 (mmtt) REVERT: A 742 MET cc_start: 0.4813 (mmm) cc_final: 0.3416 (mtp) REVERT: A 760 PHE cc_start: 0.7182 (t80) cc_final: 0.6950 (m-80) REVERT: A 798 MET cc_start: 0.6226 (mtt) cc_final: 0.5791 (ptm) REVERT: A 820 LEU cc_start: 0.7317 (OUTLIER) cc_final: 0.7055 (mm) REVERT: A 822 GLU cc_start: 0.7235 (mm-30) cc_final: 0.7018 (mm-30) REVERT: A 1251 LYS cc_start: 0.6368 (mtpt) cc_final: 0.6134 (mptt) REVERT: A 1287 LYS cc_start: 0.8253 (tppt) cc_final: 0.7646 (mtpp) REVERT: A 1305 GLU cc_start: 0.7103 (OUTLIER) cc_final: 0.6538 (tt0) REVERT: A 1349 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6445 (pm20) REVERT: A 1435 ILE cc_start: 0.7197 (OUTLIER) cc_final: 0.6913 (pt) REVERT: A 1465 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8019 (pptt) REVERT: A 1466 LYS cc_start: 0.8346 (mtpt) cc_final: 0.8090 (mtpt) REVERT: A 1486 LYS cc_start: 0.7927 (ttpt) cc_final: 0.7685 (ttpt) REVERT: A 1541 GLN cc_start: 0.8281 (tp40) cc_final: 0.8076 (tp40) REVERT: A 1727 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6729 (mt-10) REVERT: B 69 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7673 (ttpt) REVERT: B 162 MET cc_start: 0.6173 (tpt) cc_final: 0.5925 (tpt) REVERT: B 182 TYR cc_start: 0.7790 (t80) cc_final: 0.7428 (t80) outliers start: 59 outliers final: 35 residues processed: 253 average time/residue: 0.2272 time to fit residues: 83.0275 Evaluate side-chains 247 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 205 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 859 ILE Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1238 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1351 ILE Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1421 VAL Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1485 MET Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1672 GLU Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 93 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 137 optimal weight: 0.2980 chunk 114 optimal weight: 4.9990 chunk 63 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 132 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.2484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11965 Z= 0.184 Angle : 0.588 10.297 16214 Z= 0.304 Chirality : 0.041 0.281 1886 Planarity : 0.004 0.038 1978 Dihedral : 6.571 78.378 1769 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 5.08 % Allowed : 25.10 % Favored : 69.82 % 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: -0.57 (0.22), residues: 1419 helix: 0.45 (0.18), residues: 842 sheet: -0.58 (0.47), residues: 120 loop : -1.81 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 151 HIS 0.002 0.001 HIS A 766 PHE 0.014 0.001 PHE A1740 TYR 0.020 0.001 TYR A1348 ARG 0.002 0.000 ARG A1367 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 214 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.6641 (ttp) cc_final: 0.6392 (ttp) REVERT: A 300 ARG cc_start: 0.7355 (ttm-80) cc_final: 0.7130 (mtt-85) REVERT: A 301 LYS cc_start: 0.7455 (mtmt) cc_final: 0.7141 (mmtt) REVERT: A 742 MET cc_start: 0.4730 (mmm) cc_final: 0.3532 (mtp) REVERT: A 760 PHE cc_start: 0.7130 (t80) cc_final: 0.6885 (m-80) REVERT: A 798 MET cc_start: 0.6260 (mtt) cc_final: 0.5802 (ptm) REVERT: A 820 LEU cc_start: 0.7405 (OUTLIER) cc_final: 0.7133 (mm) REVERT: A 822 GLU cc_start: 0.7272 (mm-30) cc_final: 0.7044 (mm-30) REVERT: A 1251 LYS cc_start: 0.6433 (mtpt) cc_final: 0.6178 (mptt) REVERT: A 1287 LYS cc_start: 0.8204 (tppt) cc_final: 0.7669 (mtpp) REVERT: A 1290 ARG cc_start: 0.8532 (ttm-80) cc_final: 0.8329 (ttm-80) REVERT: A 1305 GLU cc_start: 0.7148 (OUTLIER) cc_final: 0.6578 (tt0) REVERT: A 1349 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.6459 (pt0) REVERT: A 1435 ILE cc_start: 0.7224 (OUTLIER) cc_final: 0.6932 (pt) REVERT: A 1486 LYS cc_start: 0.7961 (ttpt) cc_final: 0.7691 (ttpt) REVERT: A 1540 SER cc_start: 0.7311 (t) cc_final: 0.7107 (m) REVERT: A 1541 GLN cc_start: 0.8274 (tp40) cc_final: 0.7877 (tp40) REVERT: A 1727 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.6719 (mt-10) REVERT: B 28 THR cc_start: 0.8328 (p) cc_final: 0.8090 (t) REVERT: B 69 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7539 (ttpt) REVERT: B 162 MET cc_start: 0.6206 (tpt) cc_final: 0.5969 (tpt) REVERT: B 182 TYR cc_start: 0.7814 (t80) cc_final: 0.7474 (t80) REVERT: F 79 MET cc_start: -0.0219 (tmm) cc_final: -0.0639 (ptp) outliers start: 65 outliers final: 36 residues processed: 263 average time/residue: 0.2329 time to fit residues: 88.8526 Evaluate side-chains 249 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 207 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 247 ASP Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 1192 SER 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 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1368 SER Chi-restraints excluded: chain A residue 1376 VAL Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1421 VAL Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1485 MET Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 137 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.8980 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 136 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 84 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6436 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 : 0.003 0.031 11965 Z= 0.188 Angle : 0.595 11.016 16214 Z= 0.303 Chirality : 0.042 0.288 1886 Planarity : 0.004 0.037 1978 Dihedral : 6.292 78.083 1765 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 4.30 % Allowed : 25.88 % Favored : 69.82 % 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: -0.48 (0.22), residues: 1419 helix: 0.49 (0.18), residues: 844 sheet: -0.46 (0.47), residues: 120 loop : -1.72 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 151 HIS 0.002 0.000 HIS B 134 PHE 0.018 0.001 PHE A 165 TYR 0.018 0.001 TYR A1348 ARG 0.005 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 216 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: A 130 MET cc_start: 0.6643 (ttp) cc_final: 0.6425 (ttp) REVERT: A 141 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8191 (mt) REVERT: A 164 THR cc_start: 0.8739 (OUTLIER) cc_final: 0.8376 (p) REVERT: A 300 ARG cc_start: 0.7428 (ttm-80) cc_final: 0.7210 (mtt-85) REVERT: A 301 LYS cc_start: 0.7392 (mtmt) cc_final: 0.7115 (mmtt) REVERT: A 742 MET cc_start: 0.4817 (mmm) cc_final: 0.3708 (mtp) REVERT: A 760 PHE cc_start: 0.7066 (t80) cc_final: 0.6848 (m-80) REVERT: A 798 MET cc_start: 0.6186 (mtt) cc_final: 0.5984 (mtp) REVERT: A 820 LEU cc_start: 0.7348 (OUTLIER) cc_final: 0.7086 (mm) REVERT: A 822 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7097 (mm-30) REVERT: A 1251 LYS cc_start: 0.6458 (mtpt) cc_final: 0.6159 (mptt) REVERT: A 1287 LYS cc_start: 0.8131 (tppt) cc_final: 0.7638 (mttp) REVERT: A 1290 ARG cc_start: 0.8525 (ttm-80) cc_final: 0.8310 (ttm-80) REVERT: A 1305 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6547 (tt0) REVERT: A 1349 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.6518 (pt0) REVERT: A 1435 ILE cc_start: 0.7249 (OUTLIER) cc_final: 0.6956 (pt) REVERT: A 1486 LYS cc_start: 0.7962 (ttpt) cc_final: 0.7707 (ttpt) REVERT: A 1540 SER cc_start: 0.7442 (t) cc_final: 0.7210 (m) REVERT: A 1541 GLN cc_start: 0.8273 (tp40) cc_final: 0.7873 (tp40) REVERT: A 1727 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6716 (mt-10) REVERT: B 28 THR cc_start: 0.8340 (p) cc_final: 0.8130 (t) REVERT: B 69 LYS cc_start: 0.8062 (OUTLIER) cc_final: 0.7506 (ttpt) REVERT: B 162 MET cc_start: 0.6276 (tpt) cc_final: 0.6027 (tpt) REVERT: B 182 TYR cc_start: 0.7764 (t80) cc_final: 0.7426 (t80) outliers start: 55 outliers final: 38 residues processed: 256 average time/residue: 0.2220 time to fit residues: 82.6985 Evaluate side-chains 253 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 207 time to evaluate : 1.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 ILE Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 764 GLU Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1368 SER Chi-restraints excluded: chain A residue 1388 ASN Chi-restraints excluded: chain A residue 1421 VAL Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1485 MET Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 69 LYS Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 137 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 131 optimal weight: 30.0000 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6474 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11965 Z= 0.244 Angle : 0.618 9.383 16214 Z= 0.319 Chirality : 0.043 0.287 1886 Planarity : 0.004 0.038 1978 Dihedral : 6.319 78.344 1765 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 4.77 % Allowed : 25.96 % Favored : 69.27 % 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: -0.55 (0.22), residues: 1419 helix: 0.41 (0.18), residues: 845 sheet: -0.42 (0.47), residues: 120 loop : -1.74 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 151 HIS 0.003 0.001 HIS A 766 PHE 0.017 0.001 PHE A1740 TYR 0.020 0.002 TYR A1348 ARG 0.003 0.000 ARG A 214 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 214 time to evaluate : 1.233 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.6655 (ttp) cc_final: 0.6447 (ttp) REVERT: A 164 THR cc_start: 0.8736 (OUTLIER) cc_final: 0.8373 (p) REVERT: A 243 LYS cc_start: 0.7595 (mtpt) cc_final: 0.7380 (mtpp) REVERT: A 300 ARG cc_start: 0.7422 (ttm-80) cc_final: 0.7206 (mtt-85) REVERT: A 301 LYS cc_start: 0.7425 (mtmt) cc_final: 0.7137 (mmtt) REVERT: A 742 MET cc_start: 0.4966 (mmm) cc_final: 0.3830 (mtp) REVERT: A 820 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.6967 (mm) REVERT: A 822 GLU cc_start: 0.7357 (mm-30) cc_final: 0.7105 (mm-30) REVERT: A 1251 LYS cc_start: 0.6485 (mtpt) cc_final: 0.6176 (mptt) REVERT: A 1287 LYS cc_start: 0.8159 (tppt) cc_final: 0.7663 (mttp) REVERT: A 1305 GLU cc_start: 0.7167 (OUTLIER) cc_final: 0.6570 (tt0) REVERT: A 1349 GLU cc_start: 0.7801 (OUTLIER) cc_final: 0.6555 (pt0) REVERT: A 1435 ILE cc_start: 0.7221 (OUTLIER) cc_final: 0.6895 (pt) REVERT: A 1486 LYS cc_start: 0.7995 (ttpt) cc_final: 0.7745 (ttpt) REVERT: A 1540 SER cc_start: 0.7451 (t) cc_final: 0.7208 (m) REVERT: A 1541 GLN cc_start: 0.8200 (tp40) cc_final: 0.7808 (tp40) REVERT: A 1565 LYS cc_start: 0.8282 (pttm) cc_final: 0.7819 (ptpt) REVERT: A 1727 GLU cc_start: 0.7336 (OUTLIER) cc_final: 0.6845 (mt-10) REVERT: B 28 THR cc_start: 0.8351 (p) cc_final: 0.8128 (t) REVERT: B 162 MET cc_start: 0.6288 (tpt) cc_final: 0.6038 (tpt) REVERT: B 182 TYR cc_start: 0.7754 (t80) cc_final: 0.7431 (t80) REVERT: F 79 MET cc_start: 0.0431 (tmm) cc_final: -0.0593 (mmt) outliers start: 61 outliers final: 44 residues processed: 261 average time/residue: 0.2263 time to fit residues: 86.0599 Evaluate side-chains 260 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 210 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1368 SER Chi-restraints excluded: chain A residue 1421 VAL Chi-restraints excluded: chain A residue 1435 ILE Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1485 MET Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1672 GLU Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 70 ILE Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 137 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 chunk 131 optimal weight: 30.0000 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 134 optimal weight: 20.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11965 Z= 0.398 Angle : 0.712 10.809 16214 Z= 0.368 Chirality : 0.047 0.324 1886 Planarity : 0.005 0.041 1978 Dihedral : 6.622 79.211 1765 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 4.46 % Allowed : 26.19 % Favored : 69.35 % 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: -0.97 (0.22), residues: 1419 helix: 0.05 (0.17), residues: 848 sheet: -0.60 (0.45), residues: 126 loop : -1.88 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 151 HIS 0.004 0.001 HIS A 766 PHE 0.021 0.002 PHE A1740 TYR 0.023 0.002 TYR A1348 ARG 0.004 0.000 ARG A 922 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 211 time to evaluate : 1.074 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.8015 (tt0) cc_final: 0.7797 (tt0) REVERT: A 301 LYS cc_start: 0.7483 (mtmt) cc_final: 0.7180 (mmtt) REVERT: A 742 MET cc_start: 0.5101 (mmm) cc_final: 0.3862 (mtp) REVERT: A 820 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6927 (mm) REVERT: A 1251 LYS cc_start: 0.6588 (mtpt) cc_final: 0.6200 (mptt) REVERT: A 1287 LYS cc_start: 0.8226 (tppt) cc_final: 0.7688 (mttp) REVERT: A 1305 GLU cc_start: 0.7325 (OUTLIER) cc_final: 0.6846 (tt0) REVERT: A 1349 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.6663 (pm20) REVERT: A 1464 LYS cc_start: 0.7515 (tttm) cc_final: 0.7254 (ttmm) REVERT: A 1486 LYS cc_start: 0.8049 (ttpt) cc_final: 0.7803 (ttpt) REVERT: A 1540 SER cc_start: 0.7356 (t) cc_final: 0.7100 (m) REVERT: A 1541 GLN cc_start: 0.8219 (tp40) cc_final: 0.7815 (tp40) REVERT: A 1565 LYS cc_start: 0.8336 (pttm) cc_final: 0.7870 (ptpt) REVERT: A 1727 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7090 (mt-10) REVERT: A 1756 ILE cc_start: 0.8435 (mm) cc_final: 0.8194 (mm) REVERT: B 99 LYS cc_start: 0.7062 (tppp) cc_final: 0.6580 (tppt) REVERT: B 152 ARG cc_start: 0.8479 (ptm160) cc_final: 0.7703 (ptt90) REVERT: B 162 MET cc_start: 0.6233 (tpt) cc_final: 0.6009 (tpt) REVERT: B 182 TYR cc_start: 0.7827 (t80) cc_final: 0.7516 (t80) outliers start: 57 outliers final: 42 residues processed: 254 average time/residue: 0.2347 time to fit residues: 86.2328 Evaluate side-chains 248 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 202 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 760 PHE Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 896 VAL Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1368 SER Chi-restraints excluded: chain A residue 1421 VAL Chi-restraints excluded: chain A residue 1471 ASP Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1608 LEU Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 137 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.6980 chunk 63 optimal weight: 0.6980 chunk 93 optimal weight: 7.9990 chunk 141 optimal weight: 50.0000 chunk 130 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11965 Z= 0.265 Angle : 0.644 10.354 16214 Z= 0.331 Chirality : 0.044 0.284 1886 Planarity : 0.004 0.037 1978 Dihedral : 6.381 78.358 1763 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.41 % Favored : 93.59 % Rotamer: Outliers : 3.75 % Allowed : 27.13 % Favored : 69.12 % 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: -0.72 (0.22), residues: 1419 helix: 0.28 (0.17), residues: 838 sheet: -0.55 (0.46), residues: 123 loop : -1.77 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP A 151 HIS 0.003 0.001 HIS A 766 PHE 0.016 0.001 PHE A1740 TYR 0.022 0.002 TYR A1348 ARG 0.002 0.000 ARG A 922 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2838 Ramachandran restraints generated. 1419 Oldfield, 0 Emsley, 1419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 212 time to evaluate : 1.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 MET cc_start: 0.6638 (ttp) cc_final: 0.6349 (ttp) REVERT: A 164 THR cc_start: 0.8573 (OUTLIER) cc_final: 0.8223 (p) REVERT: A 301 LYS cc_start: 0.7511 (mtmt) cc_final: 0.7180 (mmtt) REVERT: A 742 MET cc_start: 0.4950 (mmm) cc_final: 0.3836 (mtp) REVERT: A 820 LEU cc_start: 0.7286 (OUTLIER) cc_final: 0.6946 (mm) REVERT: A 1227 GLU cc_start: 0.7596 (tt0) cc_final: 0.7248 (tp30) REVERT: A 1251 LYS cc_start: 0.6616 (mtpt) cc_final: 0.6223 (mptt) REVERT: A 1287 LYS cc_start: 0.8168 (tppt) cc_final: 0.7662 (mttp) REVERT: A 1305 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6707 (tt0) REVERT: A 1349 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.6566 (pm20) REVERT: A 1464 LYS cc_start: 0.7508 (tttm) cc_final: 0.7262 (ttmm) REVERT: A 1540 SER cc_start: 0.7427 (t) cc_final: 0.7169 (m) REVERT: A 1541 GLN cc_start: 0.8186 (tp40) cc_final: 0.7788 (tp40) REVERT: A 1565 LYS cc_start: 0.8259 (pttm) cc_final: 0.7879 (ptpt) REVERT: A 1727 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.6930 (mt-10) REVERT: A 1739 TYR cc_start: 0.7896 (t80) cc_final: 0.7663 (t80) REVERT: B 99 LYS cc_start: 0.7009 (tppp) cc_final: 0.6344 (tppt) REVERT: B 162 MET cc_start: 0.6235 (tpt) cc_final: 0.6010 (tpt) REVERT: B 182 TYR cc_start: 0.7797 (t80) cc_final: 0.7470 (t80) outliers start: 48 outliers final: 39 residues processed: 250 average time/residue: 0.2384 time to fit residues: 85.7863 Evaluate side-chains 254 residues out of total 1287 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 210 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 196 ILE Chi-restraints excluded: chain A residue 206 ASN Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 324 CYS Chi-restraints excluded: chain A residue 346 THR Chi-restraints excluded: chain A residue 348 SER Chi-restraints excluded: chain A residue 354 LEU Chi-restraints excluded: chain A residue 746 VAL Chi-restraints excluded: chain A residue 820 LEU Chi-restraints excluded: chain A residue 825 LEU Chi-restraints excluded: chain A residue 836 SER Chi-restraints excluded: chain A residue 902 ASP Chi-restraints excluded: chain A residue 925 CYS Chi-restraints excluded: chain A residue 934 ASP Chi-restraints excluded: chain A residue 963 PHE Chi-restraints excluded: chain A residue 970 SER Chi-restraints excluded: chain A residue 1192 SER Chi-restraints excluded: chain A residue 1200 LEU Chi-restraints excluded: chain A residue 1206 SER Chi-restraints excluded: chain A residue 1216 ILE Chi-restraints excluded: chain A residue 1270 LEU Chi-restraints excluded: chain A residue 1305 GLU Chi-restraints excluded: chain A residue 1325 LEU Chi-restraints excluded: chain A residue 1349 GLU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1368 SER Chi-restraints excluded: chain A residue 1421 VAL Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1575 THR Chi-restraints excluded: chain A residue 1614 LEU Chi-restraints excluded: chain A residue 1628 LYS Chi-restraints excluded: chain A residue 1710 SER Chi-restraints excluded: chain A residue 1720 VAL Chi-restraints excluded: chain A residue 1727 GLU Chi-restraints excluded: chain A residue 1734 SER Chi-restraints excluded: chain A residue 1751 VAL Chi-restraints excluded: chain A residue 1754 MET Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 93 ASN Chi-restraints excluded: chain B residue 137 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 0.1980 chunk 112 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 115 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 6 optimal weight: 20.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 360 GLN A1579 ASN ** B 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.224506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.175767 restraints weight = 12311.302| |-----------------------------------------------------------------------------| r_work (start): 0.4005 rms_B_bonded: 3.18 r_work: 0.3662 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3658 r_free = 0.3658 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3658 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11965 Z= 0.178 Angle : 0.600 9.474 16214 Z= 0.310 Chirality : 0.042 0.280 1886 Planarity : 0.004 0.038 1978 Dihedral : 6.169 77.171 1763 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 3.28 % Allowed : 27.99 % Favored : 68.73 % 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: -0.41 (0.22), residues: 1419 helix: 0.51 (0.18), residues: 838 sheet: -0.37 (0.47), residues: 123 loop : -1.61 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 151 HIS 0.004 0.000 HIS A 765 PHE 0.028 0.001 PHE A 165 TYR 0.022 0.001 TYR A1436 ARG 0.007 0.000 ARG B 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2932.67 seconds wall clock time: 53 minutes 53.51 seconds (3233.51 seconds total)