Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 16:42:11 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/04_2023/8gz2_34388_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/04_2023/8gz2_34388.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/04_2023/8gz2_34388_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/04_2023/8gz2_34388_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/04_2023/8gz2_34388_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/04_2023/8gz2_34388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/04_2023/8gz2_34388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/04_2023/8gz2_34388_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/04_2023/8gz2_34388_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.006 sd= 0.076 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 872 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: 4 Type Number sf(0) Gaussians S 99 5.16 5 C 7874 2.51 5 N 1870 2.21 5 O 2141 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 29": "OE1" <-> "OE2" Residue "D TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 52": "OE1" <-> "OE2" Residue "D PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 148": "OD1" <-> "OD2" Residue "B PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 198": "OD1" <-> "OD2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 724": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 773": "OE1" <-> "OE2" Residue "B PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 913": "OE1" <-> "OE2" Residue "B GLU 946": "OE1" <-> "OE2" Residue "B PHE 1206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1223": "OE1" <-> "OE2" Residue "B ASP 1236": "OD1" <-> "OD2" Residue "B TYR 1241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1311": "OE1" <-> "OE2" Residue "B PHE 1357": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1366": "OE1" <-> "OE2" Residue "B GLU 1368": "OE1" <-> "OE2" Residue "B GLU 1386": "OE1" <-> "OE2" Residue "B ASP 1417": "OD1" <-> "OD2" Residue "B GLU 1483": "OE1" <-> "OE2" Residue "B TYR 1489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1564": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1581": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1589": "OD1" <-> "OD2" Residue "B PHE 1663": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1679": "OE1" <-> "OE2" Residue "B GLU 1767": "OE1" <-> "OE2" Residue "C GLU 31": "OE1" <-> "OE2" Residue "C PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 11984 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1381 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 172} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 9474 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1174, 9474 Classifications: {'peptide': 1174} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 34, 'TRANS': 1139} Chain breaks: 2 Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "C" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 885 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 6, 'TRANS': 113} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 100 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 87 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "E" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 35 Unusual residues: {'NAG': 1, 'WMK': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.47, per 1000 atoms: 0.54 Number of scatterers: 11984 At special positions: 0 Unit cell: (132.08, 138.32, 115.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 99 16.00 O 2141 8.00 N 1870 7.00 C 7874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 43 " distance=2.08 Simple disulfide: pdb=" SG CYS D 40 " - pdb=" SG CYS D 121 " distance=2.04 Simple disulfide: pdb=" SG CYS B 281 " - pdb=" SG CYS B 324 " distance=2.03 Simple disulfide: pdb=" SG CYS B 904 " - pdb=" SG CYS C 55 " distance=2.03 Simple disulfide: pdb=" SG CYS B 906 " - pdb=" SG CYS B 912 " distance=2.03 Simple disulfide: pdb=" SG CYS B 944 " - pdb=" SG CYS B 953 " distance=2.03 Simple disulfide: pdb=" SG CYS B1356 " - pdb=" SG CYS B1376 " distance=2.04 Simple disulfide: pdb=" SG CYS B1721 " - pdb=" SG CYS B1736 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 127 " distance=2.03 Simple disulfide: pdb=" SG CYS C 72 " - pdb=" SG CYS C 75 " distance=2.03 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 A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG E 1 " - " NAG E 2 " " NAG E 2 " - " BMA E 3 " " NAG F 1 " - " NAG F 2 " " NAG F 2 " - " BMA F 3 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " NAG-ASN " NAG A 1 " - " ASN B 295 " " NAG B2001 " - " ASN B 289 " " NAG D 301 " - " ASN D 135 " " NAG E 1 " - " ASN B 308 " " NAG F 1 " - " ASN B 326 " " NAG G 1 " - " ASN B1358 " " NAG H 1 " - " ASN B1372 " Time building additional restraints: 5.22 Conformation dependent library (CDL) restraints added in 2.0 seconds 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2778 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 54 helices and 5 sheets defined 58.6% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.83 Creating SS restraints... Processing helix chain 'D' and resid 154 through 189 Processing helix chain 'B' and resid 120 through 130 Processing helix chain 'B' and resid 132 through 150 Processing helix chain 'B' and resid 156 through 178 removed outlier: 5.294A pdb=" N ASN B 160 " --> pdb=" O TRP B 157 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 208 removed outlier: 3.542A pdb=" N LEU B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 216 through 233 removed outlier: 4.062A pdb=" N ARG B 223 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VAL B 224 " --> pdb=" O ARG B 220 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU B 225 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG B 226 " --> pdb=" O PHE B 222 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA B 227 " --> pdb=" O ARG B 223 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR B 230 " --> pdb=" O ARG B 226 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ILE B 231 " --> pdb=" O ALA B 227 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N SER B 232 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 272 removed outlier: 3.950A pdb=" N SER B 252 " --> pdb=" O VAL B 248 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ASP B 253 " --> pdb=" O LYS B 249 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N VAL B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 278 No H-bonds generated for 'chain 'B' and resid 276 through 278' Processing helix chain 'B' and resid 288 through 290 No H-bonds generated for 'chain 'B' and resid 288 through 290' Processing helix chain 'B' and resid 302 through 305 No H-bonds generated for 'chain 'B' and resid 302 through 305' Processing helix chain 'B' and resid 309 through 311 No H-bonds generated for 'chain 'B' and resid 309 through 311' Processing helix chain 'B' and resid 347 through 349 No H-bonds generated for 'chain 'B' and resid 347 through 349' Processing helix chain 'B' and resid 356 through 368 Processing helix chain 'B' and resid 372 through 383 Processing helix chain 'B' and resid 385 through 395 removed outlier: 3.907A pdb=" N ILE B 389 " --> pdb=" O THR B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 423 Processing helix chain 'B' and resid 722 through 730 removed outlier: 3.836A pdb=" N PHE B 726 " --> pdb=" O CYS B 722 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR B 729 " --> pdb=" O LYS B 725 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 750 Processing helix chain 'B' and resid 752 through 771 removed outlier: 3.865A pdb=" N ASP B 756 " --> pdb=" O ASP B 752 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N LEU B 757 " --> pdb=" O PRO B 753 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ALA B 758 " --> pdb=" O PHE B 754 " (cutoff:3.500A) Processing helix chain 'B' and resid 779 through 806 Processing helix chain 'B' and resid 809 through 813 Processing helix chain 'B' and resid 816 through 833 removed outlier: 3.646A pdb=" N GLU B 831 " --> pdb=" O LEU B 827 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU B 832 " --> pdb=" O SER B 828 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER B 833 " --> pdb=" O LEU B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 843 through 856 removed outlier: 3.766A pdb=" N ARG B 847 " --> pdb=" O ARG B 844 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS B 856 " --> pdb=" O LYS B 853 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 871 Processing helix chain 'B' and resid 876 through 896 Processing helix chain 'B' and resid 900 through 903 No H-bonds generated for 'chain 'B' and resid 900 through 903' Processing helix chain 'B' and resid 905 through 908 No H-bonds generated for 'chain 'B' and resid 905 through 908' Processing helix chain 'B' and resid 922 through 934 Processing helix chain 'B' and resid 938 through 948 removed outlier: 4.416A pdb=" N ASP B 943 " --> pdb=" O GLU B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 980 Processing helix chain 'B' and resid 1184 through 1195 Processing helix chain 'B' and resid 1198 through 1215 removed outlier: 4.034A pdb=" N LEU B1215 " --> pdb=" O SER B1211 " (cutoff:3.500A) Processing helix chain 'B' and resid 1226 through 1254 removed outlier: 3.726A pdb=" N LYS B1237 " --> pdb=" O GLU B1233 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL B1238 " --> pdb=" O TYR B1234 " (cutoff:3.500A) Processing helix chain 'B' and resid 1256 through 1260 Processing helix chain 'B' and resid 1263 through 1283 Processing helix chain 'B' and resid 1292 through 1309 removed outlier: 3.646A pdb=" N THR B1297 " --> pdb=" O LYS B1293 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LEU B1298 " --> pdb=" O SER B1294 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG B1299 " --> pdb=" O LEU B1295 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ALA B1300 " --> pdb=" O ARG B1296 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LEU B1301 " --> pdb=" O THR B1297 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ARG B1302 " --> pdb=" O LEU B1298 " (cutoff:3.500A) Proline residue: B1303 - end of helix removed outlier: 4.863A pdb=" N ALA B1306 " --> pdb=" O ARG B1302 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU B1307 " --> pdb=" O PRO B1303 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER B1308 " --> pdb=" O LEU B1304 " (cutoff:3.500A) Processing helix chain 'B' and resid 1311 through 1349 Proline residue: B1325 - end of helix removed outlier: 4.263A pdb=" N ASN B1329 " --> pdb=" O PRO B1325 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL B1330 " --> pdb=" O SER B1326 " (cutoff:3.500A) Processing helix chain 'B' and resid 1373 through 1382 Processing helix chain 'B' and resid 1399 through 1411 Processing helix chain 'B' and resid 1415 through 1423 Processing helix chain 'B' and resid 1438 through 1450 Processing helix chain 'B' and resid 1454 through 1473 Processing helix chain 'B' and resid 1483 through 1495 Processing helix chain 'B' and resid 1510 through 1520 Processing helix chain 'B' and resid 1522 through 1540 Processing helix chain 'B' and resid 1548 through 1580 removed outlier: 8.050A pdb=" N HIS B1578 " --> pdb=" O PHE B1574 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N TYR B1579 " --> pdb=" O ALA B1575 " (cutoff:3.500A) Processing helix chain 'B' and resid 1584 through 1604 Processing helix chain 'B' and resid 1613 through 1633 removed outlier: 4.108A pdb=" N ARG B1623 " --> pdb=" O ILE B1619 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ILE B1624 " --> pdb=" O ARG B1620 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLY B1625 " --> pdb=" O LEU B1621 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N ARG B1626 " --> pdb=" O ALA B1622 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ILE B1627 " --> pdb=" O ARG B1623 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B1628 " --> pdb=" O ILE B1624 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG B1629 " --> pdb=" O GLY B1625 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU B1630 " --> pdb=" O ARG B1626 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N ILE B1631 " --> pdb=" O ILE B1627 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N LYS B1632 " --> pdb=" O LEU B1628 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N GLY B1633 " --> pdb=" O ARG B1629 " (cutoff:3.500A) Processing helix chain 'B' and resid 1636 through 1672 Proline residue: B1649 - end of helix Processing helix chain 'B' and resid 1691 through 1703 removed outlier: 4.066A pdb=" N THR B1703 " --> pdb=" O PHE B1699 " (cutoff:3.500A) Processing helix chain 'B' and resid 1707 through 1712 Processing helix chain 'B' and resid 1718 through 1720 No H-bonds generated for 'chain 'B' and resid 1718 through 1720' Processing helix chain 'B' and resid 1739 through 1771 removed outlier: 3.534A pdb=" N ASN B1759 " --> pdb=" O LEU B1755 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU B1767 " --> pdb=" O ALA B1763 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 121 No H-bonds generated for 'chain 'C' and resid 119 through 121' Processing sheet with id= A, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.386A pdb=" N GLU D 145 " --> pdb=" O ALA D 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'D' and resid 36 through 40 Processing sheet with id= C, first strand: chain 'D' and resid 134 through 144 removed outlier: 4.437A pdb=" N ASN D 50 " --> pdb=" O PHE D 128 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU D 71 " --> pdb=" O TRP D 57 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N PHE D 59 " --> pdb=" O LYS D 69 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N LYS D 69 " --> pdb=" O PHE D 59 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 37 through 40 removed outlier: 7.470A pdb=" N HIS C 143 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N VAL C 40 " --> pdb=" O HIS C 143 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLN C 145 " --> pdb=" O VAL C 40 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER C 64 " --> pdb=" O MET C 130 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU C 81 " --> pdb=" O TRP C 67 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N TYR C 69 " --> pdb=" O MET C 79 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N MET C 79 " --> pdb=" O TYR C 69 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 46 through 48 648 hydrogen bonds defined for protein. 1785 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.23 Time building geometry restraints manager: 5.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1870 1.32 - 1.45: 3507 1.45 - 1.58: 6741 1.58 - 1.71: 0 1.71 - 1.84: 160 Bond restraints: 12278 Sorted by residual: bond pdb=" C10 WMK B2002 " pdb=" N16 WMK B2002 " ideal model delta sigma weight residual 0.786 1.475 -0.689 2.00e-02 2.50e+03 1.19e+03 bond pdb=" C02 WMK B2002 " pdb=" N19 WMK B2002 " ideal model delta sigma weight residual 1.060 1.463 -0.403 2.00e-02 2.50e+03 4.06e+02 bond pdb=" C03 WMK B2002 " pdb=" C10 WMK B2002 " ideal model delta sigma weight residual 1.171 1.547 -0.376 2.00e-02 2.50e+03 3.54e+02 bond pdb=" C17 WMK B2002 " pdb=" N16 WMK B2002 " ideal model delta sigma weight residual 1.696 1.363 0.333 2.00e-02 2.50e+03 2.77e+02 bond pdb=" C03 WMK B2002 " pdb=" C04 WMK B2002 " ideal model delta sigma weight residual 1.871 1.540 0.331 2.00e-02 2.50e+03 2.75e+02 ... (remaining 12273 not shown) Histogram of bond angle deviations from ideal: 90.67 - 99.50: 9 99.50 - 108.33: 514 108.33 - 117.15: 8088 117.15 - 125.98: 7871 125.98 - 134.80: 180 Bond angle restraints: 16662 Sorted by residual: angle pdb=" N SER D 47 " pdb=" CA SER D 47 " pdb=" C SER D 47 " ideal model delta sigma weight residual 112.89 121.06 -8.17 1.24e+00 6.50e-01 4.34e+01 angle pdb=" C04 WMK B2002 " pdb=" C05 WMK B2002 " pdb=" O21 WMK B2002 " ideal model delta sigma weight residual 109.92 90.82 19.10 3.00e+00 1.11e-01 4.05e+01 angle pdb=" C06 WMK B2002 " pdb=" C05 WMK B2002 " pdb=" O21 WMK B2002 " ideal model delta sigma weight residual 109.62 90.67 18.95 3.00e+00 1.11e-01 3.99e+01 angle pdb=" N PRO C 133 " pdb=" CA PRO C 133 " pdb=" CB PRO C 133 " ideal model delta sigma weight residual 103.52 97.67 5.85 1.06e+00 8.90e-01 3.05e+01 angle pdb=" C04 WMK B2002 " pdb=" C05 WMK B2002 " pdb=" C06 WMK B2002 " ideal model delta sigma weight residual 109.47 125.29 -15.82 3.00e+00 1.11e-01 2.78e+01 ... (remaining 16657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.54: 6259 17.54 - 35.08: 641 35.08 - 52.63: 120 52.63 - 70.17: 19 70.17 - 87.71: 15 Dihedral angle restraints: 7054 sinusoidal: 2758 harmonic: 4296 Sorted by residual: dihedral pdb=" CB CYS C 72 " pdb=" SG CYS C 72 " pdb=" SG CYS C 75 " pdb=" CB CYS C 75 " ideal model delta sinusoidal sigma weight residual 93.00 179.76 -86.76 1 1.00e+01 1.00e-02 9.06e+01 dihedral pdb=" CB CYS B 944 " pdb=" SG CYS B 944 " pdb=" SG CYS B 953 " pdb=" CB CYS B 953 " ideal model delta sinusoidal sigma weight residual -86.00 -162.57 76.57 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CB CYS B1356 " pdb=" SG CYS B1356 " pdb=" SG CYS B1376 " pdb=" CB CYS B1376 " ideal model delta sinusoidal sigma weight residual -86.00 -145.22 59.22 1 1.00e+01 1.00e-02 4.69e+01 ... (remaining 7051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.580: 1950 0.580 - 1.160: 2 1.160 - 1.740: 1 1.740 - 2.320: 0 2.320 - 2.900: 1 Chirality restraints: 1954 Sorted by residual: chirality pdb=" C05 WMK B2002 " pdb=" C04 WMK B2002 " pdb=" C06 WMK B2002 " pdb=" C08 WMK B2002 " both_signs ideal model delta sigma weight residual False 2.50 -0.40 2.90 2.00e-01 2.50e+01 2.10e+02 chirality pdb=" C10 WMK B2002 " pdb=" C03 WMK B2002 " pdb=" C09 WMK B2002 " pdb=" N16 WMK B2002 " both_signs ideal model delta sigma weight residual False 0.84 2.38 -1.54 2.00e-01 2.50e+01 5.92e+01 chirality pdb=" C02 WMK B2002 " pdb=" C03 WMK B2002 " pdb=" N19 WMK B2002 " pdb=" O01 WMK B2002 " both_signs ideal model delta sigma weight residual False -2.05 -2.73 0.68 2.00e-01 2.50e+01 1.16e+01 ... (remaining 1951 not shown) Planarity restraints: 2038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B1415 " -0.030 2.00e-02 2.50e+03 2.38e-02 1.41e+01 pdb=" CG TRP B1415 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP B1415 " -0.024 2.00e-02 2.50e+03 pdb=" CD2 TRP B1415 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP B1415 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B1415 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B1415 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1415 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1415 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B1415 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B1390 " -0.011 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C LYS B1390 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS B1390 " -0.015 2.00e-02 2.50e+03 pdb=" N ASN B1391 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B1386 " -0.012 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C GLU B1386 " 0.040 2.00e-02 2.50e+03 pdb=" O GLU B1386 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE B1387 " -0.013 2.00e-02 2.50e+03 ... (remaining 2035 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1203 2.74 - 3.28: 12984 3.28 - 3.82: 19706 3.82 - 4.36: 22801 4.36 - 4.90: 38937 Nonbonded interactions: 95631 Sorted by model distance: nonbonded pdb=" O VAL B 283 " pdb=" OH TYR B 305 " model vdw 2.202 2.440 nonbonded pdb=" O ALA B 890 " pdb=" OG SER B 925 " model vdw 2.269 2.440 nonbonded pdb=" OE1 GLU B 939 " pdb=" O20 WMK B2002 " model vdw 2.272 2.440 nonbonded pdb=" O PRO B 346 " pdb=" OG1 THR B 351 " model vdw 2.274 2.440 nonbonded pdb=" N SER D 47 " pdb=" OG SER D 47 " model vdw 2.278 2.496 ... (remaining 95626 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.41 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.790 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: 4.690 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 33.720 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 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 : 0.012 0.689 12278 Z= 0.732 Angle : 0.894 19.099 16662 Z= 0.473 Chirality : 0.093 2.900 1954 Planarity : 0.004 0.050 2031 Dihedral : 14.555 87.709 4246 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 0.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.22), residues: 1457 helix: 0.67 (0.17), residues: 836 sheet: -0.44 (0.51), residues: 106 loop : -1.85 (0.29), residues: 515 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 281 time to evaluate : 1.346 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 283 average time/residue: 0.2323 time to fit residues: 96.0049 Evaluate side-chains 233 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 1.412 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1000 time to fit residues: 2.1168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 1.9990 chunk 110 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 59 optimal weight: 7.9990 chunk 114 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 132 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 143 HIS B 332 GLN B 404 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1586 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 12278 Z= 0.323 Angle : 0.760 26.730 16662 Z= 0.369 Chirality : 0.068 2.259 1954 Planarity : 0.004 0.053 2031 Dihedral : 5.155 27.355 1564 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer Outliers : 2.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1457 helix: 0.80 (0.17), residues: 835 sheet: -0.34 (0.49), residues: 105 loop : -1.73 (0.29), residues: 517 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 239 time to evaluate : 1.365 Fit side-chains revert: symmetry clash outliers start: 27 outliers final: 14 residues processed: 249 average time/residue: 0.2312 time to fit residues: 84.7308 Evaluate side-chains 242 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 228 time to evaluate : 1.323 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.1153 time to fit residues: 4.9464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 118 optimal weight: 8.9990 chunk 131 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 106 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 93 ASN B 404 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1678 HIS B1768 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 12278 Z= 0.181 Angle : 0.682 27.943 16662 Z= 0.323 Chirality : 0.066 2.245 1954 Planarity : 0.004 0.057 2031 Dihedral : 4.795 26.819 1564 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.22), residues: 1457 helix: 1.02 (0.18), residues: 833 sheet: -0.43 (0.49), residues: 98 loop : -1.51 (0.28), residues: 526 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 254 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 5 residues processed: 265 average time/residue: 0.2224 time to fit residues: 87.9126 Evaluate side-chains 235 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 230 time to evaluate : 1.361 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1144 time to fit residues: 2.9803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 63 optimal weight: 1.9990 chunk 89 optimal weight: 0.2980 chunk 133 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 chunk 38 optimal weight: 0.0770 overall best weight: 1.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 ASN B 774 HIS ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1768 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12278 Z= 0.198 Angle : 0.677 27.314 16662 Z= 0.321 Chirality : 0.066 2.278 1954 Planarity : 0.004 0.056 2031 Dihedral : 4.650 25.091 1564 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 2.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1457 helix: 1.13 (0.18), residues: 833 sheet: -0.36 (0.49), residues: 98 loop : -1.37 (0.28), residues: 526 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 243 time to evaluate : 1.360 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 255 average time/residue: 0.2299 time to fit residues: 86.7986 Evaluate side-chains 242 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 227 time to evaluate : 1.322 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.1199 time to fit residues: 5.1460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 2 optimal weight: 6.9990 chunk 105 optimal weight: 8.9990 chunk 58 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 0 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 chunk 126 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1768 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 12278 Z= 0.261 Angle : 0.703 27.103 16662 Z= 0.333 Chirality : 0.067 2.283 1954 Planarity : 0.004 0.056 2031 Dihedral : 4.626 24.856 1564 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.22), residues: 1457 helix: 1.11 (0.18), residues: 828 sheet: -0.34 (0.51), residues: 95 loop : -1.32 (0.28), residues: 534 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 235 time to evaluate : 1.251 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 12 residues processed: 250 average time/residue: 0.2161 time to fit residues: 80.6070 Evaluate side-chains 237 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 225 time to evaluate : 1.250 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1131 time to fit residues: 4.3168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 5.9990 chunk 127 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 141 optimal weight: 0.0070 chunk 117 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 overall best weight: 0.6398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1768 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.036 12278 Z= 0.163 Angle : 0.675 27.794 16662 Z= 0.314 Chirality : 0.065 2.252 1954 Planarity : 0.004 0.056 2031 Dihedral : 4.462 24.539 1564 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 1.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.23), residues: 1457 helix: 1.22 (0.18), residues: 835 sheet: -0.56 (0.50), residues: 98 loop : -1.22 (0.28), residues: 524 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 254 time to evaluate : 1.317 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 266 average time/residue: 0.2219 time to fit residues: 88.2052 Evaluate side-chains 244 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 232 time to evaluate : 1.379 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1222 time to fit residues: 4.6680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 136 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 80 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 118 optimal weight: 9.9990 chunk 78 optimal weight: 0.9990 chunk 140 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 85 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1768 ASN C 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 12278 Z= 0.264 Angle : 0.720 26.831 16662 Z= 0.342 Chirality : 0.067 2.297 1954 Planarity : 0.004 0.056 2031 Dihedral : 4.560 23.989 1564 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 1.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.23), residues: 1457 helix: 1.21 (0.18), residues: 822 sheet: -0.66 (0.50), residues: 98 loop : -1.18 (0.28), residues: 537 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 230 time to evaluate : 1.392 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 238 average time/residue: 0.2309 time to fit residues: 81.2538 Evaluate side-chains 226 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 218 time to evaluate : 1.369 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1231 time to fit residues: 3.7434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 4.9990 chunk 56 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 27 optimal weight: 0.0570 chunk 89 optimal weight: 0.5980 chunk 95 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 110 optimal weight: 9.9990 chunk 128 optimal weight: 0.0770 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS B 728 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1768 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 12278 Z= 0.156 Angle : 0.681 27.778 16662 Z= 0.319 Chirality : 0.065 2.256 1954 Planarity : 0.003 0.056 2031 Dihedral : 4.385 23.502 1564 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.23), residues: 1457 helix: 1.30 (0.18), residues: 828 sheet: -0.66 (0.50), residues: 97 loop : -1.13 (0.28), residues: 532 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 244 time to evaluate : 1.657 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 249 average time/residue: 0.2195 time to fit residues: 81.7921 Evaluate side-chains 239 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 233 time to evaluate : 1.340 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1288 time to fit residues: 3.2754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 131 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 57 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 5.9990 chunk 118 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 130 optimal weight: 6.9990 chunk 86 optimal weight: 0.2980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS B 404 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1768 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.050 12278 Z= 0.178 Angle : 0.697 27.344 16662 Z= 0.329 Chirality : 0.066 2.280 1954 Planarity : 0.004 0.055 2031 Dihedral : 4.361 22.993 1564 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1457 helix: 1.31 (0.18), residues: 828 sheet: -0.57 (0.51), residues: 97 loop : -1.15 (0.28), residues: 532 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 246 time to evaluate : 1.342 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 249 average time/residue: 0.2241 time to fit residues: 83.4881 Evaluate side-chains 235 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 232 time to evaluate : 1.366 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1173 time to fit residues: 2.5177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 145 optimal weight: 50.0000 chunk 133 optimal weight: 0.8980 chunk 115 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS B 404 ASN ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1512 GLN B1768 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 12278 Z= 0.188 Angle : 0.711 27.488 16662 Z= 0.338 Chirality : 0.066 2.270 1954 Planarity : 0.004 0.055 2031 Dihedral : 4.349 22.760 1564 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.23), residues: 1457 helix: 1.28 (0.18), residues: 827 sheet: -0.31 (0.51), residues: 100 loop : -1.14 (0.28), residues: 530 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2914 Ramachandran restraints generated. 1457 Oldfield, 0 Emsley, 1457 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 231 time to evaluate : 1.275 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 235 average time/residue: 0.2182 time to fit residues: 76.8966 Evaluate side-chains 233 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 231 time to evaluate : 1.374 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1408 time to fit residues: 2.3669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 123 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 106 optimal weight: 9.9990 chunk 17 optimal weight: 0.0070 chunk 32 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 48 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 0.5980 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1768 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.183554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.131148 restraints weight = 17785.574| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.11 r_work: 0.3430 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 12278 Z= 0.187 Angle : 0.701 27.506 16662 Z= 0.333 Chirality : 0.066 2.269 1954 Planarity : 0.004 0.055 2031 Dihedral : 4.308 22.414 1564 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1457 helix: 1.30 (0.18), residues: 826 sheet: -0.32 (0.51), residues: 100 loop : -1.13 (0.29), residues: 531 =============================================================================== Job complete usr+sys time: 2697.85 seconds wall clock time: 49 minutes 32.66 seconds (2972.66 seconds total)