Starting phenix.real_space_refine on Thu Feb 15 16:58:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/02_2024/8gz2_34388_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/02_2024/8gz2_34388.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/02_2024/8gz2_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_34388/02_2024/8gz2_34388_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/02_2024/8gz2_34388_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/02_2024/8gz2_34388.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/02_2024/8gz2_34388.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/02_2024/8gz2_34388_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gz2_34388/02_2024/8gz2_34388_updated.pdb" } resolution = 3.3 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= 0.006 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-dev-5238/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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 9 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 dihedrals: 3 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 6.99, per 1000 atoms: 0.58 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: 5.04 Conformation dependent library (CDL) restraints added in 2.2 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: 2.96 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: 3.97 Time building geometry restraints manager: 5.43 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 - 23.75: 6858 23.75 - 47.50: 437 47.50 - 71.25: 59 71.25 - 95.00: 38 95.00 - 118.75: 20 Dihedral angle restraints: 7412 sinusoidal: 3116 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 7409 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 4.210 Check model and map are aligned: 0.190 Set scattering table: 0.130 Process input model: 35.500 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: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.500 ------------------------------------------------------------------------------- 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 : 17.418 118.753 4604 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 % Allowed : 0.95 % Favored : 98.90 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP B1415 HIS 0.004 0.001 HIS B 775 PHE 0.029 0.002 PHE B1337 TYR 0.026 0.002 TYR B1488 ARG 0.007 0.001 ARG B1299 *********************** 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 : 1.305 Fit side-chains revert: symmetry clash REVERT: D 48 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8389 (pm20) REVERT: B 222 PHE cc_start: 0.6549 (m-10) cc_final: 0.6339 (m-10) REVERT: B 807 MET cc_start: 0.7586 (ptm) cc_final: 0.7102 (ptm) REVERT: B 1207 MET cc_start: 0.8780 (tpp) cc_final: 0.8523 (tpp) REVERT: B 1416 MET cc_start: 0.8019 (mmm) cc_final: 0.7701 (mmm) REVERT: C 104 ASN cc_start: 0.7403 (t0) cc_final: 0.7099 (t0) outliers start: 2 outliers final: 1 residues processed: 283 average time/residue: 0.2437 time to fit residues: 100.5762 Evaluate side-chains 235 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 233 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 GLU 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: 0.4980 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: 1.6986 ------------------------------------------------------------------------------- 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 ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1586 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.1174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12278 Z= 0.273 Angle : 0.746 27.106 16662 Z= 0.358 Chirality : 0.068 2.306 1954 Planarity : 0.004 0.054 2031 Dihedral : 12.243 86.436 1926 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.21 % Allowed : 9.93 % Favored : 87.86 % 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: -0.21 (0.22), residues: 1457 helix: 0.85 (0.18), residues: 835 sheet: -0.42 (0.51), residues: 98 loop : -1.69 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B1415 HIS 0.006 0.001 HIS B 131 PHE 0.027 0.002 PHE B 726 TYR 0.024 0.002 TYR B1488 ARG 0.005 0.001 ARG B1617 *********************** 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 273 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 245 time to evaluate : 1.530 Fit side-chains revert: symmetry clash REVERT: B 1185 TRP cc_start: 0.5990 (t60) cc_final: 0.5509 (t60) REVERT: B 1207 MET cc_start: 0.8816 (tpp) cc_final: 0.8434 (tpp) REVERT: B 1265 CYS cc_start: 0.7538 (m) cc_final: 0.7165 (m) REVERT: B 1645 MET cc_start: 0.7686 (tpt) cc_final: 0.7335 (tpt) REVERT: B 1768 ASN cc_start: 0.8408 (OUTLIER) cc_final: 0.8202 (t0) REVERT: C 104 ASN cc_start: 0.7429 (t0) cc_final: 0.7136 (t0) outliers start: 28 outliers final: 16 residues processed: 257 average time/residue: 0.2320 time to fit residues: 87.1843 Evaluate side-chains 247 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 230 time to evaluate : 1.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1722 SER Chi-restraints excluded: chain B residue 1748 SER Chi-restraints excluded: chain B residue 1768 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 73 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 110 optimal weight: 0.8980 chunk 90 optimal weight: 0.6980 chunk 36 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 143 optimal weight: 0.0060 chunk 118 optimal weight: 9.9990 chunk 131 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- 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** B1678 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.1547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12278 Z= 0.172 Angle : 0.681 27.664 16662 Z= 0.319 Chirality : 0.067 2.273 1954 Planarity : 0.004 0.055 2031 Dihedral : 9.308 66.499 1926 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 2.29 % Allowed : 12.92 % Favored : 84.79 % 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: 0.05 (0.22), residues: 1457 helix: 1.06 (0.18), residues: 835 sheet: -0.48 (0.50), residues: 99 loop : -1.52 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B1185 HIS 0.005 0.001 HIS B 131 PHE 0.020 0.001 PHE B 171 TYR 0.025 0.001 TYR B1488 ARG 0.003 0.000 ARG B 844 *********************** 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 281 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 252 time to evaluate : 1.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 777 MET cc_start: 0.7025 (mmm) cc_final: 0.6091 (mtt) REVERT: B 827 LEU cc_start: 0.8990 (mp) cc_final: 0.8735 (mt) REVERT: B 917 TRP cc_start: 0.7166 (m-10) cc_final: 0.6527 (m100) REVERT: B 1207 MET cc_start: 0.8778 (tpp) cc_final: 0.8398 (tpp) REVERT: B 1406 LEU cc_start: 0.8775 (tp) cc_final: 0.8446 (mp) REVERT: B 1526 ILE cc_start: 0.8414 (pt) cc_final: 0.8122 (mm) REVERT: B 1645 MET cc_start: 0.7757 (tpt) cc_final: 0.7466 (tpt) REVERT: B 1768 ASN cc_start: 0.8442 (OUTLIER) cc_final: 0.8234 (t0) REVERT: C 104 ASN cc_start: 0.7479 (t0) cc_final: 0.7168 (t0) outliers start: 29 outliers final: 17 residues processed: 267 average time/residue: 0.2374 time to fit residues: 93.5952 Evaluate side-chains 245 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 227 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 933 LEU Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1244 ILE Chi-restraints excluded: chain B residue 1249 LEU Chi-restraints excluded: chain B residue 1429 ASP Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1768 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 131 optimal weight: 0.5980 chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 14 optimal weight: 9.9990 chunk 63 optimal weight: 0.8980 chunk 89 optimal weight: 0.0870 chunk 133 optimal weight: 4.9990 chunk 141 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 126 optimal weight: 0.0980 chunk 38 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 12278 Z= 0.158 Angle : 0.667 27.341 16662 Z= 0.312 Chirality : 0.067 2.291 1954 Planarity : 0.003 0.056 2031 Dihedral : 7.375 59.756 1926 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.52 % Allowed : 15.52 % Favored : 81.95 % 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: 0.27 (0.22), residues: 1457 helix: 1.19 (0.18), residues: 838 sheet: -0.40 (0.50), residues: 96 loop : -1.37 (0.28), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B1185 HIS 0.003 0.001 HIS B 131 PHE 0.020 0.001 PHE B1616 TYR 0.022 0.001 TYR B1488 ARG 0.003 0.000 ARG B1299 *********************** 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 285 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 253 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 777 MET cc_start: 0.7013 (mmm) cc_final: 0.6259 (mtt) REVERT: B 917 TRP cc_start: 0.7145 (m-10) cc_final: 0.6423 (m100) REVERT: B 1207 MET cc_start: 0.8770 (tpp) cc_final: 0.8366 (tpp) REVERT: B 1265 CYS cc_start: 0.7553 (m) cc_final: 0.7247 (m) REVERT: B 1406 LEU cc_start: 0.8683 (tp) cc_final: 0.8235 (mp) REVERT: B 1534 LEU cc_start: 0.9159 (OUTLIER) cc_final: 0.8953 (tt) REVERT: B 1645 MET cc_start: 0.7715 (tpt) cc_final: 0.7428 (tpt) REVERT: B 1768 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8234 (t0) REVERT: C 104 ASN cc_start: 0.7484 (t0) cc_final: 0.7169 (t0) outliers start: 32 outliers final: 20 residues processed: 268 average time/residue: 0.2172 time to fit residues: 85.2849 Evaluate side-chains 259 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 237 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 751 MET Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 933 LEU Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 1429 ASP Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1534 LEU Chi-restraints excluded: chain B residue 1722 SER Chi-restraints excluded: chain B residue 1768 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 117 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 97 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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** ** B1678 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1768 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.067 12278 Z= 0.459 Angle : 0.790 26.148 16662 Z= 0.384 Chirality : 0.070 2.332 1954 Planarity : 0.004 0.058 2031 Dihedral : 7.666 59.240 1926 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer: Outliers : 3.94 % Allowed : 16.15 % Favored : 79.91 % 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: 0.92 (0.18), residues: 829 sheet: -0.25 (0.52), residues: 95 loop : -1.47 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 917 HIS 0.005 0.001 HIS D 134 PHE 0.029 0.002 PHE B1447 TYR 0.028 0.002 TYR B 376 ARG 0.006 0.001 ARG B 365 *********************** 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 276 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 226 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 48 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8566 (mp0) REVERT: B 139 MET cc_start: 0.5365 (mmp) cc_final: 0.4783 (mmp) REVERT: B 777 MET cc_start: 0.7022 (mmm) cc_final: 0.6512 (mtt) REVERT: B 1265 CYS cc_start: 0.7830 (m) cc_final: 0.7430 (m) REVERT: C 104 ASN cc_start: 0.7640 (t0) cc_final: 0.7326 (t0) outliers start: 50 outliers final: 38 residues processed: 258 average time/residue: 0.2135 time to fit residues: 81.9818 Evaluate side-chains 258 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 219 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 131 ASN Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 751 MET Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 772 MET Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 790 LEU Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 933 LEU Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1202 THR Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1321 VAL Chi-restraints excluded: chain B residue 1337 PHE Chi-restraints excluded: chain B residue 1429 ASP Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1698 LEU Chi-restraints excluded: chain B residue 1722 SER Chi-restraints excluded: chain B residue 1748 SER Chi-restraints excluded: chain B residue 1758 VAL Chi-restraints excluded: chain B residue 1768 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 47 optimal weight: 0.8980 chunk 127 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 82 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 117 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 overall best weight: 0.6958 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12278 Z= 0.172 Angle : 0.684 27.342 16662 Z= 0.324 Chirality : 0.067 2.295 1954 Planarity : 0.004 0.057 2031 Dihedral : 6.683 59.984 1926 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.23 % Allowed : 17.18 % Favored : 79.59 % 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: 0.23 (0.23), residues: 1457 helix: 1.14 (0.18), residues: 830 sheet: -0.51 (0.51), residues: 96 loop : -1.28 (0.28), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B1185 HIS 0.003 0.001 HIS B 131 PHE 0.016 0.001 PHE B 171 TYR 0.023 0.001 TYR B1488 ARG 0.003 0.000 ARG B1299 *********************** 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 281 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 240 time to evaluate : 1.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 412 MET cc_start: 0.7322 (mtm) cc_final: 0.6986 (mtp) REVERT: B 777 MET cc_start: 0.6944 (mmm) cc_final: 0.6425 (mtt) REVERT: B 1207 MET cc_start: 0.8735 (tpp) cc_final: 0.8326 (tpp) REVERT: B 1246 GLU cc_start: 0.8000 (mm-30) cc_final: 0.7443 (tp30) REVERT: B 1265 CYS cc_start: 0.7587 (m) cc_final: 0.7299 (m) REVERT: C 104 ASN cc_start: 0.7614 (t0) cc_final: 0.7294 (t0) outliers start: 41 outliers final: 29 residues processed: 268 average time/residue: 0.2172 time to fit residues: 86.9307 Evaluate side-chains 253 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 224 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 333 CYS Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 751 MET Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1337 PHE Chi-restraints excluded: chain B residue 1387 ILE Chi-restraints excluded: chain B residue 1429 ASP Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1656 LEU Chi-restraints excluded: chain B residue 1722 SER Chi-restraints excluded: chain C residue 65 LEU 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: 0.8980 chunk 80 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 118 optimal weight: 0.0070 chunk 78 optimal weight: 3.9990 chunk 140 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.0800 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2275 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 : 0.690 27.037 16662 Z= 0.323 Chirality : 0.067 2.306 1954 Planarity : 0.004 0.056 2031 Dihedral : 6.024 59.518 1923 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.07 % Allowed : 19.62 % Favored : 77.30 % 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: 0.30 (0.23), residues: 1457 helix: 1.23 (0.18), residues: 825 sheet: -0.63 (0.51), residues: 98 loop : -1.27 (0.28), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1185 HIS 0.005 0.001 HIS B 131 PHE 0.030 0.001 PHE B1447 TYR 0.019 0.001 TYR B 376 ARG 0.003 0.000 ARG D 152 *********************** 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 275 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 236 time to evaluate : 1.507 Fit side-chains revert: symmetry clash REVERT: B 412 MET cc_start: 0.7369 (mtm) cc_final: 0.7037 (mtp) REVERT: B 777 MET cc_start: 0.7049 (mmm) cc_final: 0.6624 (mtt) REVERT: B 1207 MET cc_start: 0.8771 (tpp) cc_final: 0.8349 (tpp) REVERT: B 1246 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7403 (tp30) REVERT: B 1265 CYS cc_start: 0.7679 (m) cc_final: 0.7462 (m) REVERT: C 104 ASN cc_start: 0.7615 (t0) cc_final: 0.7313 (t0) outliers start: 39 outliers final: 27 residues processed: 259 average time/residue: 0.2206 time to fit residues: 86.0201 Evaluate side-chains 254 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 227 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 953 CYS Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1337 PHE Chi-restraints excluded: chain B residue 1387 ILE Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1656 LEU Chi-restraints excluded: chain B residue 1722 SER Chi-restraints excluded: chain B residue 1758 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 87 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 42 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 89 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 7.9990 chunk 110 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12278 Z= 0.196 Angle : 0.698 27.224 16662 Z= 0.326 Chirality : 0.067 2.293 1954 Planarity : 0.004 0.056 2031 Dihedral : 5.782 58.057 1922 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.35 % Favored : 94.65 % Rotamer: Outliers : 3.15 % Allowed : 19.46 % Favored : 77.38 % 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: 0.30 (0.23), residues: 1457 helix: 1.23 (0.18), residues: 828 sheet: -0.60 (0.52), residues: 92 loop : -1.27 (0.28), residues: 537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP B1185 HIS 0.005 0.001 HIS B 131 PHE 0.028 0.001 PHE B1447 TYR 0.023 0.001 TYR B1488 ARG 0.003 0.000 ARG B1299 *********************** 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 275 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 235 time to evaluate : 1.419 Fit side-chains REVERT: B 412 MET cc_start: 0.7356 (mtm) cc_final: 0.7036 (mtp) REVERT: B 777 MET cc_start: 0.6997 (mmm) cc_final: 0.6641 (mtt) REVERT: B 1207 MET cc_start: 0.8787 (tpp) cc_final: 0.8354 (tpp) REVERT: B 1246 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7377 (tp30) REVERT: B 1265 CYS cc_start: 0.7692 (m) cc_final: 0.7485 (m) REVERT: B 1406 LEU cc_start: 0.8692 (mt) cc_final: 0.8291 (mt) REVERT: B 1529 MET cc_start: 0.7297 (ptm) cc_final: 0.7003 (ptt) REVERT: B 1530 MET cc_start: 0.6778 (mmt) cc_final: 0.6545 (mmm) REVERT: B 1581 PHE cc_start: 0.8697 (m-80) cc_final: 0.8468 (m-80) REVERT: B 1617 ARG cc_start: 0.7315 (mtm110) cc_final: 0.6989 (mtm-85) REVERT: C 104 ASN cc_start: 0.7593 (t0) cc_final: 0.7288 (t0) outliers start: 40 outliers final: 34 residues processed: 259 average time/residue: 0.2189 time to fit residues: 85.4182 Evaluate side-chains 263 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 229 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 TRP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 768 LEU Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 860 THR Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 953 CYS Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1337 PHE Chi-restraints excluded: chain B residue 1387 ILE Chi-restraints excluded: chain B residue 1429 ASP Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1656 LEU Chi-restraints excluded: chain B residue 1722 SER Chi-restraints excluded: chain B residue 1758 VAL Chi-restraints excluded: chain C residue 65 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 134 optimal weight: 8.9990 chunk 122 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 102 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 86 optimal weight: 0.0070 overall best weight: 1.3804 ------------------------------------------------------------------------------- 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: 0.7600 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12278 Z= 0.226 Angle : 0.705 27.054 16662 Z= 0.333 Chirality : 0.067 2.301 1954 Planarity : 0.004 0.056 2031 Dihedral : 5.713 56.403 1922 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.23 % Allowed : 19.86 % Favored : 76.91 % 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: 1.20 (0.18), residues: 827 sheet: -0.43 (0.51), residues: 100 loop : -1.24 (0.28), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP B1185 HIS 0.007 0.001 HIS B 131 PHE 0.025 0.001 PHE B1447 TYR 0.025 0.001 TYR B1555 ARG 0.003 0.000 ARG B 931 *********************** 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 272 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 231 time to evaluate : 1.448 Fit side-chains REVERT: B 412 MET cc_start: 0.7321 (mtm) cc_final: 0.6989 (mtp) REVERT: B 777 MET cc_start: 0.6942 (mmm) cc_final: 0.6600 (mtt) REVERT: B 1189 LYS cc_start: 0.7885 (mtmt) cc_final: 0.7547 (mtmm) REVERT: B 1207 MET cc_start: 0.8797 (tpp) cc_final: 0.8375 (tpp) REVERT: B 1246 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7338 (tp30) REVERT: B 1529 MET cc_start: 0.7326 (ptm) cc_final: 0.7012 (ptt) REVERT: B 1530 MET cc_start: 0.6749 (mmt) cc_final: 0.6504 (mmm) REVERT: B 1581 PHE cc_start: 0.8743 (m-80) cc_final: 0.8519 (m-80) REVERT: B 1617 ARG cc_start: 0.7363 (mtm110) cc_final: 0.6961 (mtm-85) REVERT: C 104 ASN cc_start: 0.7626 (t0) cc_final: 0.7315 (t0) outliers start: 41 outliers final: 34 residues processed: 257 average time/residue: 0.2136 time to fit residues: 81.7866 Evaluate side-chains 259 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 225 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain D residue 48 GLU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 TRP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 860 THR Chi-restraints excluded: chain B residue 863 MET Chi-restraints excluded: chain B residue 867 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 953 CYS Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1195 VAL Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1337 PHE Chi-restraints excluded: chain B residue 1429 ASP Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1656 LEU Chi-restraints excluded: chain B residue 1698 LEU Chi-restraints excluded: chain B residue 1722 SER Chi-restraints excluded: chain B residue 1758 VAL Chi-restraints excluded: chain C residue 65 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 138 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 145 optimal weight: 40.0000 chunk 133 optimal weight: 2.9990 chunk 115 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 89 optimal weight: 0.3980 chunk 71 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.7556 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12278 Z= 0.174 Angle : 0.688 27.302 16662 Z= 0.322 Chirality : 0.067 2.293 1954 Planarity : 0.004 0.057 2031 Dihedral : 5.421 52.716 1922 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.44 % Allowed : 20.65 % Favored : 76.91 % 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: 0.41 (0.23), residues: 1457 helix: 1.30 (0.18), residues: 824 sheet: -0.36 (0.52), residues: 100 loop : -1.22 (0.28), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.001 TRP B1185 HIS 0.008 0.001 HIS B 131 PHE 0.023 0.001 PHE B1616 TYR 0.027 0.001 TYR B1488 ARG 0.003 0.000 ARG B1299 ********************** 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 274 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 243 time to evaluate : 1.234 Fit side-chains REVERT: D 183 LYS cc_start: 0.8283 (mmtt) cc_final: 0.7823 (mptt) REVERT: B 777 MET cc_start: 0.6909 (mmm) cc_final: 0.6699 (mtt) REVERT: B 1207 MET cc_start: 0.8774 (tpp) cc_final: 0.8381 (tpp) REVERT: B 1265 CYS cc_start: 0.7655 (m) cc_final: 0.7273 (m) REVERT: B 1529 MET cc_start: 0.7319 (ptm) cc_final: 0.7040 (ptt) REVERT: B 1530 MET cc_start: 0.6747 (mmt) cc_final: 0.6543 (mmm) REVERT: B 1581 PHE cc_start: 0.8672 (m-80) cc_final: 0.8463 (m-80) REVERT: B 1617 ARG cc_start: 0.7330 (mtm110) cc_final: 0.6964 (mtm-85) REVERT: C 104 ASN cc_start: 0.7721 (t0) cc_final: 0.7428 (t0) outliers start: 31 outliers final: 29 residues processed: 261 average time/residue: 0.2121 time to fit residues: 81.7572 Evaluate side-chains 262 residues out of total 1312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 233 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 21 CYS Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 150 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 196 TRP Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 255 MET Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 421 THR Chi-restraints excluded: chain B residue 750 VAL Chi-restraints excluded: chain B residue 754 PHE Chi-restraints excluded: chain B residue 767 THR Chi-restraints excluded: chain B residue 780 GLN Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 858 TRP Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 953 CYS Chi-restraints excluded: chain B residue 961 MET Chi-restraints excluded: chain B residue 976 LEU Chi-restraints excluded: chain B residue 1227 THR Chi-restraints excluded: chain B residue 1337 PHE Chi-restraints excluded: chain B residue 1429 ASP Chi-restraints excluded: chain B residue 1463 ILE Chi-restraints excluded: chain B residue 1468 ASN Chi-restraints excluded: chain B residue 1656 LEU Chi-restraints excluded: chain B residue 1722 SER Chi-restraints excluded: chain C residue 65 LEU 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: 0.7980 chunk 106 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 48 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 14 optimal weight: 10.0000 chunk 21 optimal weight: 0.2980 chunk 101 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 131 HIS ** B 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4305 r_free = 0.4305 target = 0.184280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.128316 restraints weight = 17768.445| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.47 r_work: 0.3463 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12278 Z= 0.163 Angle : 0.686 27.303 16662 Z= 0.321 Chirality : 0.066 2.293 1954 Planarity : 0.004 0.056 2031 Dihedral : 5.231 52.831 1922 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.60 % Allowed : 21.04 % Favored : 76.36 % 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: 0.52 (0.23), residues: 1457 helix: 1.39 (0.18), residues: 823 sheet: -0.19 (0.52), residues: 98 loop : -1.19 (0.28), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.001 TRP B1185 HIS 0.009 0.001 HIS B 131 PHE 0.025 0.001 PHE B1659 TYR 0.028 0.001 TYR B1488 ARG 0.003 0.000 ARG D 152 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3122.14 seconds wall clock time: 57 minutes 37.11 seconds (3457.11 seconds total)