Starting phenix.real_space_refine on Fri Mar 6 21:56:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wlt_32592/03_2026/7wlt_32592.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wlt_32592/03_2026/7wlt_32592.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wlt_32592/03_2026/7wlt_32592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wlt_32592/03_2026/7wlt_32592.map" model { file = "/net/cci-nas-00/data/ceres_data/7wlt_32592/03_2026/7wlt_32592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wlt_32592/03_2026/7wlt_32592.cif" } resolution = 3.46 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 27 5.49 5 S 195 5.16 5 C 22455 2.51 5 N 5466 2.21 5 O 5769 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 267 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33912 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 10835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1353, 10835 Classifications: {'peptide': 1353} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 57, 'TRANS': 1295} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 4, 'ARG:plan': 7, 'GLN:plan1': 6, 'GLU:plan': 6, 'HIS:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 170 Chain: "C" Number of atoms: 10835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1353, 10835 Classifications: {'peptide': 1353} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 57, 'TRANS': 1295} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 4, 'ARG:plan': 7, 'GLN:plan1': 6, 'GLU:plan': 6, 'HIS:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 170 Chain: "E" Number of atoms: 10835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1353, 10835 Classifications: {'peptide': 1353} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 85} Link IDs: {'PTRANS': 57, 'TRANS': 1295} Chain breaks: 11 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 320 Unresolved non-hydrogen angles: 411 Unresolved non-hydrogen dihedrals: 259 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'ASP:plan': 1, 'PHE:plan': 4, 'ARG:plan': 7, 'GLN:plan1': 6, 'GLU:plan': 6, 'HIS:plan': 4, 'ASN:plan1': 4, 'TYR:plan': 4} Unresolved non-hydrogen planarities: 170 Chain: "A" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 469 Unusual residues: {'PEE': 1, 'PLX': 7} Classifications: {'peptide': 1, 'undetermined': 8} Link IDs: {None: 8} Chain: "C" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 469 Unusual residues: {'PEE': 1, 'PLX': 7} Classifications: {'peptide': 1, 'undetermined': 8} Link IDs: {None: 8} Chain: "E" Number of atoms: 469 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 469 Unusual residues: {'PEE': 1, 'PLX': 7} Classifications: {'peptide': 1, 'undetermined': 8} Link IDs: {None: 8} Time building chain proxies: 8.76, per 1000 atoms: 0.26 Number of scatterers: 33912 At special positions: 0 Unit cell: (198.738, 200.934, 157.014, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 195 16.00 P 27 15.00 O 5769 8.00 N 5466 7.00 C 22455 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A1243 " - pdb=" SG CYS A1271 " distance=2.04 Simple disulfide: pdb=" SG CYS C1243 " - pdb=" SG CYS C1271 " distance=2.04 Simple disulfide: pdb=" SG CYS E1243 " - pdb=" SG CYS E1271 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.52 Conformation dependent library (CDL) restraints added in 1.2 seconds 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7794 Finding SS restraints... Secondary structure from input PDB file: 159 helices and 12 sheets defined 68.2% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 784 through 824 removed outlier: 4.180A pdb=" N ARG A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE A 810 " --> pdb=" O GLU A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 826 through 840 Processing helix chain 'A' and resid 845 through 868 removed outlier: 3.990A pdb=" N THR A 854 " --> pdb=" O SER A 850 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 950 Processing helix chain 'A' and resid 973 through 985 Processing helix chain 'A' and resid 989 through 1006 Processing helix chain 'A' and resid 1007 through 1023 removed outlier: 3.723A pdb=" N ILE A1011 " --> pdb=" O ASN A1007 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG A1023 " --> pdb=" O ALA A1019 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1053 removed outlier: 3.545A pdb=" N ILE A1029 " --> pdb=" O ARG A1025 " (cutoff:3.500A) Proline residue: A1034 - end of helix Processing helix chain 'A' and resid 1073 through 1080 Processing helix chain 'A' and resid 1093 through 1114 removed outlier: 3.935A pdb=" N ASP A1097 " --> pdb=" O ASN A1093 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1160 Processing helix chain 'A' and resid 1161 through 1176 removed outlier: 3.760A pdb=" N ARG A1176 " --> pdb=" O ALA A1172 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1201 removed outlier: 5.645A pdb=" N THR A1196 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1228 Processing helix chain 'A' and resid 1229 through 1232 Processing helix chain 'A' and resid 1242 through 1250 removed outlier: 3.790A pdb=" N ILE A1246 " --> pdb=" O PHE A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1267 Processing helix chain 'A' and resid 1280 through 1299 Processing helix chain 'A' and resid 1299 through 1365 removed outlier: 3.926A pdb=" N LEU A1303 " --> pdb=" O SER A1299 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N SER A1317 " --> pdb=" O ALA A1313 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG A1318 " --> pdb=" O LEU A1314 " (cutoff:3.500A) Processing helix chain 'A' and resid 1403 through 1408 Processing helix chain 'A' and resid 1411 through 1416 removed outlier: 3.565A pdb=" N GLU A1416 " --> pdb=" O PHE A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1494 through 1548 removed outlier: 5.252A pdb=" N HIS A1526 " --> pdb=" O ALA A1522 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS A1527 " --> pdb=" O PHE A1523 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN A1543 " --> pdb=" O TYR A1539 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU A1544 " --> pdb=" O LEU A1540 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1557 Processing helix chain 'A' and resid 1656 through 1669 removed outlier: 3.809A pdb=" N GLU A1660 " --> pdb=" O ILE A1656 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN A1669 " --> pdb=" O PHE A1665 " (cutoff:3.500A) Processing helix chain 'A' and resid 1672 through 1686 Processing helix chain 'A' and resid 1686 through 1701 Processing helix chain 'A' and resid 1704 through 1717 removed outlier: 4.895A pdb=" N LEU A1710 " --> pdb=" O ALA A1706 " (cutoff:3.500A) Proline residue: A1711 - end of helix Processing helix chain 'A' and resid 1726 through 1749 removed outlier: 3.535A pdb=" N TRP A1730 " --> pdb=" O SER A1726 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE A1749 " --> pdb=" O TYR A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1758 through 1763 Processing helix chain 'A' and resid 1769 through 1775 Processing helix chain 'A' and resid 1786 through 1803 Processing helix chain 'A' and resid 1947 through 1968 Proline residue: A1957 - end of helix Processing helix chain 'A' and resid 1976 through 1997 Processing helix chain 'A' and resid 2016 through 2041 removed outlier: 3.994A pdb=" N PHE A2022 " --> pdb=" O GLN A2018 " (cutoff:3.500A) Processing helix chain 'A' and resid 2042 through 2063 Processing helix chain 'A' and resid 2063 through 2069 Processing helix chain 'A' and resid 2076 through 2100 Processing helix chain 'A' and resid 2108 through 2112 removed outlier: 3.519A pdb=" N THR A2111 " --> pdb=" O ASN A2108 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS A2112 " --> pdb=" O PHE A2109 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2108 through 2112' Processing helix chain 'A' and resid 2115 through 2128 Processing helix chain 'A' and resid 2130 through 2143 removed outlier: 3.559A pdb=" N LEU A2134 " --> pdb=" O PHE A2130 " (cutoff:3.500A) Processing helix chain 'A' and resid 2148 through 2175 Processing helix chain 'A' and resid 2184 through 2214 Proline residue: A2206 - end of helix removed outlier: 3.665A pdb=" N ARG A2214 " --> pdb=" O MET A2210 " (cutoff:3.500A) Processing helix chain 'A' and resid 2252 through 2263 Processing helix chain 'A' and resid 2266 through 2276 removed outlier: 3.714A pdb=" N TYR A2276 " --> pdb=" O PHE A2272 " (cutoff:3.500A) Processing helix chain 'A' and resid 2277 through 2279 No H-bonds generated for 'chain 'A' and resid 2277 through 2279' Processing helix chain 'A' and resid 2297 through 2310 Processing helix chain 'A' and resid 2348 through 2358 Processing helix chain 'A' and resid 2422 through 2424 No H-bonds generated for 'chain 'A' and resid 2422 through 2424' Processing helix chain 'A' and resid 2466 through 2483 Processing helix chain 'A' and resid 2488 through 2493 removed outlier: 4.308A pdb=" N MET A2493 " --> pdb=" O HIS A2490 " (cutoff:3.500A) Processing helix chain 'A' and resid 2500 through 2517 Processing helix chain 'A' and resid 2518 through 2535 removed outlier: 3.542A pdb=" N GLU A2522 " --> pdb=" O GLU A2518 " (cutoff:3.500A) Processing helix chain 'A' and resid 2535 through 2543 Processing helix chain 'C' and resid 785 through 824 removed outlier: 4.180A pdb=" N ARG C 803 " --> pdb=" O VAL C 799 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU C 807 " --> pdb=" O ARG C 803 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE C 810 " --> pdb=" O GLU C 806 " (cutoff:3.500A) Processing helix chain 'C' and resid 826 through 840 Processing helix chain 'C' and resid 845 through 868 removed outlier: 3.990A pdb=" N THR C 854 " --> pdb=" O SER C 850 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N VAL C 855 " --> pdb=" O CYS C 851 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 950 Processing helix chain 'C' and resid 973 through 985 Processing helix chain 'C' and resid 989 through 1006 Processing helix chain 'C' and resid 1007 through 1023 removed outlier: 3.723A pdb=" N ILE C1011 " --> pdb=" O ASN C1007 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG C1023 " --> pdb=" O ALA C1019 " (cutoff:3.500A) Processing helix chain 'C' and resid 1025 through 1053 removed outlier: 3.545A pdb=" N ILE C1029 " --> pdb=" O ARG C1025 " (cutoff:3.500A) Proline residue: C1034 - end of helix Processing helix chain 'C' and resid 1073 through 1080 Processing helix chain 'C' and resid 1093 through 1114 removed outlier: 3.935A pdb=" N ASP C1097 " --> pdb=" O ASN C1093 " (cutoff:3.500A) Processing helix chain 'C' and resid 1148 through 1160 Processing helix chain 'C' and resid 1161 through 1176 removed outlier: 3.760A pdb=" N ARG C1176 " --> pdb=" O ALA C1172 " (cutoff:3.500A) Processing helix chain 'C' and resid 1180 through 1201 removed outlier: 5.646A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N THR C1197 " --> pdb=" O LEU C1193 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1228 Processing helix chain 'C' and resid 1229 through 1232 Processing helix chain 'C' and resid 1242 through 1250 removed outlier: 3.789A pdb=" N ILE C1246 " --> pdb=" O PHE C1242 " (cutoff:3.500A) Processing helix chain 'C' and resid 1263 through 1267 Processing helix chain 'C' and resid 1280 through 1299 Processing helix chain 'C' and resid 1299 through 1365 removed outlier: 3.926A pdb=" N LEU C1303 " --> pdb=" O SER C1299 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N SER C1317 " --> pdb=" O ALA C1313 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG C1318 " --> pdb=" O LEU C1314 " (cutoff:3.500A) Processing helix chain 'C' and resid 1403 through 1408 Processing helix chain 'C' and resid 1411 through 1416 removed outlier: 3.565A pdb=" N GLU C1416 " --> pdb=" O PHE C1413 " (cutoff:3.500A) Processing helix chain 'C' and resid 1494 through 1548 removed outlier: 5.252A pdb=" N HIS C1526 " --> pdb=" O ALA C1522 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N HIS C1527 " --> pdb=" O PHE C1523 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN C1543 " --> pdb=" O TYR C1539 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLU C1544 " --> pdb=" O LEU C1540 " (cutoff:3.500A) Processing helix chain 'C' and resid 1552 through 1557 Processing helix chain 'C' and resid 1656 through 1669 removed outlier: 3.810A pdb=" N GLU C1660 " --> pdb=" O ILE C1656 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN C1669 " --> pdb=" O PHE C1665 " (cutoff:3.500A) Processing helix chain 'C' and resid 1672 through 1686 Processing helix chain 'C' and resid 1686 through 1701 Processing helix chain 'C' and resid 1704 through 1717 removed outlier: 4.895A pdb=" N LEU C1710 " --> pdb=" O ALA C1706 " (cutoff:3.500A) Proline residue: C1711 - end of helix Processing helix chain 'C' and resid 1726 through 1749 removed outlier: 3.535A pdb=" N TRP C1730 " --> pdb=" O SER C1726 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE C1749 " --> pdb=" O TYR C1745 " (cutoff:3.500A) Processing helix chain 'C' and resid 1758 through 1763 Processing helix chain 'C' and resid 1769 through 1775 Processing helix chain 'C' and resid 1786 through 1803 Processing helix chain 'C' and resid 1947 through 1968 Proline residue: C1957 - end of helix Processing helix chain 'C' and resid 1976 through 1997 Processing helix chain 'C' and resid 2016 through 2041 removed outlier: 3.994A pdb=" N PHE C2022 " --> pdb=" O GLN C2018 " (cutoff:3.500A) Processing helix chain 'C' and resid 2042 through 2063 Processing helix chain 'C' and resid 2063 through 2069 Processing helix chain 'C' and resid 2076 through 2100 Processing helix chain 'C' and resid 2108 through 2112 removed outlier: 3.519A pdb=" N THR C2111 " --> pdb=" O ASN C2108 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS C2112 " --> pdb=" O PHE C2109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2108 through 2112' Processing helix chain 'C' and resid 2115 through 2128 Processing helix chain 'C' and resid 2130 through 2143 removed outlier: 3.560A pdb=" N LEU C2134 " --> pdb=" O PHE C2130 " (cutoff:3.500A) Processing helix chain 'C' and resid 2148 through 2175 Processing helix chain 'C' and resid 2184 through 2214 Proline residue: C2206 - end of helix removed outlier: 3.665A pdb=" N ARG C2214 " --> pdb=" O MET C2210 " (cutoff:3.500A) Processing helix chain 'C' and resid 2252 through 2263 Processing helix chain 'C' and resid 2266 through 2276 removed outlier: 3.714A pdb=" N TYR C2276 " --> pdb=" O PHE C2272 " (cutoff:3.500A) Processing helix chain 'C' and resid 2277 through 2279 No H-bonds generated for 'chain 'C' and resid 2277 through 2279' Processing helix chain 'C' and resid 2297 through 2310 Processing helix chain 'C' and resid 2348 through 2358 Processing helix chain 'C' and resid 2422 through 2424 No H-bonds generated for 'chain 'C' and resid 2422 through 2424' Processing helix chain 'C' and resid 2466 through 2483 Processing helix chain 'C' and resid 2488 through 2493 removed outlier: 4.308A pdb=" N MET C2493 " --> pdb=" O HIS C2490 " (cutoff:3.500A) Processing helix chain 'C' and resid 2500 through 2517 Processing helix chain 'C' and resid 2518 through 2535 removed outlier: 3.541A pdb=" N GLU C2522 " --> pdb=" O GLU C2518 " (cutoff:3.500A) Processing helix chain 'C' and resid 2535 through 2543 Processing helix chain 'E' and resid 785 through 824 removed outlier: 4.180A pdb=" N ARG E 803 " --> pdb=" O VAL E 799 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU E 807 " --> pdb=" O ARG E 803 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N PHE E 810 " --> pdb=" O GLU E 806 " (cutoff:3.500A) Processing helix chain 'E' and resid 826 through 840 Processing helix chain 'E' and resid 845 through 868 removed outlier: 3.989A pdb=" N THR E 854 " --> pdb=" O SER E 850 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL E 855 " --> pdb=" O CYS E 851 " (cutoff:3.500A) Processing helix chain 'E' and resid 924 through 950 Processing helix chain 'E' and resid 973 through 985 Processing helix chain 'E' and resid 989 through 1006 Processing helix chain 'E' and resid 1007 through 1023 removed outlier: 3.723A pdb=" N ILE E1011 " --> pdb=" O ASN E1007 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ARG E1023 " --> pdb=" O ALA E1019 " (cutoff:3.500A) Processing helix chain 'E' and resid 1025 through 1053 removed outlier: 3.545A pdb=" N ILE E1029 " --> pdb=" O ARG E1025 " (cutoff:3.500A) Proline residue: E1034 - end of helix Processing helix chain 'E' and resid 1073 through 1080 Processing helix chain 'E' and resid 1093 through 1114 removed outlier: 3.935A pdb=" N ASP E1097 " --> pdb=" O ASN E1093 " (cutoff:3.500A) Processing helix chain 'E' and resid 1148 through 1160 Processing helix chain 'E' and resid 1161 through 1176 removed outlier: 3.761A pdb=" N ARG E1176 " --> pdb=" O ALA E1172 " (cutoff:3.500A) Processing helix chain 'E' and resid 1180 through 1201 removed outlier: 5.645A pdb=" N THR E1196 " --> pdb=" O LEU E1192 " (cutoff:3.500A) removed outlier: 6.038A pdb=" N THR E1197 " --> pdb=" O LEU E1193 " (cutoff:3.500A) Processing helix chain 'E' and resid 1202 through 1228 Processing helix chain 'E' and resid 1229 through 1232 Processing helix chain 'E' and resid 1242 through 1250 removed outlier: 3.790A pdb=" N ILE E1246 " --> pdb=" O PHE E1242 " (cutoff:3.500A) Processing helix chain 'E' and resid 1263 through 1267 Processing helix chain 'E' and resid 1280 through 1299 Processing helix chain 'E' and resid 1299 through 1365 removed outlier: 3.926A pdb=" N LEU E1303 " --> pdb=" O SER E1299 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N SER E1317 " --> pdb=" O ALA E1313 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ARG E1318 " --> pdb=" O LEU E1314 " (cutoff:3.500A) Processing helix chain 'E' and resid 1403 through 1408 Processing helix chain 'E' and resid 1411 through 1416 removed outlier: 3.566A pdb=" N GLU E1416 " --> pdb=" O PHE E1413 " (cutoff:3.500A) Processing helix chain 'E' and resid 1494 through 1548 removed outlier: 5.251A pdb=" N HIS E1526 " --> pdb=" O ALA E1522 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N HIS E1527 " --> pdb=" O PHE E1523 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLN E1543 " --> pdb=" O TYR E1539 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N GLU E1544 " --> pdb=" O LEU E1540 " (cutoff:3.500A) Processing helix chain 'E' and resid 1552 through 1557 Processing helix chain 'E' and resid 1656 through 1669 removed outlier: 3.809A pdb=" N GLU E1660 " --> pdb=" O ILE E1656 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLN E1669 " --> pdb=" O PHE E1665 " (cutoff:3.500A) Processing helix chain 'E' and resid 1672 through 1686 Processing helix chain 'E' and resid 1686 through 1701 Processing helix chain 'E' and resid 1704 through 1717 removed outlier: 4.895A pdb=" N LEU E1710 " --> pdb=" O ALA E1706 " (cutoff:3.500A) Proline residue: E1711 - end of helix Processing helix chain 'E' and resid 1726 through 1749 removed outlier: 3.535A pdb=" N TRP E1730 " --> pdb=" O SER E1726 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N PHE E1749 " --> pdb=" O TYR E1745 " (cutoff:3.500A) Processing helix chain 'E' and resid 1758 through 1763 Processing helix chain 'E' and resid 1769 through 1775 Processing helix chain 'E' and resid 1786 through 1803 Processing helix chain 'E' and resid 1947 through 1968 Proline residue: E1957 - end of helix Processing helix chain 'E' and resid 1976 through 1997 Processing helix chain 'E' and resid 2016 through 2041 removed outlier: 3.994A pdb=" N PHE E2022 " --> pdb=" O GLN E2018 " (cutoff:3.500A) Processing helix chain 'E' and resid 2042 through 2063 Processing helix chain 'E' and resid 2063 through 2069 Processing helix chain 'E' and resid 2076 through 2100 Processing helix chain 'E' and resid 2108 through 2112 removed outlier: 3.519A pdb=" N THR E2111 " --> pdb=" O ASN E2108 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS E2112 " --> pdb=" O PHE E2109 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2108 through 2112' Processing helix chain 'E' and resid 2115 through 2128 Processing helix chain 'E' and resid 2130 through 2143 removed outlier: 3.559A pdb=" N LEU E2134 " --> pdb=" O PHE E2130 " (cutoff:3.500A) Processing helix chain 'E' and resid 2148 through 2175 Processing helix chain 'E' and resid 2184 through 2214 Proline residue: E2206 - end of helix removed outlier: 3.665A pdb=" N ARG E2214 " --> pdb=" O MET E2210 " (cutoff:3.500A) Processing helix chain 'E' and resid 2252 through 2263 Processing helix chain 'E' and resid 2266 through 2276 removed outlier: 3.715A pdb=" N TYR E2276 " --> pdb=" O PHE E2272 " (cutoff:3.500A) Processing helix chain 'E' and resid 2277 through 2279 No H-bonds generated for 'chain 'E' and resid 2277 through 2279' Processing helix chain 'E' and resid 2297 through 2310 Processing helix chain 'E' and resid 2348 through 2358 Processing helix chain 'E' and resid 2422 through 2424 No H-bonds generated for 'chain 'E' and resid 2422 through 2424' Processing helix chain 'E' and resid 2466 through 2483 Processing helix chain 'E' and resid 2488 through 2493 removed outlier: 4.308A pdb=" N MET E2493 " --> pdb=" O HIS E2490 " (cutoff:3.500A) Processing helix chain 'E' and resid 2500 through 2517 Processing helix chain 'E' and resid 2518 through 2535 removed outlier: 3.542A pdb=" N GLU E2522 " --> pdb=" O GLU E2518 " (cutoff:3.500A) Processing helix chain 'E' and resid 2535 through 2543 Processing sheet with id=AA1, first strand: chain 'A' and resid 2236 through 2243 removed outlier: 6.926A pdb=" N LEU A2232 " --> pdb=" O PRO A2237 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2248 through 2250 Processing sheet with id=AA3, first strand: chain 'A' and resid 2286 through 2287 Processing sheet with id=AA4, first strand: chain 'A' and resid 2366 through 2372 removed outlier: 5.231A pdb=" N VAL A2367 " --> pdb=" O ILE A2403 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE A2403 " --> pdb=" O VAL A2367 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL A2401 " --> pdb=" O PRO A2369 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU A2399 " --> pdb=" O LEU A2371 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 2236 through 2243 removed outlier: 6.926A pdb=" N LEU C2232 " --> pdb=" O PRO C2237 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 2248 through 2250 Processing sheet with id=AA7, first strand: chain 'C' and resid 2286 through 2287 Processing sheet with id=AA8, first strand: chain 'C' and resid 2366 through 2372 removed outlier: 5.231A pdb=" N VAL C2367 " --> pdb=" O ILE C2403 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE C2403 " --> pdb=" O VAL C2367 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL C2401 " --> pdb=" O PRO C2369 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU C2399 " --> pdb=" O LEU C2371 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2236 through 2243 removed outlier: 6.926A pdb=" N LEU E2232 " --> pdb=" O PRO E2237 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 2248 through 2250 Processing sheet with id=AB2, first strand: chain 'E' and resid 2286 through 2287 Processing sheet with id=AB3, first strand: chain 'E' and resid 2366 through 2372 removed outlier: 5.232A pdb=" N VAL E2367 " --> pdb=" O ILE E2403 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE E2403 " --> pdb=" O VAL E2367 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N VAL E2401 " --> pdb=" O PRO E2369 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N LEU E2399 " --> pdb=" O LEU E2371 " (cutoff:3.500A) 2140 hydrogen bonds defined for protein. 6339 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: 6.81 Time building geometry restraints manager: 4.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6384 1.33 - 1.45: 8653 1.45 - 1.57: 19286 1.57 - 1.70: 78 1.70 - 1.82: 303 Bond restraints: 34704 Sorted by residual: bond pdb=" O16 P5S A2607 " pdb=" P12 P5S A2607 " ideal model delta sigma weight residual 1.635 1.707 -0.072 2.00e-02 2.50e+03 1.29e+01 bond pdb=" O16 P5S C2608 " pdb=" P12 P5S C2608 " ideal model delta sigma weight residual 1.635 1.707 -0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C30 PEE E2608 " pdb=" O3 PEE E2608 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" C30 PEE C2607 " pdb=" O3 PEE C2607 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.27e+01 bond pdb=" O16 P5S E2609 " pdb=" P12 P5S E2609 " ideal model delta sigma weight residual 1.635 1.706 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 34699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.81: 44712 2.81 - 5.61: 1754 5.61 - 8.42: 298 8.42 - 11.22: 50 11.22 - 14.03: 25 Bond angle restraints: 46839 Sorted by residual: angle pdb=" C GLY E2463 " pdb=" N TYR E2464 " pdb=" CA TYR E2464 " ideal model delta sigma weight residual 121.54 133.16 -11.62 1.91e+00 2.74e-01 3.70e+01 angle pdb=" C GLY A2463 " pdb=" N TYR A2464 " pdb=" CA TYR A2464 " ideal model delta sigma weight residual 121.54 133.14 -11.60 1.91e+00 2.74e-01 3.69e+01 angle pdb=" C GLY C2463 " pdb=" N TYR C2464 " pdb=" CA TYR C2464 " ideal model delta sigma weight residual 121.54 133.12 -11.58 1.91e+00 2.74e-01 3.68e+01 angle pdb=" N ASN E1142 " pdb=" CA ASN E1142 " pdb=" C ASN E1142 " ideal model delta sigma weight residual 110.70 119.18 -8.48 1.55e+00 4.16e-01 2.99e+01 angle pdb=" N ASN A1142 " pdb=" CA ASN A1142 " pdb=" C ASN A1142 " ideal model delta sigma weight residual 110.70 119.16 -8.46 1.55e+00 4.16e-01 2.98e+01 ... (remaining 46834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.63: 20016 28.63 - 57.25: 957 57.25 - 85.88: 108 85.88 - 114.50: 27 114.50 - 143.13: 45 Dihedral angle restraints: 21153 sinusoidal: 9171 harmonic: 11982 Sorted by residual: dihedral pdb=" CA TYR E1259 " pdb=" C TYR E1259 " pdb=" N ASP E1260 " pdb=" CA ASP E1260 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA TYR A1259 " pdb=" C TYR A1259 " pdb=" N ASP A1260 " pdb=" CA ASP A1260 " ideal model delta harmonic sigma weight residual 180.00 158.08 21.92 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" C41 PEE E2608 " pdb=" C42 PEE E2608 " pdb=" C43 PEE E2608 " pdb=" C44 PEE E2608 " ideal model delta sinusoidal sigma weight residual 179.49 36.36 143.13 1 3.00e+01 1.11e-03 1.92e+01 ... (remaining 21150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.096: 4652 0.096 - 0.191: 464 0.191 - 0.287: 44 0.287 - 0.383: 12 0.383 - 0.479: 9 Chirality restraints: 5181 Sorted by residual: chirality pdb=" CB ILE E1722 " pdb=" CA ILE E1722 " pdb=" CG1 ILE E1722 " pdb=" CG2 ILE E1722 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.73e+00 chirality pdb=" CB ILE A1722 " pdb=" CA ILE A1722 " pdb=" CG1 ILE A1722 " pdb=" CG2 ILE A1722 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.72e+00 chirality pdb=" CB ILE C1722 " pdb=" CA ILE C1722 " pdb=" CG1 ILE C1722 " pdb=" CG2 ILE C1722 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.69e+00 ... (remaining 5178 not shown) Planarity restraints: 5667 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A1244 " 0.020 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP A1244 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP A1244 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP A1244 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A1244 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A1244 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A1244 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A1244 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A1244 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A1244 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E1244 " 0.020 2.00e-02 2.50e+03 2.10e-02 1.10e+01 pdb=" CG TRP E1244 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TRP E1244 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP E1244 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP E1244 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E1244 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP E1244 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP E1244 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP E1244 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP E1244 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C1244 " 0.020 2.00e-02 2.50e+03 2.09e-02 1.09e+01 pdb=" CG TRP C1244 " -0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP C1244 " 0.027 2.00e-02 2.50e+03 pdb=" CD2 TRP C1244 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C1244 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C1244 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C1244 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP C1244 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C1244 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP C1244 " -0.001 2.00e-02 2.50e+03 ... (remaining 5664 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 1176 2.69 - 3.25: 35414 3.25 - 3.80: 53864 3.80 - 4.35: 62502 4.35 - 4.90: 106847 Nonbonded interactions: 259803 Sorted by model distance: nonbonded pdb=" N GLU E2518 " pdb=" OE1 GLU E2518 " model vdw 2.142 3.120 nonbonded pdb=" N GLU A2518 " pdb=" OE1 GLU A2518 " model vdw 2.143 3.120 nonbonded pdb=" N GLU C2518 " pdb=" OE1 GLU C2518 " model vdw 2.143 3.120 nonbonded pdb=" O TRP E2542 " pdb=" NH2 ARG E2546 " model vdw 2.200 3.120 nonbonded pdb=" O TRP A2542 " pdb=" NH2 ARG A2546 " model vdw 2.200 3.120 ... (remaining 259798 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = (chain 'A' and resid 784 through 2605) selection = (chain 'C' and resid 784 through 2605) selection = (chain 'E' and resid 784 through 2605) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 4.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 32.520 Find NCS groups from input model: 1.030 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 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 : 0.011 0.079 34707 Z= 0.525 Angle : 1.284 14.030 46845 Z= 0.632 Chirality : 0.063 0.479 5181 Planarity : 0.007 0.074 5667 Dihedral : 17.715 143.128 13350 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 20.70 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.94 % Favored : 93.91 % Rotamer: Outliers : 0.89 % Allowed : 0.95 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.14), residues: 3987 helix: 2.60 (0.10), residues: 2646 sheet: -0.37 (0.33), residues: 261 loop : -1.97 (0.18), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.001 ARG C1664 TYR 0.029 0.003 TYR A1757 PHE 0.049 0.003 PHE E2426 TRP 0.057 0.003 TRP E1244 HIS 0.014 0.002 HIS A1145 Details of bonding type rmsd covalent geometry : bond 0.01138 (34704) covalent geometry : angle 1.28355 (46839) SS BOND : bond 0.00601 ( 3) SS BOND : angle 1.95556 ( 6) hydrogen bonds : bond 0.12519 ( 2140) hydrogen bonds : angle 5.38394 ( 6339) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 407 time to evaluate : 1.406 Fit side-chains REVERT: A 897 ASN cc_start: 0.7354 (t0) cc_final: 0.7036 (t0) REVERT: A 1142 ASN cc_start: 0.6838 (p0) cc_final: 0.6431 (p0) REVERT: A 1144 ILE cc_start: 0.8167 (pt) cc_final: 0.7904 (pt) REVERT: A 1226 MET cc_start: 0.7733 (ttm) cc_final: 0.7343 (tpp) REVERT: A 2153 MET cc_start: 0.8458 (mmm) cc_final: 0.7958 (mtt) REVERT: A 2270 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7819 (mmm) REVERT: A 2446 MET cc_start: 0.8884 (ttt) cc_final: 0.8402 (ttt) REVERT: C 1226 MET cc_start: 0.7900 (ttm) cc_final: 0.7582 (tpp) REVERT: C 1264 MET cc_start: 0.6932 (mmt) cc_final: 0.5838 (mmt) REVERT: C 1323 TYR cc_start: 0.8440 (t80) cc_final: 0.7965 (t80) REVERT: C 1495 MET cc_start: 0.3070 (mpp) cc_final: 0.1925 (ttt) REVERT: C 2061 MET cc_start: 0.8676 (tpp) cc_final: 0.8389 (tpp) REVERT: C 2153 MET cc_start: 0.8358 (mmm) cc_final: 0.7820 (mtt) REVERT: E 2061 MET cc_start: 0.8572 (tpp) cc_final: 0.8223 (tpp) REVERT: E 2153 MET cc_start: 0.8370 (mmm) cc_final: 0.7791 (mtt) outliers start: 30 outliers final: 7 residues processed: 410 average time/residue: 0.2000 time to fit residues: 138.2939 Evaluate side-chains 341 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 333 time to evaluate : 1.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1143 PHE Chi-restraints excluded: chain A residue 1238 MET Chi-restraints excluded: chain A residue 2270 MET Chi-restraints excluded: chain C residue 1143 PHE Chi-restraints excluded: chain C residue 2270 MET Chi-restraints excluded: chain E residue 1143 PHE Chi-restraints excluded: chain E residue 2270 MET Chi-restraints excluded: chain E residue 2493 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.8980 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1967 HIS ** C1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1967 HIS E1047 GLN ** E1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1967 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.134754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.101706 restraints weight = 63916.764| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.84 r_work: 0.3095 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34707 Z= 0.145 Angle : 0.665 7.973 46845 Z= 0.330 Chirality : 0.041 0.179 5181 Planarity : 0.005 0.052 5667 Dihedral : 15.778 132.489 5916 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.24 % Allowed : 8.63 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.14), residues: 3987 helix: 2.30 (0.10), residues: 2712 sheet: -0.14 (0.34), residues: 258 loop : -1.92 (0.19), residues: 1017 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1176 TYR 0.021 0.001 TYR E1803 PHE 0.024 0.002 PHE A1954 TRP 0.022 0.001 TRP C1244 HIS 0.011 0.001 HIS C1304 Details of bonding type rmsd covalent geometry : bond 0.00299 (34704) covalent geometry : angle 0.66481 (46839) SS BOND : bond 0.00235 ( 3) SS BOND : angle 0.47563 ( 6) hydrogen bonds : bond 0.05152 ( 2140) hydrogen bonds : angle 4.26564 ( 6339) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 411 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 TYR cc_start: 0.7626 (t80) cc_final: 0.7304 (t80) REVERT: A 1009 MET cc_start: 0.6327 (mmm) cc_final: 0.5973 (mmm) REVERT: A 1142 ASN cc_start: 0.7306 (p0) cc_final: 0.6807 (p0) REVERT: A 1283 ASP cc_start: 0.7931 (m-30) cc_final: 0.7714 (m-30) REVERT: A 1336 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8490 (mm-40) REVERT: A 1525 LYS cc_start: 0.8897 (tppt) cc_final: 0.8635 (tppt) REVERT: A 1664 ARG cc_start: 0.9095 (pmt170) cc_final: 0.8861 (ptt-90) REVERT: A 2139 ASP cc_start: 0.9075 (m-30) cc_final: 0.8765 (m-30) REVERT: A 2464 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.5569 (m-80) REVERT: C 1142 ASN cc_start: 0.7324 (p0) cc_final: 0.6857 (p0) REVERT: C 1144 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8154 (mp) REVERT: C 1206 GLN cc_start: 0.7820 (mt0) cc_final: 0.7536 (mt0) REVERT: C 1264 MET cc_start: 0.6729 (mmt) cc_final: 0.5651 (mmt) REVERT: C 1323 TYR cc_start: 0.8379 (t80) cc_final: 0.7948 (t80) REVERT: C 1336 GLN cc_start: 0.9165 (mm-40) cc_final: 0.8942 (mm-40) REVERT: C 1791 MET cc_start: 0.8743 (mmm) cc_final: 0.8526 (mmm) REVERT: C 2033 ILE cc_start: 0.9304 (OUTLIER) cc_final: 0.9098 (mp) REVERT: C 2061 MET cc_start: 0.9399 (tpp) cc_final: 0.9061 (tpp) REVERT: C 2139 ASP cc_start: 0.9096 (m-30) cc_final: 0.8813 (m-30) REVERT: C 2235 TYR cc_start: 0.8043 (m-80) cc_final: 0.7247 (m-80) REVERT: C 2464 TYR cc_start: 0.6766 (OUTLIER) cc_final: 0.5232 (m-80) REVERT: E 1144 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8239 (mp) REVERT: E 1336 GLN cc_start: 0.8936 (mm-40) cc_final: 0.8598 (mm-40) REVERT: E 1494 MET cc_start: 0.5472 (mmp) cc_final: 0.5199 (mmt) REVERT: E 1791 MET cc_start: 0.8841 (mmm) cc_final: 0.8640 (mmm) REVERT: E 2235 TYR cc_start: 0.8058 (m-10) cc_final: 0.7415 (m-10) REVERT: E 2464 TYR cc_start: 0.7029 (OUTLIER) cc_final: 0.5733 (m-80) outliers start: 42 outliers final: 20 residues processed: 429 average time/residue: 0.2098 time to fit residues: 150.2974 Evaluate side-chains 388 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 362 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 1350 LYS Chi-restraints excluded: chain A residue 1709 VAL Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1967 HIS Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain A residue 2486 SER Chi-restraints excluded: chain C residue 813 VAL Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 1015 CYS Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1709 VAL Chi-restraints excluded: chain C residue 1776 LEU Chi-restraints excluded: chain C residue 2033 ILE Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2486 SER Chi-restraints excluded: chain E residue 813 VAL Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 840 LEU Chi-restraints excluded: chain E residue 1144 ILE Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 310 optimal weight: 0.8980 chunk 297 optimal weight: 3.9990 chunk 367 optimal weight: 0.9990 chunk 173 optimal weight: 0.5980 chunk 208 optimal weight: 0.9980 chunk 120 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 307 optimal weight: 0.7980 chunk 336 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1047 GLN ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1503 GLN C1047 GLN ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1315 GLN C1503 GLN C1543 GLN C1967 HIS ** E1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1503 GLN E1967 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.135466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.103472 restraints weight = 63649.268| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 3.00 r_work: 0.3098 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 34707 Z= 0.130 Angle : 0.593 7.709 46845 Z= 0.297 Chirality : 0.039 0.164 5181 Planarity : 0.004 0.050 5667 Dihedral : 14.334 120.174 5895 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.71 % Allowed : 12.94 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.14), residues: 3987 helix: 2.41 (0.10), residues: 2700 sheet: -0.07 (0.34), residues: 258 loop : -1.88 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1176 TYR 0.024 0.001 TYR C1803 PHE 0.041 0.001 PHE A1954 TRP 0.015 0.001 TRP A1519 HIS 0.031 0.001 HIS A1967 Details of bonding type rmsd covalent geometry : bond 0.00270 (34704) covalent geometry : angle 0.59321 (46839) SS BOND : bond 0.00130 ( 3) SS BOND : angle 0.34562 ( 6) hydrogen bonds : bond 0.04596 ( 2140) hydrogen bonds : angle 4.00398 ( 6339) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 411 time to evaluate : 1.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1142 ASN cc_start: 0.7351 (p0) cc_final: 0.6984 (p0) REVERT: A 1143 PHE cc_start: 0.6098 (m-80) cc_final: 0.5198 (m-80) REVERT: A 1184 TYR cc_start: 0.8825 (m-10) cc_final: 0.8524 (m-10) REVERT: A 2139 ASP cc_start: 0.9034 (m-30) cc_final: 0.8755 (m-30) REVERT: A 2153 MET cc_start: 0.8772 (mmt) cc_final: 0.8335 (mtt) REVERT: A 2270 MET cc_start: 0.7317 (mmm) cc_final: 0.7025 (mmm) REVERT: A 2388 LYS cc_start: 0.8560 (mmpt) cc_final: 0.8275 (mmmt) REVERT: A 2464 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.5583 (m-80) REVERT: C 1107 GLN cc_start: 0.7551 (tm-30) cc_final: 0.7338 (tp40) REVERT: C 1142 ASN cc_start: 0.7550 (p0) cc_final: 0.7032 (p0) REVERT: C 1206 GLN cc_start: 0.7808 (mt0) cc_final: 0.7566 (mt0) REVERT: C 1264 MET cc_start: 0.6625 (mmt) cc_final: 0.6019 (mmt) REVERT: C 1323 TYR cc_start: 0.8391 (t80) cc_final: 0.8142 (t80) REVERT: C 1495 MET cc_start: 0.1884 (mpp) cc_final: 0.0973 (ttt) REVERT: C 1660 GLU cc_start: 0.8957 (pm20) cc_final: 0.8599 (pm20) REVERT: C 1664 ARG cc_start: 0.8984 (pmt170) cc_final: 0.8712 (ptt-90) REVERT: C 1791 MET cc_start: 0.8818 (mmm) cc_final: 0.8566 (mmm) REVERT: C 2061 MET cc_start: 0.9434 (tpp) cc_final: 0.9062 (tpp) REVERT: C 2139 ASP cc_start: 0.9067 (m-30) cc_final: 0.8799 (m-30) REVERT: C 2235 TYR cc_start: 0.8040 (m-80) cc_final: 0.7301 (m-80) REVERT: C 2464 TYR cc_start: 0.6914 (OUTLIER) cc_final: 0.5514 (m-80) REVERT: E 1107 GLN cc_start: 0.7783 (tm-30) cc_final: 0.7564 (tp40) REVERT: E 1142 ASN cc_start: 0.7294 (p0) cc_final: 0.6558 (p0) REVERT: E 1143 PHE cc_start: 0.6341 (m-80) cc_final: 0.5857 (m-80) REVERT: E 1525 LYS cc_start: 0.8659 (pptt) cc_final: 0.8230 (tppt) REVERT: E 1548 VAL cc_start: 0.7809 (OUTLIER) cc_final: 0.7556 (m) REVERT: E 2153 MET cc_start: 0.8721 (mmt) cc_final: 0.8513 (mtp) REVERT: E 2228 VAL cc_start: 0.9344 (OUTLIER) cc_final: 0.9046 (m) REVERT: E 2235 TYR cc_start: 0.8056 (m-80) cc_final: 0.7390 (m-10) REVERT: E 2270 MET cc_start: 0.7412 (mmm) cc_final: 0.7063 (mmm) REVERT: E 2464 TYR cc_start: 0.7041 (OUTLIER) cc_final: 0.5553 (m-80) outliers start: 58 outliers final: 26 residues processed: 445 average time/residue: 0.2088 time to fit residues: 155.1805 Evaluate side-chains 392 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 361 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 2191 MET Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain C residue 840 LEU Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 1013 HIS Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1246 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1548 VAL Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2472 SER Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 840 LEU Chi-restraints excluded: chain E residue 981 PHE Chi-restraints excluded: chain E residue 1013 HIS Chi-restraints excluded: chain E residue 1246 ILE Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1548 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 2138 MET Chi-restraints excluded: chain E residue 2228 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 30 optimal weight: 2.9990 chunk 243 optimal weight: 0.9980 chunk 296 optimal weight: 9.9990 chunk 258 optimal weight: 1.9990 chunk 376 optimal weight: 0.0770 chunk 313 optimal weight: 7.9990 chunk 64 optimal weight: 9.9990 chunk 340 optimal weight: 0.7980 chunk 353 optimal weight: 0.4980 chunk 358 optimal weight: 8.9990 chunk 135 optimal weight: 60.0000 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN A1967 HIS C 910 ASN C1967 HIS E 910 ASN ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1503 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.136141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.104112 restraints weight = 63653.344| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 3.11 r_work: 0.3094 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 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 : 0.003 0.034 34707 Z= 0.123 Angle : 0.578 8.819 46845 Z= 0.288 Chirality : 0.039 0.167 5181 Planarity : 0.004 0.048 5667 Dihedral : 13.660 116.057 5895 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 1.74 % Allowed : 15.13 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.14), residues: 3987 helix: 2.46 (0.10), residues: 2703 sheet: -0.00 (0.34), residues: 258 loop : -1.89 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A2546 TYR 0.014 0.001 TYR E1803 PHE 0.040 0.001 PHE E1954 TRP 0.016 0.001 TRP E1754 HIS 0.011 0.001 HIS C1304 Details of bonding type rmsd covalent geometry : bond 0.00262 (34704) covalent geometry : angle 0.57830 (46839) SS BOND : bond 0.00106 ( 3) SS BOND : angle 0.35982 ( 6) hydrogen bonds : bond 0.04262 ( 2140) hydrogen bonds : angle 3.86355 ( 6339) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 403 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1142 ASN cc_start: 0.7571 (p0) cc_final: 0.7197 (p0) REVERT: A 1495 MET cc_start: 0.2056 (mpt) cc_final: 0.1132 (ttt) REVERT: A 1525 LYS cc_start: 0.8570 (pptt) cc_final: 0.8309 (ptpt) REVERT: A 1548 VAL cc_start: 0.7610 (OUTLIER) cc_final: 0.7386 (m) REVERT: A 1754 TRP cc_start: 0.7670 (m-90) cc_final: 0.7397 (m-90) REVERT: A 2139 ASP cc_start: 0.9055 (m-30) cc_final: 0.8782 (m-30) REVERT: A 2464 TYR cc_start: 0.6954 (OUTLIER) cc_final: 0.5511 (m-80) REVERT: C 1206 GLN cc_start: 0.7891 (mt0) cc_final: 0.7618 (mt0) REVERT: C 1264 MET cc_start: 0.6378 (mmt) cc_final: 0.5930 (mmt) REVERT: C 1323 TYR cc_start: 0.8274 (t80) cc_final: 0.7767 (t80) REVERT: C 1495 MET cc_start: 0.2269 (mpp) cc_final: 0.1377 (ttt) REVERT: C 1754 TRP cc_start: 0.7470 (m-90) cc_final: 0.7165 (m-90) REVERT: C 1791 MET cc_start: 0.8874 (mmm) cc_final: 0.8627 (mmm) REVERT: C 2061 MET cc_start: 0.9463 (tpp) cc_final: 0.9025 (tpp) REVERT: C 2139 ASP cc_start: 0.9102 (m-30) cc_final: 0.8818 (m-30) REVERT: C 2235 TYR cc_start: 0.8024 (m-80) cc_final: 0.7319 (m-80) REVERT: C 2464 TYR cc_start: 0.6768 (OUTLIER) cc_final: 0.5297 (m-80) REVERT: E 1142 ASN cc_start: 0.7537 (p0) cc_final: 0.6849 (p0) REVERT: E 1494 MET cc_start: 0.5386 (mmt) cc_final: 0.5177 (mmp) REVERT: E 1525 LYS cc_start: 0.8693 (pptt) cc_final: 0.8341 (ptpt) REVERT: E 1995 PHE cc_start: 0.8224 (t80) cc_final: 0.8012 (t80) REVERT: E 2228 VAL cc_start: 0.9363 (OUTLIER) cc_final: 0.9068 (m) REVERT: E 2235 TYR cc_start: 0.8007 (m-80) cc_final: 0.7317 (m-80) REVERT: E 2270 MET cc_start: 0.7559 (mmm) cc_final: 0.7328 (mmm) REVERT: E 2464 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.5497 (m-80) outliers start: 59 outliers final: 30 residues processed: 442 average time/residue: 0.1992 time to fit residues: 146.6919 Evaluate side-chains 400 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 365 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1548 VAL Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 2191 MET Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 1013 HIS Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1246 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1548 VAL Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 840 LEU Chi-restraints excluded: chain E residue 981 PHE Chi-restraints excluded: chain E residue 1246 ILE Chi-restraints excluded: chain E residue 1322 LEU Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 2138 MET Chi-restraints excluded: chain E residue 2228 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 390 optimal weight: 5.9990 chunk 315 optimal weight: 0.9980 chunk 243 optimal weight: 0.6980 chunk 63 optimal weight: 6.9990 chunk 181 optimal weight: 1.9990 chunk 341 optimal weight: 0.9980 chunk 331 optimal weight: 0.8980 chunk 200 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 268 optimal weight: 0.7980 chunk 382 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 910 ASN A1225 ASN ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1503 GLN C1967 HIS ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1503 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.136521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.103637 restraints weight = 63766.996| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.91 r_work: 0.3101 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34707 Z= 0.121 Angle : 0.571 9.016 46845 Z= 0.284 Chirality : 0.038 0.159 5181 Planarity : 0.004 0.048 5667 Dihedral : 13.257 116.909 5895 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 2.39 % Allowed : 15.81 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.96 (0.14), residues: 3987 helix: 2.54 (0.10), residues: 2697 sheet: 0.09 (0.34), residues: 258 loop : -1.91 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C2407 TYR 0.020 0.001 TYR E1323 PHE 0.048 0.001 PHE C1954 TRP 0.010 0.001 TRP C1244 HIS 0.009 0.001 HIS C1304 Details of bonding type rmsd covalent geometry : bond 0.00259 (34704) covalent geometry : angle 0.57081 (46839) SS BOND : bond 0.00143 ( 3) SS BOND : angle 0.36831 ( 6) hydrogen bonds : bond 0.04115 ( 2140) hydrogen bonds : angle 3.80189 ( 6339) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 402 time to evaluate : 1.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1142 ASN cc_start: 0.7723 (p0) cc_final: 0.7306 (p0) REVERT: A 1238 MET cc_start: 0.8667 (mmp) cc_final: 0.8461 (mmp) REVERT: A 1495 MET cc_start: 0.2130 (mpt) cc_final: 0.1145 (ttt) REVERT: A 1525 LYS cc_start: 0.8504 (pptt) cc_final: 0.8228 (ptpt) REVERT: A 2139 ASP cc_start: 0.9033 (m-30) cc_final: 0.8762 (m-30) REVERT: A 2464 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.5508 (m-80) REVERT: C 1206 GLN cc_start: 0.7943 (mt0) cc_final: 0.7625 (mt0) REVERT: C 1495 MET cc_start: 0.2214 (mpp) cc_final: 0.1281 (ttt) REVERT: C 1754 TRP cc_start: 0.7515 (m-90) cc_final: 0.7199 (m-90) REVERT: C 1791 MET cc_start: 0.8867 (mmm) cc_final: 0.8586 (mmm) REVERT: C 2061 MET cc_start: 0.9436 (tpp) cc_final: 0.8974 (tpp) REVERT: C 2139 ASP cc_start: 0.9126 (m-30) cc_final: 0.8863 (m-30) REVERT: C 2235 TYR cc_start: 0.7975 (m-80) cc_final: 0.7285 (m-80) REVERT: C 2464 TYR cc_start: 0.6822 (OUTLIER) cc_final: 0.5471 (m-80) REVERT: E 1142 ASN cc_start: 0.7399 (p0) cc_final: 0.6975 (p0) REVERT: E 1494 MET cc_start: 0.5357 (mmt) cc_final: 0.5020 (mmp) REVERT: E 1495 MET cc_start: 0.0685 (mpp) cc_final: -0.0136 (ttt) REVERT: E 1525 LYS cc_start: 0.8741 (pptt) cc_final: 0.8383 (ptpt) REVERT: E 1995 PHE cc_start: 0.8297 (t80) cc_final: 0.8064 (t80) REVERT: E 2228 VAL cc_start: 0.9358 (OUTLIER) cc_final: 0.9072 (m) REVERT: E 2235 TYR cc_start: 0.8063 (m-80) cc_final: 0.7466 (m-80) REVERT: E 2464 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.5580 (m-80) outliers start: 81 outliers final: 36 residues processed: 459 average time/residue: 0.2092 time to fit residues: 159.5659 Evaluate side-chains 401 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 361 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 840 LEU Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 2191 MET Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 1013 HIS Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1548 VAL Chi-restraints excluded: chain C residue 1800 LEU Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2472 SER Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 981 PHE Chi-restraints excluded: chain E residue 1013 HIS Chi-restraints excluded: chain E residue 1155 VAL Chi-restraints excluded: chain E residue 1161 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1246 ILE Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1414 LEU Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 1967 HIS Chi-restraints excluded: chain E residue 2138 MET Chi-restraints excluded: chain E residue 2228 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 237 optimal weight: 0.8980 chunk 304 optimal weight: 6.9990 chunk 52 optimal weight: 6.9990 chunk 126 optimal weight: 6.9990 chunk 356 optimal weight: 0.9990 chunk 131 optimal weight: 0.9980 chunk 226 optimal weight: 0.0570 chunk 224 optimal weight: 0.9990 chunk 276 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 chunk 163 optimal weight: 10.0000 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1699 HIS C1967 HIS ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.136522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.104004 restraints weight = 63415.648| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 2.94 r_work: 0.3105 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34707 Z= 0.118 Angle : 0.566 8.378 46845 Z= 0.283 Chirality : 0.038 0.169 5181 Planarity : 0.004 0.047 5667 Dihedral : 13.037 122.750 5895 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.07 % Allowed : 16.46 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.00 (0.14), residues: 3987 helix: 2.58 (0.10), residues: 2694 sheet: 0.09 (0.34), residues: 258 loop : -1.91 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C2407 TYR 0.017 0.001 TYR E1323 PHE 0.054 0.001 PHE E1954 TRP 0.010 0.001 TRP A2429 HIS 0.009 0.001 HIS C1304 Details of bonding type rmsd covalent geometry : bond 0.00253 (34704) covalent geometry : angle 0.56652 (46839) SS BOND : bond 0.00126 ( 3) SS BOND : angle 0.34644 ( 6) hydrogen bonds : bond 0.03998 ( 2140) hydrogen bonds : angle 3.74529 ( 6339) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 395 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1495 MET cc_start: 0.2350 (mpt) cc_final: 0.1380 (ttt) REVERT: A 1525 LYS cc_start: 0.8513 (pptt) cc_final: 0.8278 (ptpt) REVERT: A 1754 TRP cc_start: 0.7843 (m-90) cc_final: 0.7543 (m-90) REVERT: A 2133 GLU cc_start: 0.8872 (mp0) cc_final: 0.8649 (mp0) REVERT: A 2139 ASP cc_start: 0.9069 (m-30) cc_final: 0.8780 (m-30) REVERT: A 2281 ILE cc_start: 0.9270 (mt) cc_final: 0.8949 (mt) REVERT: A 2388 LYS cc_start: 0.8613 (mmpt) cc_final: 0.8269 (mmmt) REVERT: A 2464 TYR cc_start: 0.7014 (OUTLIER) cc_final: 0.5358 (m-80) REVERT: C 838 PHE cc_start: 0.7649 (OUTLIER) cc_final: 0.7089 (m-80) REVERT: C 1206 GLN cc_start: 0.8016 (mt0) cc_final: 0.7689 (mt0) REVERT: C 1495 MET cc_start: 0.2187 (mpp) cc_final: 0.1256 (ttt) REVERT: C 1502 MET cc_start: 0.6619 (ppp) cc_final: 0.6285 (ppp) REVERT: C 1754 TRP cc_start: 0.7514 (m-90) cc_final: 0.7188 (m-90) REVERT: C 1791 MET cc_start: 0.8901 (mmm) cc_final: 0.8621 (mmm) REVERT: C 1800 LEU cc_start: 0.8023 (OUTLIER) cc_final: 0.7792 (mt) REVERT: C 2061 MET cc_start: 0.9421 (tpp) cc_final: 0.8989 (tpp) REVERT: C 2139 ASP cc_start: 0.9157 (m-30) cc_final: 0.8847 (m-30) REVERT: C 2153 MET cc_start: 0.8990 (mmp) cc_final: 0.8387 (mtp) REVERT: C 2179 LYS cc_start: 0.7885 (mttm) cc_final: 0.7635 (mttp) REVERT: C 2235 TYR cc_start: 0.7931 (m-80) cc_final: 0.7283 (m-80) REVERT: C 2308 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8500 (mp) REVERT: C 2464 TYR cc_start: 0.6847 (OUTLIER) cc_final: 0.5387 (m-80) REVERT: E 1494 MET cc_start: 0.5326 (mmt) cc_final: 0.4945 (mmp) REVERT: E 1495 MET cc_start: 0.0707 (mpp) cc_final: -0.0113 (ttt) REVERT: E 1525 LYS cc_start: 0.8721 (pptt) cc_final: 0.8362 (ptpt) REVERT: E 2061 MET cc_start: 0.9349 (tpp) cc_final: 0.9081 (tpp) REVERT: E 2228 VAL cc_start: 0.9361 (OUTLIER) cc_final: 0.9074 (m) REVERT: E 2235 TYR cc_start: 0.8017 (m-80) cc_final: 0.7438 (m-80) REVERT: E 2270 MET cc_start: 0.7255 (mmm) cc_final: 0.6918 (mmm) REVERT: E 2464 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.5485 (m-80) outliers start: 70 outliers final: 38 residues processed: 441 average time/residue: 0.2114 time to fit residues: 154.9539 Evaluate side-chains 411 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 366 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1013 HIS Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 2191 MET Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 838 PHE Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1235 VAL Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1548 VAL Chi-restraints excluded: chain C residue 1800 LEU Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2308 LEU Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2472 SER Chi-restraints excluded: chain C residue 2493 MET Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 981 PHE Chi-restraints excluded: chain E residue 1022 THR Chi-restraints excluded: chain E residue 1155 VAL Chi-restraints excluded: chain E residue 1161 LEU Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1414 LEU Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 1967 HIS Chi-restraints excluded: chain E residue 2138 MET Chi-restraints excluded: chain E residue 2228 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 49 optimal weight: 9.9990 chunk 373 optimal weight: 6.9990 chunk 317 optimal weight: 5.9990 chunk 117 optimal weight: 0.9980 chunk 242 optimal weight: 0.0060 chunk 123 optimal weight: 0.9980 chunk 251 optimal weight: 0.0980 chunk 397 optimal weight: 3.9990 chunk 141 optimal weight: 0.0980 chunk 351 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1699 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1967 HIS ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1543 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.138314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.107281 restraints weight = 63757.439| |-----------------------------------------------------------------------------| r_work (start): 0.3403 rms_B_bonded: 3.02 r_work: 0.3146 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 34707 Z= 0.110 Angle : 0.569 10.204 46845 Z= 0.281 Chirality : 0.038 0.158 5181 Planarity : 0.004 0.046 5667 Dihedral : 12.621 127.122 5895 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.04 % Allowed : 16.99 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.14), residues: 3987 helix: 2.59 (0.10), residues: 2697 sheet: 0.12 (0.34), residues: 258 loop : -1.88 (0.18), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C2407 TYR 0.016 0.001 TYR E1323 PHE 0.052 0.001 PHE E1954 TRP 0.012 0.001 TRP E1754 HIS 0.009 0.001 HIS E1304 Details of bonding type rmsd covalent geometry : bond 0.00227 (34704) covalent geometry : angle 0.56944 (46839) SS BOND : bond 0.00144 ( 3) SS BOND : angle 0.37399 ( 6) hydrogen bonds : bond 0.03718 ( 2140) hydrogen bonds : angle 3.66857 ( 6339) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 399 time to evaluate : 1.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 838 PHE cc_start: 0.7716 (OUTLIER) cc_final: 0.7221 (m-80) REVERT: A 1350 LYS cc_start: 0.9090 (tmmt) cc_final: 0.8838 (tppp) REVERT: A 1495 MET cc_start: 0.2345 (mpt) cc_final: 0.1387 (ttt) REVERT: A 1525 LYS cc_start: 0.8585 (pptt) cc_final: 0.8360 (ptpt) REVERT: A 1754 TRP cc_start: 0.7833 (m-90) cc_final: 0.7566 (m-90) REVERT: A 1800 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7631 (mt) REVERT: A 2139 ASP cc_start: 0.9034 (m-30) cc_final: 0.8757 (m-30) REVERT: A 2235 TYR cc_start: 0.7608 (m-80) cc_final: 0.7083 (m-80) REVERT: A 2308 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8572 (mt) REVERT: A 2464 TYR cc_start: 0.7086 (OUTLIER) cc_final: 0.5119 (m-80) REVERT: C 1206 GLN cc_start: 0.7952 (mt0) cc_final: 0.7644 (mt0) REVERT: C 1495 MET cc_start: 0.2305 (mpp) cc_final: 0.1351 (ttt) REVERT: C 1502 MET cc_start: 0.6792 (ppp) cc_final: 0.6546 (ppp) REVERT: C 1791 MET cc_start: 0.8872 (mmm) cc_final: 0.8596 (mmm) REVERT: C 1800 LEU cc_start: 0.7996 (OUTLIER) cc_final: 0.7792 (mt) REVERT: C 2061 MET cc_start: 0.9366 (tpp) cc_final: 0.8941 (tpp) REVERT: C 2153 MET cc_start: 0.8901 (mmp) cc_final: 0.8418 (mtp) REVERT: C 2179 LYS cc_start: 0.7906 (mttm) cc_final: 0.7668 (mttp) REVERT: C 2464 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.5169 (m-80) REVERT: E 1226 MET cc_start: 0.7644 (tpp) cc_final: 0.7368 (tpp) REVERT: E 1238 MET cc_start: 0.8415 (mmp) cc_final: 0.8214 (mmp) REVERT: E 1495 MET cc_start: 0.0464 (mpp) cc_final: -0.0265 (ttt) REVERT: E 1525 LYS cc_start: 0.8617 (pptt) cc_final: 0.8321 (ptpt) REVERT: E 1791 MET cc_start: 0.8928 (mmm) cc_final: 0.8693 (mmm) REVERT: E 1800 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7874 (mt) REVERT: E 2061 MET cc_start: 0.9227 (tpp) cc_final: 0.8975 (tpp) REVERT: E 2235 TYR cc_start: 0.7861 (m-80) cc_final: 0.7284 (m-80) REVERT: E 2270 MET cc_start: 0.7143 (mmm) cc_final: 0.6822 (mmm) REVERT: E 2464 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.5142 (m-80) outliers start: 69 outliers final: 35 residues processed: 444 average time/residue: 0.2105 time to fit residues: 155.6450 Evaluate side-chains 406 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 363 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1800 LEU Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 1153 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1157 VAL Chi-restraints excluded: chain C residue 1235 VAL Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1548 VAL Chi-restraints excluded: chain C residue 1800 LEU Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2472 SER Chi-restraints excluded: chain C residue 2493 MET Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 981 PHE Chi-restraints excluded: chain E residue 1022 THR Chi-restraints excluded: chain E residue 1155 VAL Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1342 LEU Chi-restraints excluded: chain E residue 1414 LEU Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 1800 LEU Chi-restraints excluded: chain E residue 1967 HIS Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 75 optimal weight: 0.0870 chunk 375 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 56 optimal weight: 7.9990 chunk 259 optimal weight: 0.9990 chunk 209 optimal weight: 5.9990 chunk 313 optimal weight: 0.2980 chunk 262 optimal weight: 1.9990 chunk 301 optimal weight: 1.9990 chunk 334 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1967 HIS ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.137023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.105692 restraints weight = 63336.819| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 2.95 r_work: 0.3125 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 34707 Z= 0.120 Angle : 0.581 10.059 46845 Z= 0.287 Chirality : 0.039 0.184 5181 Planarity : 0.004 0.045 5667 Dihedral : 12.450 125.086 5895 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 1.92 % Allowed : 17.85 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.14), residues: 3987 helix: 2.60 (0.10), residues: 2697 sheet: 0.11 (0.34), residues: 258 loop : -1.88 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C2407 TYR 0.029 0.001 TYR A1539 PHE 0.048 0.001 PHE A1954 TRP 0.015 0.001 TRP C1754 HIS 0.009 0.001 HIS A1304 Details of bonding type rmsd covalent geometry : bond 0.00261 (34704) covalent geometry : angle 0.58115 (46839) SS BOND : bond 0.00127 ( 3) SS BOND : angle 0.40441 ( 6) hydrogen bonds : bond 0.03840 ( 2140) hydrogen bonds : angle 3.67254 ( 6339) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 381 time to evaluate : 1.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 838 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.7319 (m-80) REVERT: A 1143 PHE cc_start: 0.6499 (m-80) cc_final: 0.5800 (t80) REVERT: A 1350 LYS cc_start: 0.9071 (tmmt) cc_final: 0.8846 (tppp) REVERT: A 1495 MET cc_start: 0.2425 (mpt) cc_final: 0.1459 (ttt) REVERT: A 1525 LYS cc_start: 0.8547 (pptt) cc_final: 0.8323 (ptpt) REVERT: A 1754 TRP cc_start: 0.7852 (m-90) cc_final: 0.7385 (m-90) REVERT: A 2139 ASP cc_start: 0.9080 (m-30) cc_final: 0.8779 (m-30) REVERT: A 2308 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8639 (mp) REVERT: A 2388 LYS cc_start: 0.8695 (tppt) cc_final: 0.8317 (tppt) REVERT: A 2464 TYR cc_start: 0.7103 (OUTLIER) cc_final: 0.5346 (m-80) REVERT: C 1206 GLN cc_start: 0.7931 (mt0) cc_final: 0.7608 (mt0) REVERT: C 1264 MET cc_start: 0.6414 (mmt) cc_final: 0.6061 (mtt) REVERT: C 1495 MET cc_start: 0.2559 (mpp) cc_final: 0.1562 (ttt) REVERT: C 1502 MET cc_start: 0.6792 (ppp) cc_final: 0.6580 (ppp) REVERT: C 1791 MET cc_start: 0.8913 (mmm) cc_final: 0.8642 (mmm) REVERT: C 1800 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7797 (mt) REVERT: C 2061 MET cc_start: 0.9354 (tpp) cc_final: 0.8903 (tpp) REVERT: C 2139 ASP cc_start: 0.9083 (m-30) cc_final: 0.8737 (m-30) REVERT: C 2153 MET cc_start: 0.8935 (mmp) cc_final: 0.8466 (mtp) REVERT: C 2235 TYR cc_start: 0.7917 (m-80) cc_final: 0.7297 (m-80) REVERT: C 2308 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8476 (mp) REVERT: C 2464 TYR cc_start: 0.6778 (OUTLIER) cc_final: 0.5263 (m-80) REVERT: E 1143 PHE cc_start: 0.6470 (m-80) cc_final: 0.6057 (m-80) REVERT: E 1226 MET cc_start: 0.7657 (tpp) cc_final: 0.7361 (tpp) REVERT: E 1238 MET cc_start: 0.8374 (mmp) cc_final: 0.8156 (mmp) REVERT: E 1494 MET cc_start: 0.5630 (mmp) cc_final: 0.5148 (mmt) REVERT: E 1495 MET cc_start: 0.0595 (mpp) cc_final: -0.0222 (ttt) REVERT: E 1525 LYS cc_start: 0.8641 (pptt) cc_final: 0.8365 (ptpt) REVERT: E 1800 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7857 (mt) REVERT: E 2061 MET cc_start: 0.9230 (tpp) cc_final: 0.8968 (tpp) REVERT: E 2235 TYR cc_start: 0.8010 (m-80) cc_final: 0.7400 (m-80) REVERT: E 2270 MET cc_start: 0.7260 (mmm) cc_final: 0.7009 (mmm) REVERT: E 2464 TYR cc_start: 0.7136 (OUTLIER) cc_final: 0.5355 (m-80) REVERT: E 2518 GLU cc_start: 0.8241 (mp0) cc_final: 0.7916 (mp0) outliers start: 65 outliers final: 43 residues processed: 425 average time/residue: 0.2128 time to fit residues: 150.3555 Evaluate side-chains 417 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 366 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1530 MET Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1967 HIS Chi-restraints excluded: chain A residue 2191 MET Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 1153 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1235 VAL Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1407 ILE Chi-restraints excluded: chain C residue 1548 VAL Chi-restraints excluded: chain C residue 1800 LEU Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2308 LEU Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2472 SER Chi-restraints excluded: chain C residue 2493 MET Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 981 PHE Chi-restraints excluded: chain E residue 1022 THR Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1246 ILE Chi-restraints excluded: chain E residue 1342 LEU Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1414 LEU Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 1800 LEU Chi-restraints excluded: chain E residue 2191 MET Chi-restraints excluded: chain E residue 2228 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 86 optimal weight: 0.8980 chunk 142 optimal weight: 6.9990 chunk 361 optimal weight: 2.9990 chunk 123 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 133 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 209 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 258 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1967 HIS ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.133832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.102245 restraints weight = 63368.969| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.92 r_work: 0.3065 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 34707 Z= 0.160 Angle : 0.622 10.075 46845 Z= 0.309 Chirality : 0.040 0.181 5181 Planarity : 0.004 0.046 5667 Dihedral : 12.661 116.637 5895 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.13 % Allowed : 18.11 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.14), residues: 3987 helix: 2.58 (0.10), residues: 2673 sheet: 0.03 (0.34), residues: 258 loop : -1.87 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG C2407 TYR 0.024 0.001 TYR A1539 PHE 0.050 0.002 PHE A1954 TRP 0.013 0.001 TRP C2082 HIS 0.010 0.001 HIS E1304 Details of bonding type rmsd covalent geometry : bond 0.00372 (34704) covalent geometry : angle 0.62216 (46839) SS BOND : bond 0.00065 ( 3) SS BOND : angle 0.37271 ( 6) hydrogen bonds : bond 0.04351 ( 2140) hydrogen bonds : angle 3.83971 ( 6339) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 368 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 838 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.7573 (m-80) REVERT: A 1350 LYS cc_start: 0.9093 (tmmt) cc_final: 0.8873 (tppp) REVERT: A 1495 MET cc_start: 0.2368 (mpt) cc_final: 0.1364 (ttt) REVERT: A 1525 LYS cc_start: 0.8592 (pptt) cc_final: 0.8365 (ptpt) REVERT: A 2139 ASP cc_start: 0.9138 (m-30) cc_final: 0.8880 (m-30) REVERT: A 2281 ILE cc_start: 0.9162 (mt) cc_final: 0.8911 (mt) REVERT: A 2308 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8655 (mp) REVERT: A 2464 TYR cc_start: 0.6988 (OUTLIER) cc_final: 0.5170 (m-80) REVERT: C 1206 GLN cc_start: 0.7883 (mt0) cc_final: 0.7583 (mt0) REVERT: C 1495 MET cc_start: 0.2343 (mpp) cc_final: 0.1489 (ttt) REVERT: C 1525 LYS cc_start: 0.8540 (pptt) cc_final: 0.8090 (ptpt) REVERT: C 1791 MET cc_start: 0.8914 (mmm) cc_final: 0.8660 (mmm) REVERT: C 1800 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7853 (mt) REVERT: C 2061 MET cc_start: 0.9399 (tpp) cc_final: 0.8934 (tpp) REVERT: C 2139 ASP cc_start: 0.9106 (m-30) cc_final: 0.8742 (m-30) REVERT: C 2153 MET cc_start: 0.8957 (mmp) cc_final: 0.8484 (mtp) REVERT: C 2235 TYR cc_start: 0.8251 (m-80) cc_final: 0.7520 (m-80) REVERT: C 2308 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8394 (mp) REVERT: C 2464 TYR cc_start: 0.6752 (OUTLIER) cc_final: 0.5111 (m-80) REVERT: E 1494 MET cc_start: 0.5291 (mmp) cc_final: 0.5062 (mmp) REVERT: E 1495 MET cc_start: 0.2047 (mpp) cc_final: 0.1048 (ttt) REVERT: E 1525 LYS cc_start: 0.8671 (pptt) cc_final: 0.8404 (ptpt) REVERT: E 2061 MET cc_start: 0.9360 (tpp) cc_final: 0.9026 (tpp) REVERT: E 2235 TYR cc_start: 0.8387 (m-80) cc_final: 0.7903 (m-80) REVERT: E 2464 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.5257 (m-80) REVERT: E 2518 GLU cc_start: 0.8296 (mp0) cc_final: 0.8004 (mp0) outliers start: 72 outliers final: 47 residues processed: 419 average time/residue: 0.2147 time to fit residues: 149.3073 Evaluate side-chains 404 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 350 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 838 PHE Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1298 LEU Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1530 MET Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1967 HIS Chi-restraints excluded: chain A residue 2191 MET Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 1013 HIS Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1153 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1251 LEU Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1414 LEU Chi-restraints excluded: chain C residue 1548 VAL Chi-restraints excluded: chain C residue 1800 LEU Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2308 LEU Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2472 SER Chi-restraints excluded: chain C residue 2493 MET Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 981 PHE Chi-restraints excluded: chain E residue 1013 HIS Chi-restraints excluded: chain E residue 1155 VAL Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1246 ILE Chi-restraints excluded: chain E residue 1342 LEU Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 1967 HIS Chi-restraints excluded: chain E residue 1982 LEU Chi-restraints excluded: chain E residue 2138 MET Chi-restraints excluded: chain E residue 2228 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 114 optimal weight: 3.9990 chunk 55 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 7.9990 chunk 239 optimal weight: 0.6980 chunk 84 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 173 optimal weight: 2.9990 chunk 247 optimal weight: 2.9990 chunk 342 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1967 HIS ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.134110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.102591 restraints weight = 63883.337| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 3.00 r_work: 0.3067 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 34707 Z= 0.150 Angle : 0.626 10.173 46845 Z= 0.309 Chirality : 0.040 0.175 5181 Planarity : 0.004 0.045 5667 Dihedral : 12.728 116.146 5895 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 1.65 % Allowed : 18.59 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.94 (0.14), residues: 3987 helix: 2.56 (0.10), residues: 2673 sheet: -0.01 (0.34), residues: 258 loop : -1.89 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C2407 TYR 0.021 0.001 TYR A1539 PHE 0.056 0.002 PHE E1954 TRP 0.015 0.001 TRP C1754 HIS 0.022 0.001 HIS A1304 Details of bonding type rmsd covalent geometry : bond 0.00345 (34704) covalent geometry : angle 0.62568 (46839) SS BOND : bond 0.00062 ( 3) SS BOND : angle 0.38039 ( 6) hydrogen bonds : bond 0.04269 ( 2140) hydrogen bonds : angle 3.82903 ( 6339) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7974 Ramachandran restraints generated. 3987 Oldfield, 0 Emsley, 3987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 363 time to evaluate : 1.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1143 PHE cc_start: 0.6966 (m-80) cc_final: 0.6157 (t80) REVERT: A 1350 LYS cc_start: 0.9101 (tmmt) cc_final: 0.8879 (tppp) REVERT: A 1495 MET cc_start: 0.2604 (mpt) cc_final: 0.1632 (ttt) REVERT: A 1525 LYS cc_start: 0.8606 (pptt) cc_final: 0.8399 (ptpt) REVERT: A 2139 ASP cc_start: 0.9149 (m-30) cc_final: 0.8900 (m-30) REVERT: A 2281 ILE cc_start: 0.9207 (mt) cc_final: 0.8956 (mt) REVERT: A 2308 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8638 (mp) REVERT: A 2464 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.5429 (m-80) REVERT: C 1206 GLN cc_start: 0.7937 (mt0) cc_final: 0.7596 (mt0) REVERT: C 1276 GLU cc_start: 0.8140 (pm20) cc_final: 0.7441 (tp30) REVERT: C 1495 MET cc_start: 0.2509 (mpp) cc_final: 0.1697 (ttt) REVERT: C 1995 PHE cc_start: 0.8104 (t80) cc_final: 0.7835 (t80) REVERT: C 2061 MET cc_start: 0.9426 (tpp) cc_final: 0.8978 (tpp) REVERT: C 2153 MET cc_start: 0.8937 (mmp) cc_final: 0.8519 (mtp) REVERT: C 2235 TYR cc_start: 0.8172 (m-80) cc_final: 0.7465 (m-80) REVERT: C 2308 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8431 (mp) REVERT: C 2464 TYR cc_start: 0.6850 (OUTLIER) cc_final: 0.5174 (m-80) REVERT: E 1226 MET cc_start: 0.7768 (tpp) cc_final: 0.7478 (tpp) REVERT: E 1238 MET cc_start: 0.8497 (mmp) cc_final: 0.8128 (mmp) REVERT: E 1494 MET cc_start: 0.5467 (mmp) cc_final: 0.5254 (mmp) REVERT: E 1495 MET cc_start: 0.1465 (mpp) cc_final: 0.0502 (ttt) REVERT: E 1525 LYS cc_start: 0.8653 (pptt) cc_final: 0.8382 (ptpt) REVERT: E 2061 MET cc_start: 0.9397 (tpp) cc_final: 0.9088 (tpp) REVERT: E 2235 TYR cc_start: 0.8310 (m-80) cc_final: 0.7823 (m-80) REVERT: E 2464 TYR cc_start: 0.7087 (OUTLIER) cc_final: 0.5205 (m-80) REVERT: E 2518 GLU cc_start: 0.8271 (mp0) cc_final: 0.7958 (mp0) outliers start: 56 outliers final: 41 residues processed: 399 average time/residue: 0.2098 time to fit residues: 139.5426 Evaluate side-chains 401 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 355 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 981 PHE Chi-restraints excluded: chain A residue 1022 THR Chi-restraints excluded: chain A residue 1167 VAL Chi-restraints excluded: chain A residue 1246 ILE Chi-restraints excluded: chain A residue 1251 LEU Chi-restraints excluded: chain A residue 1342 LEU Chi-restraints excluded: chain A residue 1407 ILE Chi-restraints excluded: chain A residue 1731 MET Chi-restraints excluded: chain A residue 1798 SER Chi-restraints excluded: chain A residue 1967 HIS Chi-restraints excluded: chain A residue 2191 MET Chi-restraints excluded: chain A residue 2308 LEU Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2464 TYR Chi-restraints excluded: chain C residue 822 LEU Chi-restraints excluded: chain C residue 825 VAL Chi-restraints excluded: chain C residue 981 PHE Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1246 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1414 LEU Chi-restraints excluded: chain C residue 1548 VAL Chi-restraints excluded: chain C residue 1776 LEU Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2251 PHE Chi-restraints excluded: chain C residue 2308 LEU Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2472 SER Chi-restraints excluded: chain C residue 2493 MET Chi-restraints excluded: chain E residue 825 VAL Chi-restraints excluded: chain E residue 838 PHE Chi-restraints excluded: chain E residue 981 PHE Chi-restraints excluded: chain E residue 1155 VAL Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1246 ILE Chi-restraints excluded: chain E residue 1342 LEU Chi-restraints excluded: chain E residue 1516 LEU Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 1967 HIS Chi-restraints excluded: chain E residue 1982 LEU Chi-restraints excluded: chain E residue 2138 MET Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2464 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 338 optimal weight: 0.9990 chunk 399 optimal weight: 1.9990 chunk 257 optimal weight: 0.0070 chunk 344 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 315 optimal weight: 0.9980 chunk 258 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 339 optimal weight: 0.0370 chunk 364 optimal weight: 0.6980 chunk 15 optimal weight: 30.0000 overall best weight: 0.4476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1239 GLN ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1344 GLN C1239 GLN C1699 HIS C1967 HIS ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1344 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.137421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.106218 restraints weight = 62929.692| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.95 r_work: 0.3132 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 34707 Z= 0.114 Angle : 0.604 10.149 46845 Z= 0.295 Chirality : 0.038 0.172 5181 Planarity : 0.004 0.045 5667 Dihedral : 12.406 120.502 5895 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 1.48 % Allowed : 18.97 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.14), residues: 3987 helix: 2.56 (0.10), residues: 2694 sheet: 0.04 (0.33), residues: 258 loop : -1.91 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C2407 TYR 0.020 0.001 TYR A1539 PHE 0.055 0.001 PHE A1954 TRP 0.014 0.001 TRP C1754 HIS 0.020 0.001 HIS A1304 Details of bonding type rmsd covalent geometry : bond 0.00239 (34704) covalent geometry : angle 0.60408 (46839) SS BOND : bond 0.00168 ( 3) SS BOND : angle 0.44510 ( 6) hydrogen bonds : bond 0.03762 ( 2140) hydrogen bonds : angle 3.69354 ( 6339) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9499.99 seconds wall clock time: 163 minutes 2.85 seconds (9782.85 seconds total)