Starting phenix.real_space_refine on Sun Jun 29 21:03:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wlt_32592/06_2025/7wlt_32592.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wlt_32592/06_2025/7wlt_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_32592/06_2025/7wlt_32592.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wlt_32592/06_2025/7wlt_32592.map" model { file = "/net/cci-nas-00/data/ceres_data/7wlt_32592/06_2025/7wlt_32592.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wlt_32592/06_2025/7wlt_32592.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.83s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 6, 'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} 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: {'GLN:plan1': 6, 'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} 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: {'GLN:plan1': 6, 'ASP:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'HIS:plan': 4, 'PHE:plan': 4, 'GLU:plan': 6, 'ARG:plan': 7} 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: 19.22, per 1000 atoms: 0.57 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: 8.80 Conformation dependent library (CDL) restraints added in 3.8 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: 3.23 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: 11.99 Time building geometry restraints manager: 10.32 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: 0.10 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 784 through 2547 or resid 2601 through 2605)) selection = (chain 'C' and (resid 784 through 2547 or resid 2601 through 2605)) selection = (chain 'E' and (resid 784 through 2547 or resid 2601 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: 3.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.410 Check model and map are aligned: 0.240 Set scattering table: 0.280 Process input model: 71.160 Find NCS groups from input model: 2.090 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 80.980 ------------------------------------------------------------------------------- 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 : 20.69 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (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 TRP 0.057 0.003 TRP E1244 HIS 0.014 0.002 HIS A1145 PHE 0.049 0.003 PHE E2426 TYR 0.029 0.003 TYR A1757 ARG 0.025 0.001 ARG C1664 Details of bonding type rmsd hydrogen bonds : bond 0.12519 ( 2140) hydrogen bonds : angle 5.38394 ( 6339) SS BOND : bond 0.00601 ( 3) SS BOND : angle 1.95556 ( 6) covalent geometry : bond 0.01138 (34704) covalent geometry : angle 1.28355 (46839) *********************** 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 : 3.668 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: 0.7957 (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: 0.7583 (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: 0.1924 (ttt) REVERT: C 2061 MET cc_start: 0.8676 (tpp) cc_final: 0.8388 (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: 0.8222 (tpp) REVERT: E 2153 MET cc_start: 0.8370 (mmm) cc_final: 0.7792 (mtt) outliers start: 30 outliers final: 7 residues processed: 410 average time/residue: 0.4309 time to fit residues: 296.2583 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 : 3.990 ------------------------------------------------------------------------------- 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 341 optimal weight: 0.7980 chunk 306 optimal weight: 4.9990 chunk 170 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 317 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 236 optimal weight: 0.9980 chunk 367 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.134168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.101036 restraints weight = 63616.662| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.83 r_work: 0.3087 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1504 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= 0.150 Angle : 0.668 7.953 46845 Z= 0.333 Chirality : 0.041 0.181 5181 Planarity : 0.005 0.052 5667 Dihedral : 15.950 133.024 5916 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.15 % Allowed : 8.66 % Favored : 90.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.14), residues: 3987 helix: 2.36 (0.10), residues: 2694 sheet: -0.14 (0.34), residues: 258 loop : -1.88 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C1244 HIS 0.011 0.001 HIS C1304 PHE 0.026 0.002 PHE A2426 TYR 0.019 0.001 TYR E1539 ARG 0.004 0.000 ARG C1664 Details of bonding type rmsd hydrogen bonds : bond 0.05312 ( 2140) hydrogen bonds : angle 4.29411 ( 6339) SS BOND : bond 0.00224 ( 3) SS BOND : angle 0.49437 ( 6) covalent geometry : bond 0.00313 (34704) covalent geometry : angle 0.66830 (46839) *********************** 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 443 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 404 time to evaluate : 4.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 816 TYR cc_start: 0.7618 (t80) cc_final: 0.7376 (t80) REVERT: A 1009 MET cc_start: 0.6368 (mmm) cc_final: 0.6014 (mmm) REVERT: A 1142 ASN cc_start: 0.7249 (p0) cc_final: 0.6727 (p0) REVERT: A 1525 LYS cc_start: 0.8874 (tppt) cc_final: 0.8626 (tppt) REVERT: A 1664 ARG cc_start: 0.9095 (pmt170) cc_final: 0.8867 (ptt-90) REVERT: A 2139 ASP cc_start: 0.9084 (m-30) cc_final: 0.8757 (m-30) REVERT: A 2270 MET cc_start: 0.7793 (mmm) cc_final: 0.7587 (mmm) REVERT: A 2464 TYR cc_start: 0.6967 (OUTLIER) cc_final: 0.5552 (m-80) REVERT: C 1142 ASN cc_start: 0.7293 (p0) cc_final: 0.6822 (p0) REVERT: C 1144 ILE cc_start: 0.8484 (OUTLIER) cc_final: 0.8154 (mp) REVERT: C 1206 GLN cc_start: 0.7766 (mt0) cc_final: 0.7512 (mt0) REVERT: C 1264 MET cc_start: 0.6748 (mmt) cc_final: 0.5728 (mmt) REVERT: C 1323 TYR cc_start: 0.8358 (t80) cc_final: 0.7952 (t80) REVERT: C 1336 GLN cc_start: 0.9168 (mm-40) cc_final: 0.8946 (mm-40) REVERT: C 2033 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9125 (mp) REVERT: C 2061 MET cc_start: 0.9419 (tpp) cc_final: 0.9054 (tpp) REVERT: C 2139 ASP cc_start: 0.9105 (m-30) cc_final: 0.8823 (m-30) REVERT: C 2235 TYR cc_start: 0.8074 (m-80) cc_final: 0.7250 (m-80) REVERT: C 2464 TYR cc_start: 0.6728 (OUTLIER) cc_final: 0.5183 (m-80) REVERT: E 1144 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8238 (mp) REVERT: E 1494 MET cc_start: 0.5476 (mmp) cc_final: 0.5200 (mmt) REVERT: E 2235 TYR cc_start: 0.8120 (m-10) cc_final: 0.7508 (m-10) REVERT: E 2464 TYR cc_start: 0.7044 (OUTLIER) cc_final: 0.5708 (m-80) outliers start: 39 outliers final: 17 residues processed: 422 average time/residue: 0.4357 time to fit residues: 306.0001 Evaluate side-chains 384 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 361 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 117 optimal weight: 0.2980 chunk 303 optimal weight: 3.9990 chunk 74 optimal weight: 0.0060 chunk 286 optimal weight: 8.9990 chunk 126 optimal weight: 7.9990 chunk 265 optimal weight: 0.9980 chunk 196 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 104 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- 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 ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1503 GLN E1967 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.136395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.104613 restraints weight = 64223.714| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 3.06 r_work: 0.3101 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34707 Z= 0.125 Angle : 0.593 7.556 46845 Z= 0.296 Chirality : 0.039 0.165 5181 Planarity : 0.004 0.050 5667 Dihedral : 14.479 121.509 5895 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.68 % Allowed : 12.85 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.14), residues: 3987 helix: 2.38 (0.10), residues: 2700 sheet: -0.04 (0.34), residues: 258 loop : -1.94 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1519 HIS 0.025 0.001 HIS A1967 PHE 0.039 0.001 PHE A1954 TYR 0.025 0.001 TYR C1803 ARG 0.003 0.000 ARG C1176 Details of bonding type rmsd hydrogen bonds : bond 0.04564 ( 2140) hydrogen bonds : angle 4.00477 ( 6339) SS BOND : bond 0.00128 ( 3) SS BOND : angle 0.33313 ( 6) covalent geometry : bond 0.00257 (34704) covalent geometry : angle 0.59335 (46839) *********************** 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 471 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 414 time to evaluate : 3.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1142 ASN cc_start: 0.7331 (p0) cc_final: 0.6976 (p0) REVERT: A 1143 PHE cc_start: 0.6094 (m-80) cc_final: 0.5155 (m-80) REVERT: A 2139 ASP cc_start: 0.9034 (m-30) cc_final: 0.8768 (m-30) REVERT: A 2235 TYR cc_start: 0.7977 (m-80) cc_final: 0.7344 (m-80) REVERT: A 2270 MET cc_start: 0.7734 (mmm) cc_final: 0.7517 (mmm) REVERT: A 2388 LYS cc_start: 0.8627 (mmpt) cc_final: 0.8309 (mmpt) REVERT: A 2464 TYR cc_start: 0.7027 (OUTLIER) cc_final: 0.5594 (m-80) REVERT: C 1107 GLN cc_start: 0.7521 (tm-30) cc_final: 0.7314 (tp40) REVERT: C 1142 ASN cc_start: 0.7485 (p0) cc_final: 0.6944 (p0) REVERT: C 1206 GLN cc_start: 0.7813 (mt0) cc_final: 0.7570 (mt0) REVERT: C 1264 MET cc_start: 0.6632 (mmt) cc_final: 0.6016 (mmt) REVERT: C 1323 TYR cc_start: 0.8378 (t80) cc_final: 0.8130 (t80) REVERT: C 1495 MET cc_start: 0.1899 (mpp) cc_final: 0.0959 (ttt) REVERT: C 1525 LYS cc_start: 0.8603 (pptt) cc_final: 0.8265 (ptpt) REVERT: C 1664 ARG cc_start: 0.8978 (pmt170) cc_final: 0.8703 (ptt-90) REVERT: C 1995 PHE cc_start: 0.7919 (t80) cc_final: 0.7562 (t80) REVERT: C 2061 MET cc_start: 0.9438 (tpp) cc_final: 0.9070 (tpp) REVERT: C 2139 ASP cc_start: 0.9072 (m-30) cc_final: 0.8806 (m-30) REVERT: C 2235 TYR cc_start: 0.7969 (m-80) cc_final: 0.7258 (m-80) REVERT: C 2464 TYR cc_start: 0.6866 (OUTLIER) cc_final: 0.5473 (m-80) REVERT: E 1107 GLN cc_start: 0.7668 (tm-30) cc_final: 0.7458 (tp40) REVERT: E 1142 ASN cc_start: 0.7271 (p0) cc_final: 0.6533 (p0) REVERT: E 1143 PHE cc_start: 0.6337 (m-80) cc_final: 0.5809 (m-80) REVERT: E 1548 VAL cc_start: 0.7829 (OUTLIER) cc_final: 0.7576 (m) REVERT: E 2153 MET cc_start: 0.8713 (mmt) cc_final: 0.8085 (mtt) REVERT: E 2228 VAL cc_start: 0.9356 (OUTLIER) cc_final: 0.9050 (m) REVERT: E 2235 TYR cc_start: 0.7989 (m-80) cc_final: 0.7310 (m-10) REVERT: E 2270 MET cc_start: 0.7393 (mmm) cc_final: 0.7036 (mmm) REVERT: E 2464 TYR cc_start: 0.7045 (OUTLIER) cc_final: 0.5552 (m-80) outliers start: 57 outliers final: 26 residues processed: 447 average time/residue: 0.4327 time to fit residues: 320.7245 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 : 3.621 ------------------------------------------------------------------------------- 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 2295 ARG 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 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 1967 HIS 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 360 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 397 optimal weight: 1.9990 chunk 351 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 50 optimal weight: 7.9990 chunk 9 optimal weight: 0.0970 chunk 180 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 362 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1543 GLN A1967 HIS C 910 ASN ** C1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3838 r_free = 0.3838 target = 0.136617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.103857 restraints weight = 63900.036| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.99 r_work: 0.3105 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2334 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= 0.118 Angle : 0.577 9.113 46845 Z= 0.287 Chirality : 0.039 0.166 5181 Planarity : 0.004 0.047 5667 Dihedral : 13.829 118.205 5895 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 1.57 % Allowed : 14.89 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.14), residues: 3987 helix: 2.45 (0.10), residues: 2697 sheet: 0.02 (0.34), residues: 258 loop : -1.93 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E1754 HIS 0.028 0.001 HIS E1967 PHE 0.045 0.001 PHE E1954 TYR 0.014 0.001 TYR E1803 ARG 0.003 0.000 ARG C2407 Details of bonding type rmsd hydrogen bonds : bond 0.04258 ( 2140) hydrogen bonds : angle 3.86756 ( 6339) SS BOND : bond 0.00124 ( 3) SS BOND : angle 0.35713 ( 6) covalent geometry : bond 0.00246 (34704) covalent geometry : angle 0.57672 (46839) *********************** 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 453 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 400 time to evaluate : 3.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1142 ASN cc_start: 0.7462 (p0) cc_final: 0.7176 (p0) REVERT: A 1143 PHE cc_start: 0.6170 (m-80) cc_final: 0.5709 (m-80) REVERT: A 1525 LYS cc_start: 0.8545 (pptt) cc_final: 0.8237 (tppt) REVERT: A 1548 VAL cc_start: 0.7692 (OUTLIER) cc_final: 0.7485 (m) REVERT: A 1754 TRP cc_start: 0.7693 (m-90) cc_final: 0.7428 (m-90) REVERT: A 2139 ASP cc_start: 0.9025 (m-30) cc_final: 0.8755 (m-30) REVERT: A 2235 TYR cc_start: 0.7921 (m-80) cc_final: 0.7341 (m-80) REVERT: A 2270 MET cc_start: 0.7716 (mmm) cc_final: 0.7476 (mmm) REVERT: A 2388 LYS cc_start: 0.8655 (mmpt) cc_final: 0.8296 (mmpt) REVERT: A 2464 TYR cc_start: 0.6968 (OUTLIER) cc_final: 0.5576 (m-80) REVERT: C 1206 GLN cc_start: 0.7817 (mt0) cc_final: 0.7568 (mt0) REVERT: C 1264 MET cc_start: 0.6521 (mmt) cc_final: 0.6066 (mmt) REVERT: C 1525 LYS cc_start: 0.8631 (pptt) cc_final: 0.8309 (ptpt) REVERT: C 1754 TRP cc_start: 0.7405 (m-90) cc_final: 0.7128 (m-90) REVERT: C 1995 PHE cc_start: 0.8006 (t80) cc_final: 0.7664 (t80) REVERT: C 2061 MET cc_start: 0.9461 (tpp) cc_final: 0.9050 (tpp) REVERT: C 2139 ASP cc_start: 0.9094 (m-30) cc_final: 0.8798 (m-30) REVERT: C 2235 TYR cc_start: 0.7917 (m-80) cc_final: 0.7240 (m-80) REVERT: C 2464 TYR cc_start: 0.6814 (OUTLIER) cc_final: 0.5325 (m-80) REVERT: E 1142 ASN cc_start: 0.7381 (p0) cc_final: 0.6595 (p0) REVERT: E 1143 PHE cc_start: 0.6687 (m-80) cc_final: 0.6431 (m-80) REVERT: E 1494 MET cc_start: 0.5680 (mmt) cc_final: 0.5461 (mmp) REVERT: E 1525 LYS cc_start: 0.8653 (pptt) cc_final: 0.8181 (tppt) REVERT: E 1548 VAL cc_start: 0.7600 (OUTLIER) cc_final: 0.7389 (m) REVERT: E 2153 MET cc_start: 0.8821 (mmt) cc_final: 0.8248 (mtt) REVERT: E 2228 VAL cc_start: 0.9344 (OUTLIER) cc_final: 0.9049 (m) REVERT: E 2235 TYR cc_start: 0.7941 (m-80) cc_final: 0.7217 (m-80) REVERT: E 2270 MET cc_start: 0.7491 (mmm) cc_final: 0.7271 (mmm) REVERT: E 2464 TYR cc_start: 0.7043 (OUTLIER) cc_final: 0.5536 (m-80) outliers start: 53 outliers final: 27 residues processed: 435 average time/residue: 0.4572 time to fit residues: 331.8126 Evaluate side-chains 398 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 365 time to evaluate : 3.686 ------------------------------------------------------------------------------- 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 1144 ILE Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1342 LEU 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 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 1192 LEU Chi-restraints excluded: chain E residue 1407 ILE Chi-restraints excluded: chain E residue 1548 VAL 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 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 233 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 105 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 156 optimal weight: 1.9990 chunk 268 optimal weight: 0.7980 chunk 177 optimal weight: 2.9990 chunk 311 optimal weight: 0.8980 chunk 269 optimal weight: 0.9980 chunk 348 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 910 ASN ** A1225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1967 HIS E 910 ASN ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1503 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.135003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.102393 restraints weight = 63915.627| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.94 r_work: 0.3075 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2439 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= 0.131 Angle : 0.580 8.825 46845 Z= 0.289 Chirality : 0.039 0.163 5181 Planarity : 0.004 0.047 5667 Dihedral : 13.456 115.362 5895 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.22 % Allowed : 15.72 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.14), residues: 3987 helix: 2.49 (0.10), residues: 2700 sheet: 0.12 (0.34), residues: 258 loop : -1.84 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A2082 HIS 0.009 0.001 HIS A1304 PHE 0.057 0.002 PHE E1954 TYR 0.019 0.001 TYR E1323 ARG 0.006 0.000 ARG E2407 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 2140) hydrogen bonds : angle 3.85826 ( 6339) SS BOND : bond 0.00115 ( 3) SS BOND : angle 0.38504 ( 6) covalent geometry : bond 0.00290 (34704) covalent geometry : angle 0.57983 (46839) *********************** 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 460 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 385 time to evaluate : 3.818 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1142 ASN cc_start: 0.7770 (p0) cc_final: 0.7469 (p0) REVERT: A 1238 MET cc_start: 0.8735 (mmp) cc_final: 0.8519 (mmp) REVERT: A 1495 MET cc_start: 0.2073 (mpt) cc_final: 0.1069 (ttt) REVERT: A 1525 LYS cc_start: 0.8548 (pptt) cc_final: 0.8234 (tppt) REVERT: A 2139 ASP cc_start: 0.9109 (m-30) cc_final: 0.8825 (m-30) REVERT: A 2270 MET cc_start: 0.7698 (mmm) cc_final: 0.7419 (mmm) REVERT: A 2388 LYS cc_start: 0.8693 (mmpt) cc_final: 0.8353 (mmpt) REVERT: A 2464 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.5548 (m-80) REVERT: C 1206 GLN cc_start: 0.7906 (mt0) cc_final: 0.7616 (mt0) REVERT: C 1264 MET cc_start: 0.6518 (mmt) cc_final: 0.6151 (mmt) REVERT: C 1403 HIS cc_start: 0.6801 (t70) cc_final: 0.6492 (t70) REVERT: C 1495 MET cc_start: 0.1567 (mpp) cc_final: 0.0613 (ttt) REVERT: C 1525 LYS cc_start: 0.8674 (pptt) cc_final: 0.8350 (ptpt) REVERT: C 1754 TRP cc_start: 0.7436 (m-90) cc_final: 0.7136 (m-90) REVERT: C 1995 PHE cc_start: 0.8063 (t80) cc_final: 0.7759 (t80) REVERT: C 2061 MET cc_start: 0.9474 (tpp) cc_final: 0.9010 (tpp) REVERT: C 2139 ASP cc_start: 0.9166 (m-30) cc_final: 0.8890 (m-30) REVERT: C 2235 TYR cc_start: 0.8070 (m-80) cc_final: 0.7387 (m-80) REVERT: C 2464 TYR cc_start: 0.6811 (OUTLIER) cc_final: 0.5336 (m-80) REVERT: E 1142 ASN cc_start: 0.7529 (p0) cc_final: 0.6826 (p0) REVERT: E 1494 MET cc_start: 0.5323 (mmt) cc_final: 0.5011 (mmp) REVERT: E 1495 MET cc_start: 0.2699 (mpp) cc_final: 0.1465 (ttt) REVERT: E 1525 LYS cc_start: 0.8718 (pptt) cc_final: 0.8367 (ptpt) REVERT: E 1548 VAL cc_start: 0.7560 (OUTLIER) cc_final: 0.7359 (m) REVERT: E 2153 MET cc_start: 0.8892 (mmt) cc_final: 0.8642 (mtp) REVERT: E 2228 VAL cc_start: 0.9377 (OUTLIER) cc_final: 0.9091 (m) REVERT: E 2235 TYR cc_start: 0.8136 (m-80) cc_final: 0.7516 (m-80) REVERT: E 2464 TYR cc_start: 0.7047 (OUTLIER) cc_final: 0.5545 (m-80) outliers start: 75 outliers final: 38 residues processed: 436 average time/residue: 0.4272 time to fit residues: 309.4864 Evaluate side-chains 399 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 356 time to evaluate : 3.922 ------------------------------------------------------------------------------- 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 1155 VAL 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 1144 ILE 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 2228 VAL Chi-restraints excluded: chain C residue 2295 ARG Chi-restraints excluded: chain C residue 2464 TYR Chi-restraints excluded: chain C residue 2472 SER Chi-restraints excluded: chain C residue 2486 SER Chi-restraints excluded: chain E residue 825 VAL 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 1155 VAL Chi-restraints excluded: chain E residue 1192 LEU Chi-restraints excluded: chain E residue 1246 ILE Chi-restraints excluded: chain E residue 1251 LEU 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 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 1967 HIS 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 124 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 225 optimal weight: 1.9990 chunk 192 optimal weight: 7.9990 chunk 270 optimal weight: 60.0000 chunk 149 optimal weight: 9.9990 chunk 206 optimal weight: 0.0980 chunk 317 optimal weight: 1.9990 chunk 54 optimal weight: 0.9980 chunk 279 optimal weight: 0.0270 overall best weight: 0.6038 ------------------------------------------------------------------------------- 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 C1503 GLN C1967 HIS ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.137512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.106053 restraints weight = 63678.769| |-----------------------------------------------------------------------------| r_work (start): 0.3382 rms_B_bonded: 3.08 r_work: 0.3115 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 34707 Z= 0.113 Angle : 0.564 8.607 46845 Z= 0.281 Chirality : 0.038 0.178 5181 Planarity : 0.004 0.045 5667 Dihedral : 13.008 123.482 5895 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.80 % Allowed : 16.08 % Favored : 82.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.14), residues: 3987 helix: 2.55 (0.10), residues: 2697 sheet: 0.21 (0.34), residues: 258 loop : -1.89 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E1754 HIS 0.009 0.001 HIS A1304 PHE 0.055 0.001 PHE E1954 TYR 0.020 0.001 TYR C1323 ARG 0.007 0.000 ARG C2407 Details of bonding type rmsd hydrogen bonds : bond 0.03931 ( 2140) hydrogen bonds : angle 3.73950 ( 6339) SS BOND : bond 0.00130 ( 3) SS BOND : angle 0.38996 ( 6) covalent geometry : bond 0.00236 (34704) covalent geometry : angle 0.56444 (46839) *********************** 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 471 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 410 time to evaluate : 3.804 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: 0.7704 (p0) cc_final: 0.7275 (p0) REVERT: A 1495 MET cc_start: 0.2142 (mpt) cc_final: 0.1103 (ttt) REVERT: A 1525 LYS cc_start: 0.8506 (pptt) cc_final: 0.8255 (ptpt) REVERT: A 1754 TRP cc_start: 0.7894 (m-90) cc_final: 0.7609 (m-90) REVERT: A 2139 ASP cc_start: 0.9059 (m-30) cc_final: 0.8756 (m-30) REVERT: A 2235 TYR cc_start: 0.7825 (m-80) cc_final: 0.7293 (m-80) REVERT: A 2270 MET cc_start: 0.7686 (mmm) cc_final: 0.7408 (mmm) REVERT: A 2281 ILE cc_start: 0.9276 (mt) cc_final: 0.8955 (mt) REVERT: A 2388 LYS cc_start: 0.8717 (mmpt) cc_final: 0.8327 (mmpt) REVERT: A 2464 TYR cc_start: 0.7065 (OUTLIER) cc_final: 0.5494 (m-80) REVERT: A 2518 GLU cc_start: 0.8276 (mp0) cc_final: 0.7949 (mp0) REVERT: C 1206 GLN cc_start: 0.7958 (mt0) cc_final: 0.7653 (mt0) REVERT: C 1495 MET cc_start: 0.1793 (mpp) cc_final: 0.0859 (ttt) REVERT: C 1525 LYS cc_start: 0.8649 (pptt) cc_final: 0.8360 (ptpt) REVERT: C 1754 TRP cc_start: 0.7512 (m-90) cc_final: 0.7202 (m-90) REVERT: C 1800 LEU cc_start: 0.8058 (OUTLIER) cc_final: 0.7783 (mt) REVERT: C 1995 PHE cc_start: 0.7997 (t80) cc_final: 0.7723 (t80) REVERT: C 2061 MET cc_start: 0.9422 (tpp) cc_final: 0.8976 (tpp) REVERT: C 2139 ASP cc_start: 0.9132 (m-30) cc_final: 0.8836 (m-30) REVERT: C 2281 ILE cc_start: 0.9202 (mt) cc_final: 0.8956 (mt) REVERT: C 2464 TYR cc_start: 0.6783 (OUTLIER) cc_final: 0.5240 (m-80) REVERT: E 1142 ASN cc_start: 0.7334 (p0) cc_final: 0.6979 (p0) REVERT: E 1350 LYS cc_start: 0.9173 (tttm) cc_final: 0.8962 (tppp) REVERT: E 1494 MET cc_start: 0.5308 (mmt) cc_final: 0.4945 (mmp) REVERT: E 1495 MET cc_start: 0.2697 (mpp) cc_final: 0.1455 (ttt) REVERT: E 1525 LYS cc_start: 0.8738 (pptt) cc_final: 0.8347 (ptpt) REVERT: E 1791 MET cc_start: 0.9010 (mmm) cc_final: 0.8773 (mmm) REVERT: E 2061 MET cc_start: 0.9306 (tpp) cc_final: 0.9004 (tpp) REVERT: E 2153 MET cc_start: 0.8909 (mmt) cc_final: 0.8709 (mtm) REVERT: E 2228 VAL cc_start: 0.9333 (OUTLIER) cc_final: 0.9037 (m) REVERT: E 2235 TYR cc_start: 0.7933 (m-80) cc_final: 0.7259 (m-80) REVERT: E 2270 MET cc_start: 0.7209 (mmm) cc_final: 0.6875 (mmm) REVERT: E 2464 TYR cc_start: 0.6978 (OUTLIER) cc_final: 0.5493 (m-80) REVERT: E 2518 GLU cc_start: 0.8057 (mp0) cc_final: 0.7607 (mp0) outliers start: 61 outliers final: 27 residues processed: 453 average time/residue: 0.4491 time to fit residues: 338.9526 Evaluate side-chains 403 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 371 time to evaluate : 3.869 ------------------------------------------------------------------------------- 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 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 981 PHE Chi-restraints excluded: chain C residue 1144 ILE Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1342 LEU 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 2486 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 1516 LEU Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 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 290 optimal weight: 3.9990 chunk 300 optimal weight: 0.7980 chunk 277 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 280 optimal weight: 7.9990 chunk 324 optimal weight: 8.9990 chunk 305 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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** C1967 HIS ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1543 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.132459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.101309 restraints weight = 64150.537| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 2.95 r_work: 0.3053 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 34707 Z= 0.182 Angle : 0.629 10.031 46845 Z= 0.317 Chirality : 0.041 0.170 5181 Planarity : 0.004 0.046 5667 Dihedral : 13.149 116.215 5895 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.07 % Allowed : 16.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.14), residues: 3987 helix: 2.54 (0.10), residues: 2670 sheet: 0.00 (0.35), residues: 261 loop : -1.83 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C2082 HIS 0.009 0.001 HIS A1145 PHE 0.054 0.002 PHE E1954 TYR 0.019 0.001 TYR C1323 ARG 0.005 0.000 ARG E2407 Details of bonding type rmsd hydrogen bonds : bond 0.04669 ( 2140) hydrogen bonds : angle 3.93594 ( 6339) SS BOND : bond 0.00033 ( 3) SS BOND : angle 0.33731 ( 6) covalent geometry : bond 0.00430 (34704) covalent geometry : angle 0.62938 (46839) *********************** 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 442 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 372 time to evaluate : 3.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 838 PHE cc_start: 0.7740 (OUTLIER) cc_final: 0.7425 (m-80) REVERT: A 1350 LYS cc_start: 0.9173 (tmmt) cc_final: 0.8945 (tppp) REVERT: A 1495 MET cc_start: 0.2291 (mpt) cc_final: 0.1296 (ttt) REVERT: A 1525 LYS cc_start: 0.8507 (pptt) cc_final: 0.8282 (ptpt) REVERT: A 1754 TRP cc_start: 0.7883 (m-90) cc_final: 0.7603 (m-90) REVERT: A 2139 ASP cc_start: 0.9101 (m-30) cc_final: 0.8869 (m-30) REVERT: A 2281 ILE cc_start: 0.9212 (mt) cc_final: 0.8970 (mt) REVERT: A 2464 TYR cc_start: 0.7017 (OUTLIER) cc_final: 0.5273 (m-80) REVERT: A 2518 GLU cc_start: 0.8286 (mp0) cc_final: 0.7990 (mp0) REVERT: C 838 PHE cc_start: 0.7864 (OUTLIER) cc_final: 0.7453 (m-80) REVERT: C 1206 GLN cc_start: 0.7849 (mt0) cc_final: 0.7539 (mt0) REVERT: C 1495 MET cc_start: 0.1778 (mpp) cc_final: 0.0808 (ttt) REVERT: C 1525 LYS cc_start: 0.8700 (pptt) cc_final: 0.8408 (ptpt) REVERT: C 1995 PHE cc_start: 0.8192 (t80) cc_final: 0.7873 (t80) REVERT: C 2061 MET cc_start: 0.9430 (tpp) cc_final: 0.8944 (tpp) REVERT: C 2139 ASP cc_start: 0.9099 (m-30) cc_final: 0.8792 (m-30) REVERT: C 2235 TYR cc_start: 0.8346 (m-80) cc_final: 0.7549 (m-80) REVERT: C 2308 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8379 (mp) REVERT: C 2464 TYR cc_start: 0.6792 (OUTLIER) cc_final: 0.5098 (m-80) REVERT: E 1238 MET cc_start: 0.8503 (mmp) cc_final: 0.8287 (mmp) REVERT: E 1495 MET cc_start: 0.2513 (mpp) cc_final: 0.1394 (ttt) REVERT: E 1525 LYS cc_start: 0.8755 (pptt) cc_final: 0.8393 (ptpt) REVERT: E 1791 MET cc_start: 0.9044 (mmm) cc_final: 0.8832 (mmm) REVERT: E 2061 MET cc_start: 0.9344 (tpp) cc_final: 0.8938 (tpp) REVERT: E 2133 GLU cc_start: 0.8863 (mp0) cc_final: 0.8550 (mp0) REVERT: E 2228 VAL cc_start: 0.9434 (OUTLIER) cc_final: 0.9157 (m) REVERT: E 2446 MET cc_start: 0.8974 (ttt) cc_final: 0.8753 (ttm) REVERT: E 2464 TYR cc_start: 0.7213 (OUTLIER) cc_final: 0.5222 (m-80) REVERT: E 2518 GLU cc_start: 0.8160 (mp0) cc_final: 0.7633 (mp0) outliers start: 70 outliers final: 41 residues processed: 423 average time/residue: 0.4458 time to fit residues: 312.3832 Evaluate side-chains 398 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 350 time to evaluate : 3.943 ------------------------------------------------------------------------------- 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 1013 HIS Chi-restraints excluded: chain A residue 1155 VAL 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 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 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 1013 HIS 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 1407 ILE Chi-restraints excluded: chain C residue 1798 SER 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 2488 ILE 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 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 1982 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 25 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 282 optimal weight: 6.9990 chunk 118 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 280 optimal weight: 2.9990 chunk 221 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 315 optimal weight: 0.6980 chunk 148 optimal weight: 50.0000 chunk 44 optimal weight: 0.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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** ** C1239 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 = 0.3826 r_free = 0.3826 target = 0.135688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.104295 restraints weight = 63659.972| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 3.05 r_work: 0.3090 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34707 Z= 0.122 Angle : 0.595 10.426 46845 Z= 0.295 Chirality : 0.039 0.233 5181 Planarity : 0.004 0.045 5667 Dihedral : 12.770 116.551 5895 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 1.74 % Allowed : 17.52 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.14), residues: 3987 helix: 2.56 (0.10), residues: 2676 sheet: 0.14 (0.34), residues: 258 loop : -1.78 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E1754 HIS 0.009 0.001 HIS A1304 PHE 0.054 0.001 PHE E1954 TYR 0.018 0.001 TYR C1323 ARG 0.007 0.000 ARG E2407 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 2140) hydrogen bonds : angle 3.80046 ( 6339) SS BOND : bond 0.00101 ( 3) SS BOND : angle 0.33615 ( 6) covalent geometry : bond 0.00266 (34704) covalent geometry : angle 0.59548 (46839) *********************** 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 442 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 383 time to evaluate : 3.995 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 838 PHE cc_start: 0.7682 (OUTLIER) cc_final: 0.7390 (m-80) REVERT: A 1143 PHE cc_start: 0.7039 (m-80) cc_final: 0.6669 (t80) REVERT: A 1350 LYS cc_start: 0.9135 (tmmt) cc_final: 0.8896 (tppp) REVERT: A 1495 MET cc_start: 0.2371 (mpt) cc_final: 0.1380 (ttt) REVERT: A 1525 LYS cc_start: 0.8545 (pptt) cc_final: 0.8291 (ptpt) REVERT: A 1754 TRP cc_start: 0.7914 (m-90) cc_final: 0.7440 (m-90) REVERT: A 2139 ASP cc_start: 0.9095 (m-30) cc_final: 0.8856 (m-30) REVERT: A 2388 LYS cc_start: 0.8673 (mmpt) cc_final: 0.8405 (mmpt) REVERT: A 2464 TYR cc_start: 0.7109 (OUTLIER) cc_final: 0.5456 (m-80) REVERT: C 838 PHE cc_start: 0.7908 (OUTLIER) cc_final: 0.7486 (m-80) REVERT: C 1206 GLN cc_start: 0.7918 (mt0) cc_final: 0.7586 (mt0) REVERT: C 1495 MET cc_start: 0.1792 (mpp) cc_final: 0.0833 (ttt) REVERT: C 1502 MET cc_start: 0.6609 (ppp) cc_final: 0.6212 (ppp) REVERT: C 1525 LYS cc_start: 0.8649 (pptt) cc_final: 0.8380 (ptpt) REVERT: C 1754 TRP cc_start: 0.7508 (m-90) cc_final: 0.7194 (m-90) REVERT: C 1995 PHE cc_start: 0.8103 (t80) cc_final: 0.7812 (t80) REVERT: C 2061 MET cc_start: 0.9418 (tpp) cc_final: 0.8999 (tpp) REVERT: C 2139 ASP cc_start: 0.9098 (m-30) cc_final: 0.8734 (m-30) REVERT: C 2153 MET cc_start: 0.8983 (mmp) cc_final: 0.8389 (mtp) REVERT: C 2235 TYR cc_start: 0.7954 (m-80) cc_final: 0.7318 (m-80) REVERT: C 2464 TYR cc_start: 0.6780 (OUTLIER) cc_final: 0.5189 (m-80) REVERT: E 1494 MET cc_start: 0.5621 (mmp) cc_final: 0.5164 (mmt) REVERT: E 1495 MET cc_start: 0.2397 (mpp) cc_final: 0.1264 (ttt) REVERT: E 1525 LYS cc_start: 0.8698 (pptt) cc_final: 0.8366 (ptpt) REVERT: E 1791 MET cc_start: 0.9032 (mmm) cc_final: 0.8788 (mmm) REVERT: E 2061 MET cc_start: 0.9330 (tpp) cc_final: 0.8976 (tpp) REVERT: E 2228 VAL cc_start: 0.9354 (OUTLIER) cc_final: 0.9061 (m) REVERT: E 2235 TYR cc_start: 0.8132 (m-80) cc_final: 0.7610 (m-80) REVERT: E 2270 MET cc_start: 0.7265 (mmm) cc_final: 0.6848 (mmm) REVERT: E 2464 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.5217 (m-80) REVERT: E 2518 GLU cc_start: 0.8086 (mp0) cc_final: 0.7422 (mp0) outliers start: 59 outliers final: 34 residues processed: 425 average time/residue: 0.4307 time to fit residues: 303.4132 Evaluate side-chains 403 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 363 time to evaluate : 3.601 ------------------------------------------------------------------------------- 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 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 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 1153 LEU Chi-restraints excluded: chain C residue 1155 VAL Chi-restraints excluded: chain C residue 1235 VAL Chi-restraints excluded: chain C residue 1246 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1798 SER 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 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 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 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 319 optimal weight: 8.9990 chunk 260 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 103 optimal weight: 0.2980 chunk 392 optimal weight: 5.9990 chunk 189 optimal weight: 4.9990 chunk 266 optimal weight: 0.6980 chunk 242 optimal weight: 0.3980 chunk 354 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.134859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.103652 restraints weight = 63591.888| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 3.01 r_work: 0.3082 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 34707 Z= 0.130 Angle : 0.607 10.215 46845 Z= 0.300 Chirality : 0.039 0.221 5181 Planarity : 0.004 0.046 5667 Dihedral : 12.644 117.162 5895 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.57 % Allowed : 18.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.14), residues: 3987 helix: 2.56 (0.10), residues: 2679 sheet: 0.16 (0.34), residues: 258 loop : -1.80 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E1754 HIS 0.011 0.001 HIS E1304 PHE 0.052 0.001 PHE A1954 TYR 0.019 0.001 TYR C1323 ARG 0.007 0.000 ARG E2407 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 2140) hydrogen bonds : angle 3.77973 ( 6339) SS BOND : bond 0.00099 ( 3) SS BOND : angle 0.27664 ( 6) covalent geometry : bond 0.00291 (34704) covalent geometry : angle 0.60675 (46839) *********************** 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 430 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 377 time to evaluate : 3.702 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 838 PHE cc_start: 0.7749 (OUTLIER) cc_final: 0.7518 (m-80) REVERT: A 1143 PHE cc_start: 0.7117 (m-80) cc_final: 0.6830 (t80) REVERT: A 1350 LYS cc_start: 0.9127 (tmmt) cc_final: 0.8922 (tppp) REVERT: A 1495 MET cc_start: 0.2437 (mpt) cc_final: 0.1462 (ttt) REVERT: A 1525 LYS cc_start: 0.8562 (pptt) cc_final: 0.8343 (ptpt) REVERT: A 2139 ASP cc_start: 0.9102 (m-30) cc_final: 0.8839 (m-30) REVERT: A 2270 MET cc_start: 0.7228 (mmm) cc_final: 0.6864 (mmm) REVERT: A 2281 ILE cc_start: 0.9193 (mt) cc_final: 0.8959 (mt) REVERT: A 2308 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8609 (mp) REVERT: A 2464 TYR cc_start: 0.7009 (OUTLIER) cc_final: 0.5310 (m-80) REVERT: C 838 PHE cc_start: 0.7910 (OUTLIER) cc_final: 0.7546 (m-80) REVERT: C 1206 GLN cc_start: 0.7921 (mt0) cc_final: 0.7588 (mt0) REVERT: C 1495 MET cc_start: 0.2086 (mpp) cc_final: 0.1093 (ttt) REVERT: C 1502 MET cc_start: 0.6535 (ppp) cc_final: 0.6191 (ppp) REVERT: C 1525 LYS cc_start: 0.8650 (pptt) cc_final: 0.8381 (ptpt) REVERT: C 1995 PHE cc_start: 0.8170 (t80) cc_final: 0.7866 (t80) REVERT: C 2061 MET cc_start: 0.9424 (tpp) cc_final: 0.8976 (tpp) REVERT: C 2139 ASP cc_start: 0.9100 (m-30) cc_final: 0.8750 (m-30) REVERT: C 2153 MET cc_start: 0.8986 (mmp) cc_final: 0.8446 (mtp) REVERT: C 2235 TYR cc_start: 0.8107 (m-80) cc_final: 0.7387 (m-80) REVERT: C 2464 TYR cc_start: 0.6788 (OUTLIER) cc_final: 0.5252 (m-80) REVERT: E 1143 PHE cc_start: 0.6129 (m-10) cc_final: 0.5602 (m-10) REVERT: E 1238 MET cc_start: 0.8549 (mmp) cc_final: 0.8203 (mmp) REVERT: E 1525 LYS cc_start: 0.8631 (pptt) cc_final: 0.8352 (ptpt) REVERT: E 1791 MET cc_start: 0.8991 (mmm) cc_final: 0.8789 (mmm) REVERT: E 2061 MET cc_start: 0.9343 (tpp) cc_final: 0.8942 (tpp) REVERT: E 2228 VAL cc_start: 0.9380 (OUTLIER) cc_final: 0.9079 (m) REVERT: E 2235 TYR cc_start: 0.8225 (m-80) cc_final: 0.7676 (m-80) REVERT: E 2270 MET cc_start: 0.7370 (mmm) cc_final: 0.6970 (mmm) REVERT: E 2280 ASP cc_start: 0.8637 (t0) cc_final: 0.8251 (t0) REVERT: E 2464 TYR cc_start: 0.7069 (OUTLIER) cc_final: 0.5301 (m-80) REVERT: E 2518 GLU cc_start: 0.8209 (mp0) cc_final: 0.7708 (mp0) outliers start: 53 outliers final: 35 residues processed: 414 average time/residue: 0.4238 time to fit residues: 288.8697 Evaluate side-chains 399 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 357 time to evaluate : 3.667 ------------------------------------------------------------------------------- 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 1246 ILE Chi-restraints excluded: chain A residue 1251 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 838 PHE 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 1246 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1798 SER 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 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 1516 LEU Chi-restraints excluded: chain E residue 1709 VAL Chi-restraints excluded: chain E residue 1731 MET Chi-restraints excluded: chain E residue 1798 SER 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 215 optimal weight: 3.9990 chunk 137 optimal weight: 0.9990 chunk 288 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 128 optimal weight: 2.9990 chunk 222 optimal weight: 0.9980 chunk 316 optimal weight: 3.9990 chunk 120 optimal weight: 0.1980 chunk 143 optimal weight: 20.0000 chunk 182 optimal weight: 6.9990 chunk 168 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 ** E1138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3793 r_free = 0.3793 target = 0.132850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.101289 restraints weight = 63773.908| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.93 r_work: 0.3047 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34707 Z= 0.167 Angle : 0.638 10.261 46845 Z= 0.318 Chirality : 0.040 0.227 5181 Planarity : 0.004 0.046 5667 Dihedral : 12.802 116.323 5895 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.48 % Allowed : 18.47 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.14), residues: 3987 helix: 2.51 (0.10), residues: 2673 sheet: 0.04 (0.34), residues: 261 loop : -1.86 (0.19), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A2082 HIS 0.011 0.001 HIS E1145 PHE 0.057 0.002 PHE A1954 TYR 0.018 0.001 TYR C1323 ARG 0.008 0.000 ARG E2407 Details of bonding type rmsd hydrogen bonds : bond 0.04486 ( 2140) hydrogen bonds : angle 3.90234 ( 6339) SS BOND : bond 0.00048 ( 3) SS BOND : angle 0.30028 ( 6) covalent geometry : bond 0.00388 (34704) covalent geometry : angle 0.63758 (46839) ********************** 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 414 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 364 time to evaluate : 3.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1143 PHE cc_start: 0.7180 (m-80) cc_final: 0.6956 (t80) REVERT: A 1495 MET cc_start: 0.2334 (mpt) cc_final: 0.1338 (ttt) REVERT: A 1525 LYS cc_start: 0.8581 (pptt) cc_final: 0.8347 (ptpt) REVERT: A 2139 ASP cc_start: 0.9116 (m-30) cc_final: 0.8856 (m-30) REVERT: A 2281 ILE cc_start: 0.9204 (mt) cc_final: 0.8924 (mt) REVERT: A 2308 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8647 (mp) REVERT: A 2464 TYR cc_start: 0.7025 (OUTLIER) cc_final: 0.5396 (m-80) REVERT: C 838 PHE cc_start: 0.8092 (OUTLIER) cc_final: 0.7795 (m-80) REVERT: C 1206 GLN cc_start: 0.7879 (mt0) cc_final: 0.7541 (mt0) REVERT: C 1495 MET cc_start: 0.1793 (mpp) cc_final: 0.0975 (ttt) REVERT: C 1502 MET cc_start: 0.6545 (ppp) cc_final: 0.6175 (ppp) REVERT: C 1525 LYS cc_start: 0.8664 (pptt) cc_final: 0.8402 (ptpt) REVERT: C 1995 PHE cc_start: 0.8222 (t80) cc_final: 0.7964 (t80) REVERT: C 2061 MET cc_start: 0.9437 (tpp) cc_final: 0.8952 (tpp) REVERT: C 2139 ASP cc_start: 0.9123 (m-30) cc_final: 0.8765 (m-30) REVERT: C 2153 MET cc_start: 0.9000 (mmp) cc_final: 0.8508 (mtp) REVERT: C 2235 TYR cc_start: 0.8275 (m-80) cc_final: 0.7524 (m-80) REVERT: C 2271 GLN cc_start: 0.8395 (pp30) cc_final: 0.8102 (pp30) REVERT: C 2308 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8360 (mp) REVERT: C 2464 TYR cc_start: 0.6832 (OUTLIER) cc_final: 0.5090 (m-80) REVERT: E 1495 MET cc_start: 0.2189 (mpt) cc_final: 0.1036 (ttt) REVERT: E 1525 LYS cc_start: 0.8669 (pptt) cc_final: 0.8421 (ptpt) REVERT: E 1791 MET cc_start: 0.9024 (mmm) cc_final: 0.8787 (mmm) REVERT: E 2061 MET cc_start: 0.9395 (tpp) cc_final: 0.8981 (tpp) REVERT: E 2228 VAL cc_start: 0.9421 (OUTLIER) cc_final: 0.9138 (m) REVERT: E 2235 TYR cc_start: 0.8381 (m-80) cc_final: 0.7896 (m-80) REVERT: E 2280 ASP cc_start: 0.8646 (t0) cc_final: 0.8174 (t0) REVERT: E 2464 TYR cc_start: 0.7055 (OUTLIER) cc_final: 0.5209 (m-80) REVERT: E 2518 GLU cc_start: 0.8337 (mp0) cc_final: 0.7866 (mp0) outliers start: 50 outliers final: 40 residues processed: 398 average time/residue: 0.4480 time to fit residues: 294.8813 Evaluate side-chains 408 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 361 time to evaluate : 4.052 ------------------------------------------------------------------------------- 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 1246 ILE Chi-restraints excluded: chain A residue 1251 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 838 PHE 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 1246 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1798 SER 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 1798 SER Chi-restraints excluded: chain E residue 1967 HIS Chi-restraints excluded: chain E residue 1982 LEU 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 202 optimal weight: 6.9990 chunk 247 optimal weight: 0.9990 chunk 252 optimal weight: 0.7980 chunk 325 optimal weight: 5.9990 chunk 368 optimal weight: 4.9990 chunk 122 optimal weight: 3.9990 chunk 242 optimal weight: 0.0770 chunk 332 optimal weight: 3.9990 chunk 55 optimal weight: 6.9990 chunk 286 optimal weight: 2.9990 chunk 337 optimal weight: 0.8980 overall best weight: 1.1542 ------------------------------------------------------------------------------- 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** A1344 GLN C1967 HIS ** E1304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1344 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.134281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.102873 restraints weight = 63645.736| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 3.03 r_work: 0.3067 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 34707 Z= 0.133 Angle : 0.616 10.246 46845 Z= 0.303 Chirality : 0.039 0.213 5181 Planarity : 0.004 0.046 5667 Dihedral : 12.603 115.902 5895 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.57 % Allowed : 18.59 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.14), residues: 3987 helix: 2.53 (0.10), residues: 2679 sheet: 0.12 (0.34), residues: 258 loop : -1.85 (0.19), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C1754 HIS 0.011 0.001 HIS E1304 PHE 0.057 0.002 PHE A1954 TYR 0.018 0.001 TYR C1323 ARG 0.007 0.000 ARG E2407 Details of bonding type rmsd hydrogen bonds : bond 0.04168 ( 2140) hydrogen bonds : angle 3.81687 ( 6339) SS BOND : bond 0.00077 ( 3) SS BOND : angle 0.30178 ( 6) covalent geometry : bond 0.00298 (34704) covalent geometry : angle 0.61584 (46839) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18253.86 seconds wall clock time: 313 minutes 19.20 seconds (18799.20 seconds total)