Starting phenix.real_space_refine on Wed May 28 10:00:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ixn_35799/05_2025/8ixn_35799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ixn_35799/05_2025/8ixn_35799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ixn_35799/05_2025/8ixn_35799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ixn_35799/05_2025/8ixn_35799.map" model { file = "/net/cci-nas-00/data/ceres_data/8ixn_35799/05_2025/8ixn_35799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ixn_35799/05_2025/8ixn_35799.cif" } resolution = 4.07 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= 0.004 sd= 1.021 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 12 5.49 5 S 130 5.16 5 C 19597 2.51 5 N 4994 2.21 5 O 5310 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 30043 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 9804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 9804 Classifications: {'peptide': 1350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 343} Link IDs: {'PTRANS': 51, 'TRANS': 1298} Chain breaks: 18 Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1459 Unresolved non-hydrogen angles: 1889 Unresolved non-hydrogen dihedrals: 1288 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 7, 'TYR:plan': 23, 'ASN:plan1': 8, 'TRP:plan': 13, 'HIS:plan': 13, 'PHE:plan': 32, 'GLU:plan': 12, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 851 Chain: "A" Number of atoms: 9802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 9802 Classifications: {'peptide': 1350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 344} Link IDs: {'PTRANS': 51, 'TRANS': 1298} Chain breaks: 18 Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 1463 Unresolved non-hydrogen angles: 1894 Unresolved non-hydrogen dihedrals: 1293 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLN:plan1': 17, 'ASP:plan': 7, 'TYR:plan': 23, 'ASN:plan1': 9, 'TRP:plan': 13, 'HIS:plan': 13, 'PHE:plan': 32, 'GLU:plan': 12, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 854 Chain: "D" Number of atoms: 9810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1350, 9810 Classifications: {'peptide': 1350} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 341} Link IDs: {'PTRANS': 51, 'TRANS': 1298} Chain breaks: 18 Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1454 Unresolved non-hydrogen angles: 1883 Unresolved non-hydrogen dihedrals: 1286 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLN:plan1': 16, 'ASP:plan': 7, 'TYR:plan': 24, 'ASN:plan1': 8, 'TRP:plan': 13, 'HIS:plan': 13, 'PHE:plan': 31, 'GLU:plan': 12, 'ARG:plan': 31} Unresolved non-hydrogen planarities: 848 Chain: "C" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 209 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "A" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 209 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Chain: "D" Number of atoms: 209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 209 Unusual residues: {'PEE': 1, 'PLX': 2} Classifications: {'peptide': 1, 'undetermined': 3} Link IDs: {None: 3} Time building chain proxies: 18.06, per 1000 atoms: 0.60 Number of scatterers: 30043 At special positions: 0 Unit cell: (221.776, 205.307, 157, 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 130 16.00 P 12 15.00 O 5310 8.00 N 4994 7.00 C 19597 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C1232 " - pdb=" SG CYS C1253 " distance=2.03 Simple disulfide: pdb=" SG CYS A1232 " - pdb=" SG CYS A1253 " distance=2.03 Simple disulfide: pdb=" SG CYS D1232 " - pdb=" SG CYS D1253 " distance=2.03 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: 7.92 Conformation dependent library (CDL) restraints added in 3.9 seconds 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 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: 182 helices and 9 sheets defined 71.2% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 Creating SS restraints... Processing helix chain 'C' and resid 576 through 585 Processing helix chain 'C' and resid 586 through 598 removed outlier: 3.592A pdb=" N SER C 598 " --> pdb=" O PHE C 594 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 625 removed outlier: 3.807A pdb=" N ILE C 608 " --> pdb=" O VAL C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 631 through 648 removed outlier: 3.538A pdb=" N PHE C 635 " --> pdb=" O LEU C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 690 through 706 removed outlier: 3.584A pdb=" N PHE C 695 " --> pdb=" O LEU C 691 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR C 706 " --> pdb=" O LEU C 702 " (cutoff:3.500A) Processing helix chain 'C' and resid 707 through 716 Processing helix chain 'C' and resid 786 through 824 removed outlier: 3.955A pdb=" N LEU C 807 " --> pdb=" O ARG C 803 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N PHE C 810 " --> pdb=" O GLU C 806 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS C 811 " --> pdb=" O LEU C 807 " (cutoff:3.500A) Processing helix chain 'C' and resid 829 through 840 Processing helix chain 'C' and resid 842 through 844 No H-bonds generated for 'chain 'C' and resid 842 through 844' Processing helix chain 'C' and resid 845 through 861 Processing helix chain 'C' and resid 862 through 868 removed outlier: 3.503A pdb=" N LEU C 866 " --> pdb=" O VAL C 862 " (cutoff:3.500A) Processing helix chain 'C' and resid 921 through 950 removed outlier: 4.243A pdb=" N ASN C 926 " --> pdb=" O GLY C 922 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N HIS C 927 " --> pdb=" O TYR C 923 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLN C 950 " --> pdb=" O HIS C 946 " (cutoff:3.500A) Processing helix chain 'C' and resid 973 through 1006 removed outlier: 6.478A pdb=" N PHE C 986 " --> pdb=" O ILE C 982 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N TYR C 987 " --> pdb=" O ASN C 983 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU C 991 " --> pdb=" O TYR C 987 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N GLU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 1007 through 1022 Processing helix chain 'C' and resid 1025 through 1052 removed outlier: 3.704A 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 1110 Processing helix chain 'C' and resid 1141 through 1145 removed outlier: 4.094A pdb=" N ILE C1144 " --> pdb=" O PRO C1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 1148 through 1160 removed outlier: 3.684A pdb=" N MET C1152 " --> pdb=" O SER C1148 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU C1153 " --> pdb=" O TYR C1149 " (cutoff:3.500A) Processing helix chain 'C' and resid 1160 through 1176 removed outlier: 3.903A pdb=" N LEU C1164 " --> pdb=" O TYR C1160 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG C1176 " --> pdb=" O ALA C1172 " (cutoff:3.500A) Processing helix chain 'C' and resid 1181 through 1201 removed outlier: 5.922A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N THR C1197 " --> pdb=" O LEU C1193 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN C1200 " --> pdb=" O THR C1196 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYS C1201 " --> pdb=" O THR C1197 " (cutoff:3.500A) Processing helix chain 'C' and resid 1202 through 1232 removed outlier: 3.770A pdb=" N GLN C1206 " --> pdb=" O ASP C1202 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N LEU C1229 " --> pdb=" O ASN C1225 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU C1230 " --> pdb=" O MET C1226 " (cutoff:3.500A) Processing helix chain 'C' and resid 1242 through 1250 Processing helix chain 'C' and resid 1280 through 1299 removed outlier: 3.522A pdb=" N SER C1284 " --> pdb=" O ILE C1280 " (cutoff:3.500A) Processing helix chain 'C' and resid 1299 through 1315 removed outlier: 3.521A pdb=" N LEU C1303 " --> pdb=" O SER C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1315 through 1365 removed outlier: 3.966A pdb=" N SER C1365 " --> pdb=" O GLN C1361 " (cutoff:3.500A) Processing helix chain 'C' and resid 1411 through 1416 removed outlier: 3.767A pdb=" N GLU C1416 " --> pdb=" O PHE C1413 " (cutoff:3.500A) Processing helix chain 'C' and resid 1505 through 1545 removed outlier: 3.767A pdb=" N GLY C1509 " --> pdb=" O LEU C1505 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N HIS C1526 " --> pdb=" O ALA C1522 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N HIS C1527 " --> pdb=" O PHE C1523 " (cutoff:3.500A) Processing helix chain 'C' and resid 1552 through 1557 removed outlier: 3.646A pdb=" N VAL C1555 " --> pdb=" O ARG C1552 " (cutoff:3.500A) Processing helix chain 'C' and resid 1656 through 1669 Processing helix chain 'C' and resid 1673 through 1687 Processing helix chain 'C' and resid 1688 through 1701 Processing helix chain 'C' and resid 1708 through 1718 removed outlier: 3.579A pdb=" N VAL C1712 " --> pdb=" O LEU C1708 " (cutoff:3.500A) Processing helix chain 'C' and resid 1725 through 1748 removed outlier: 4.281A pdb=" N PHE C1729 " --> pdb=" O PRO C1725 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1801 removed outlier: 3.974A pdb=" N VAL C1788 " --> pdb=" O LYS C1784 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN C1789 " --> pdb=" O TYR C1785 " (cutoff:3.500A) Processing helix chain 'C' and resid 1957 through 1966 Processing helix chain 'C' and resid 1977 through 1994 Processing helix chain 'C' and resid 2016 through 2040 removed outlier: 3.850A pdb=" N LEU C2021 " --> pdb=" O PRO C2017 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE C2022 " --> pdb=" O GLN C2018 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG C2040 " --> pdb=" O ALA C2036 " (cutoff:3.500A) Processing helix chain 'C' and resid 2043 through 2060 Processing helix chain 'C' and resid 2061 through 2064 Processing helix chain 'C' and resid 2077 through 2100 removed outlier: 3.575A pdb=" N LEU C2081 " --> pdb=" O ALA C2077 " (cutoff:3.500A) Processing helix chain 'C' and resid 2115 through 2127 Processing helix chain 'C' and resid 2131 through 2143 Processing helix chain 'C' and resid 2148 through 2175 removed outlier: 3.542A pdb=" N TYR C2175 " --> pdb=" O THR C2171 " (cutoff:3.500A) Processing helix chain 'C' and resid 2181 through 2183 No H-bonds generated for 'chain 'C' and resid 2181 through 2183' Processing helix chain 'C' and resid 2184 through 2213 removed outlier: 3.852A pdb=" N ILE C2203 " --> pdb=" O LEU C2199 " (cutoff:3.500A) Proline residue: C2206 - end of helix Processing helix chain 'C' and resid 2252 through 2263 Processing helix chain 'C' and resid 2266 through 2276 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 2360 removed outlier: 3.669A pdb=" N GLY C2360 " --> pdb=" O GLN C2356 " (cutoff:3.500A) Processing helix chain 'C' and resid 2393 through 2397 Processing helix chain 'C' and resid 2421 through 2426 Processing helix chain 'C' and resid 2455 through 2459 removed outlier: 4.173A pdb=" N LEU C2458 " --> pdb=" O PRO C2455 " (cutoff:3.500A) Processing helix chain 'C' and resid 2465 through 2487 Processing helix chain 'C' and resid 2491 through 2495 Processing helix chain 'C' and resid 2500 through 2516 Processing helix chain 'C' and resid 2521 through 2533 Processing helix chain 'C' and resid 2535 through 2543 Processing helix chain 'A' and resid 577 through 585 Processing helix chain 'A' and resid 586 through 598 removed outlier: 3.577A pdb=" N SER A 598 " --> pdb=" O PHE A 594 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 625 removed outlier: 3.789A pdb=" N ILE A 608 " --> pdb=" O VAL A 604 " (cutoff:3.500A) Processing helix chain 'A' and resid 631 through 648 removed outlier: 3.537A pdb=" N PHE A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 687 through 689 No H-bonds generated for 'chain 'A' and resid 687 through 689' Processing helix chain 'A' and resid 690 through 706 removed outlier: 3.583A pdb=" N PHE A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 716 Processing helix chain 'A' and resid 786 through 806 Processing helix chain 'A' and resid 808 through 824 Processing helix chain 'A' and resid 829 through 840 Processing helix chain 'A' and resid 842 through 844 No H-bonds generated for 'chain 'A' and resid 842 through 844' Processing helix chain 'A' and resid 845 through 861 Processing helix chain 'A' and resid 862 through 868 Processing helix chain 'A' and resid 921 through 950 removed outlier: 4.251A pdb=" N ASN A 926 " --> pdb=" O GLY A 922 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N HIS A 927 " --> pdb=" O TYR A 923 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN A 950 " --> pdb=" O HIS A 946 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 972 removed outlier: 4.516A pdb=" N ASP A 971 " --> pdb=" O GLN A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 973 through 1006 removed outlier: 6.494A pdb=" N PHE A 986 " --> pdb=" O ILE A 982 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR A 987 " --> pdb=" O ASN A 983 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU A 991 " --> pdb=" O TYR A 987 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLU A 992 " --> pdb=" O LYS A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1022 Processing helix chain 'A' and resid 1025 through 1052 removed outlier: 3.701A 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 1110 Processing helix chain 'A' and resid 1141 through 1145 removed outlier: 4.106A pdb=" N ILE A1144 " --> pdb=" O PRO A1141 " (cutoff:3.500A) Processing helix chain 'A' and resid 1148 through 1160 removed outlier: 3.710A pdb=" N MET A1152 " --> pdb=" O SER A1148 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LEU A1153 " --> pdb=" O TYR A1149 " (cutoff:3.500A) Processing helix chain 'A' and resid 1160 through 1176 removed outlier: 3.920A pdb=" N LEU A1164 " --> pdb=" O TYR A1160 " (cutoff:3.500A) Processing helix chain 'A' and resid 1181 through 1201 removed outlier: 5.786A pdb=" N THR A1196 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N THR A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLN A1200 " --> pdb=" O THR A1196 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LYS A1201 " --> pdb=" O THR A1197 " (cutoff:3.500A) Processing helix chain 'A' and resid 1202 through 1232 removed outlier: 3.711A pdb=" N GLN A1206 " --> pdb=" O ASP A1202 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A1229 " --> pdb=" O ASN A1225 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LEU A1230 " --> pdb=" O MET A1226 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1250 Processing helix chain 'A' and resid 1280 through 1299 Processing helix chain 'A' and resid 1299 through 1315 removed outlier: 3.537A pdb=" N LEU A1303 " --> pdb=" O SER A1299 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1365 removed outlier: 3.959A pdb=" N SER A1365 " --> pdb=" O GLN A1361 " (cutoff:3.500A) Processing helix chain 'A' and resid 1411 through 1416 removed outlier: 3.789A pdb=" N GLU A1416 " --> pdb=" O PHE A1413 " (cutoff:3.500A) Processing helix chain 'A' and resid 1505 through 1545 removed outlier: 3.757A pdb=" N GLY A1509 " --> pdb=" O LEU A1505 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N HIS A1526 " --> pdb=" O ALA A1522 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N HIS A1527 " --> pdb=" O PHE A1523 " (cutoff:3.500A) Processing helix chain 'A' and resid 1552 through 1557 removed outlier: 3.639A pdb=" N VAL A1555 " --> pdb=" O ARG A1552 " (cutoff:3.500A) Processing helix chain 'A' and resid 1656 through 1669 Processing helix chain 'A' and resid 1673 through 1687 Processing helix chain 'A' and resid 1688 through 1701 Processing helix chain 'A' and resid 1708 through 1718 removed outlier: 3.631A pdb=" N VAL A1712 " --> pdb=" O LEU A1708 " (cutoff:3.500A) Processing helix chain 'A' and resid 1725 through 1749 removed outlier: 4.166A pdb=" N PHE A1729 " --> pdb=" O PRO A1725 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE A1749 " --> pdb=" O TYR A1745 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1801 removed outlier: 3.952A pdb=" N VAL A1788 " --> pdb=" O LYS A1784 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLN A1789 " --> pdb=" O TYR A1785 " (cutoff:3.500A) Processing helix chain 'A' and resid 1957 through 1966 Processing helix chain 'A' and resid 1977 through 1994 Processing helix chain 'A' and resid 2016 through 2040 removed outlier: 3.807A pdb=" N LEU A2021 " --> pdb=" O PRO A2017 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N PHE A2022 " --> pdb=" O GLN A2018 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG A2040 " --> pdb=" O ALA A2036 " (cutoff:3.500A) Processing helix chain 'A' and resid 2043 through 2060 Processing helix chain 'A' and resid 2061 through 2064 Processing helix chain 'A' and resid 2077 through 2100 removed outlier: 3.558A pdb=" N LEU A2081 " --> pdb=" O ALA A2077 " (cutoff:3.500A) Processing helix chain 'A' and resid 2115 through 2127 Processing helix chain 'A' and resid 2131 through 2143 Processing helix chain 'A' and resid 2148 through 2175 removed outlier: 3.553A pdb=" N TYR A2175 " --> pdb=" O THR A2171 " (cutoff:3.500A) Processing helix chain 'A' and resid 2181 through 2183 No H-bonds generated for 'chain 'A' and resid 2181 through 2183' Processing helix chain 'A' and resid 2184 through 2213 removed outlier: 3.895A pdb=" N ILE A2203 " --> pdb=" O LEU A2199 " (cutoff:3.500A) Proline residue: A2206 - end of helix Processing helix chain 'A' and resid 2252 through 2263 Processing helix chain 'A' and resid 2266 through 2276 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 2360 removed outlier: 3.682A pdb=" N GLY A2360 " --> pdb=" O GLN A2356 " (cutoff:3.500A) Processing helix chain 'A' and resid 2393 through 2397 Processing helix chain 'A' and resid 2421 through 2426 Processing helix chain 'A' and resid 2455 through 2459 removed outlier: 4.177A pdb=" N LEU A2458 " --> pdb=" O PRO A2455 " (cutoff:3.500A) Processing helix chain 'A' and resid 2465 through 2487 Processing helix chain 'A' and resid 2491 through 2495 Processing helix chain 'A' and resid 2500 through 2516 Processing helix chain 'A' and resid 2521 through 2534 Processing helix chain 'A' and resid 2535 through 2543 Processing helix chain 'D' and resid 577 through 585 Processing helix chain 'D' and resid 586 through 598 removed outlier: 3.580A pdb=" N SER D 598 " --> pdb=" O PHE D 594 " (cutoff:3.500A) Processing helix chain 'D' and resid 604 through 625 removed outlier: 3.780A pdb=" N ILE D 608 " --> pdb=" O VAL D 604 " (cutoff:3.500A) Processing helix chain 'D' and resid 631 through 648 removed outlier: 3.553A pdb=" N PHE D 635 " --> pdb=" O LEU D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 690 through 706 removed outlier: 3.598A pdb=" N PHE D 695 " --> pdb=" O LEU D 691 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR D 706 " --> pdb=" O LEU D 702 " (cutoff:3.500A) Processing helix chain 'D' and resid 707 through 716 Processing helix chain 'D' and resid 786 through 806 Processing helix chain 'D' and resid 808 through 824 Processing helix chain 'D' and resid 829 through 840 Processing helix chain 'D' and resid 842 through 844 No H-bonds generated for 'chain 'D' and resid 842 through 844' Processing helix chain 'D' and resid 845 through 861 Processing helix chain 'D' and resid 862 through 868 Processing helix chain 'D' and resid 921 through 950 removed outlier: 4.210A pdb=" N ASN D 926 " --> pdb=" O GLY D 922 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N HIS D 927 " --> pdb=" O TYR D 923 " (cutoff:3.500A) Processing helix chain 'D' and resid 968 through 972 removed outlier: 4.511A pdb=" N ASP D 971 " --> pdb=" O GLN D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 973 through 1006 removed outlier: 6.499A pdb=" N PHE D 986 " --> pdb=" O ILE D 982 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TYR D 987 " --> pdb=" O ASN D 983 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU D 991 " --> pdb=" O TYR D 987 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU D 992 " --> pdb=" O LYS D 988 " (cutoff:3.500A) Processing helix chain 'D' and resid 1007 through 1022 Processing helix chain 'D' and resid 1025 through 1052 removed outlier: 3.725A pdb=" N ILE D1029 " --> pdb=" O ARG D1025 " (cutoff:3.500A) Proline residue: D1034 - end of helix Processing helix chain 'D' and resid 1073 through 1080 Processing helix chain 'D' and resid 1093 through 1110 Processing helix chain 'D' and resid 1141 through 1145 removed outlier: 4.064A pdb=" N ILE D1144 " --> pdb=" O PRO D1141 " (cutoff:3.500A) Processing helix chain 'D' and resid 1148 through 1160 removed outlier: 3.713A pdb=" N MET D1152 " --> pdb=" O SER D1148 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU D1153 " --> pdb=" O TYR D1149 " (cutoff:3.500A) Processing helix chain 'D' and resid 1160 through 1176 removed outlier: 3.925A pdb=" N LEU D1164 " --> pdb=" O TYR D1160 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG D1176 " --> pdb=" O ALA D1172 " (cutoff:3.500A) Processing helix chain 'D' and resid 1181 through 1200 removed outlier: 5.814A pdb=" N THR D1196 " --> pdb=" O LEU D1192 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N THR D1197 " --> pdb=" O LEU D1193 " (cutoff:3.500A) Processing helix chain 'D' and resid 1202 through 1232 removed outlier: 3.761A pdb=" N GLN D1206 " --> pdb=" O ASP D1202 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU D1229 " --> pdb=" O ASN D1225 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N LEU D1230 " --> pdb=" O MET D1226 " (cutoff:3.500A) Processing helix chain 'D' and resid 1242 through 1250 Processing helix chain 'D' and resid 1280 through 1299 removed outlier: 3.502A pdb=" N SER D1284 " --> pdb=" O ILE D1280 " (cutoff:3.500A) Processing helix chain 'D' and resid 1299 through 1315 removed outlier: 3.560A pdb=" N LEU D1303 " --> pdb=" O SER D1299 " (cutoff:3.500A) Processing helix chain 'D' and resid 1315 through 1365 removed outlier: 3.962A pdb=" N SER D1365 " --> pdb=" O GLN D1361 " (cutoff:3.500A) Processing helix chain 'D' and resid 1411 through 1416 removed outlier: 3.768A pdb=" N GLU D1416 " --> pdb=" O PHE D1413 " (cutoff:3.500A) Processing helix chain 'D' and resid 1505 through 1545 removed outlier: 3.762A pdb=" N GLY D1509 " --> pdb=" O LEU D1505 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N HIS D1526 " --> pdb=" O ALA D1522 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N HIS D1527 " --> pdb=" O PHE D1523 " (cutoff:3.500A) Processing helix chain 'D' and resid 1552 through 1557 removed outlier: 3.644A pdb=" N VAL D1555 " --> pdb=" O ARG D1552 " (cutoff:3.500A) Processing helix chain 'D' and resid 1656 through 1669 Processing helix chain 'D' and resid 1673 through 1687 Processing helix chain 'D' and resid 1688 through 1701 Processing helix chain 'D' and resid 1708 through 1718 removed outlier: 3.584A pdb=" N VAL D1712 " --> pdb=" O LEU D1708 " (cutoff:3.500A) Processing helix chain 'D' and resid 1725 through 1748 removed outlier: 4.225A pdb=" N PHE D1729 " --> pdb=" O PRO D1725 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1801 removed outlier: 3.968A pdb=" N VAL D1788 " --> pdb=" O LYS D1784 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N GLN D1789 " --> pdb=" O TYR D1785 " (cutoff:3.500A) Processing helix chain 'D' and resid 1957 through 1966 Processing helix chain 'D' and resid 1977 through 1994 Processing helix chain 'D' and resid 2016 through 2040 removed outlier: 3.794A pdb=" N LEU D2021 " --> pdb=" O PRO D2017 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE D2022 " --> pdb=" O GLN D2018 " (cutoff:3.500A) Processing helix chain 'D' and resid 2043 through 2060 Processing helix chain 'D' and resid 2061 through 2064 removed outlier: 3.524A pdb=" N ILE D2064 " --> pdb=" O MET D2061 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2061 through 2064' Processing helix chain 'D' and resid 2077 through 2100 removed outlier: 3.523A pdb=" N LEU D2081 " --> pdb=" O ALA D2077 " (cutoff:3.500A) Processing helix chain 'D' and resid 2115 through 2127 Processing helix chain 'D' and resid 2131 through 2143 Processing helix chain 'D' and resid 2148 through 2175 removed outlier: 3.550A pdb=" N TYR D2175 " --> pdb=" O THR D2171 " (cutoff:3.500A) Processing helix chain 'D' and resid 2181 through 2183 No H-bonds generated for 'chain 'D' and resid 2181 through 2183' Processing helix chain 'D' and resid 2184 through 2213 removed outlier: 3.842A pdb=" N ILE D2203 " --> pdb=" O LEU D2199 " (cutoff:3.500A) Proline residue: D2206 - end of helix Processing helix chain 'D' and resid 2252 through 2263 Processing helix chain 'D' and resid 2266 through 2276 Processing helix chain 'D' and resid 2277 through 2279 No H-bonds generated for 'chain 'D' and resid 2277 through 2279' Processing helix chain 'D' and resid 2297 through 2310 Processing helix chain 'D' and resid 2348 through 2360 removed outlier: 3.666A pdb=" N GLY D2360 " --> pdb=" O GLN D2356 " (cutoff:3.500A) Processing helix chain 'D' and resid 2393 through 2397 Processing helix chain 'D' and resid 2421 through 2426 Processing helix chain 'D' and resid 2455 through 2459 removed outlier: 4.186A pdb=" N LEU D2458 " --> pdb=" O PRO D2455 " (cutoff:3.500A) Processing helix chain 'D' and resid 2465 through 2487 Processing helix chain 'D' and resid 2491 through 2495 Processing helix chain 'D' and resid 2500 through 2516 Processing helix chain 'D' and resid 2521 through 2534 Processing helix chain 'D' and resid 2535 through 2542 Processing sheet with id=AA1, first strand: chain 'C' and resid 2236 through 2241 removed outlier: 6.503A pdb=" N LEU C2232 " --> pdb=" O PRO C2237 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 2248 through 2250 Processing sheet with id=AA3, first strand: chain 'C' and resid 2401 through 2405 Processing sheet with id=AA4, first strand: chain 'A' and resid 2236 through 2241 removed outlier: 6.501A pdb=" N LEU A2232 " --> pdb=" O PRO A2237 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 2248 through 2250 Processing sheet with id=AA6, first strand: chain 'A' and resid 2404 through 2405 Processing sheet with id=AA7, first strand: chain 'D' and resid 2236 through 2241 removed outlier: 6.508A pdb=" N LEU D2232 " --> pdb=" O PRO D2237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 2248 through 2250 Processing sheet with id=AA9, first strand: chain 'D' and resid 2401 through 2405 2125 hydrogen bonds defined for protein. 6240 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: 11.01 Time building geometry restraints manager: 9.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 5069 1.32 - 1.45: 7742 1.45 - 1.57: 17553 1.57 - 1.70: 22 1.70 - 1.82: 200 Bond restraints: 30586 Sorted by residual: bond pdb=" C30 PEE C2603 " pdb=" O3 PEE C2603 " ideal model delta sigma weight residual 1.327 1.398 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" C30 PEE D2603 " pdb=" O3 PEE D2603 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" C30 PEE A2603 " pdb=" O3 PEE A2603 " ideal model delta sigma weight residual 1.327 1.397 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C4 PEE A2603 " pdb=" O4P PEE A2603 " ideal model delta sigma weight residual 1.409 1.346 0.063 2.00e-02 2.50e+03 9.90e+00 bond pdb=" C4 PEE C2603 " pdb=" O4P PEE C2603 " ideal model delta sigma weight residual 1.409 1.346 0.063 2.00e-02 2.50e+03 9.81e+00 ... (remaining 30581 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 40270 2.26 - 4.53: 949 4.53 - 6.79: 280 6.79 - 9.06: 60 9.06 - 11.32: 19 Bond angle restraints: 41578 Sorted by residual: angle pdb=" N VAL C1233 " pdb=" CA VAL C1233 " pdb=" C VAL C1233 " ideal model delta sigma weight residual 111.88 105.19 6.69 1.06e+00 8.90e-01 3.98e+01 angle pdb=" N VAL A1233 " pdb=" CA VAL A1233 " pdb=" C VAL A1233 " ideal model delta sigma weight residual 111.88 105.28 6.60 1.06e+00 8.90e-01 3.88e+01 angle pdb=" N VAL D1233 " pdb=" CA VAL D1233 " pdb=" C VAL D1233 " ideal model delta sigma weight residual 111.88 105.34 6.54 1.06e+00 8.90e-01 3.80e+01 angle pdb=" N GLN C2261 " pdb=" CA GLN C2261 " pdb=" CB GLN C2261 " ideal model delta sigma weight residual 110.28 117.16 -6.88 1.55e+00 4.16e-01 1.97e+01 angle pdb=" N GLN A2261 " pdb=" CA GLN A2261 " pdb=" CB GLN A2261 " ideal model delta sigma weight residual 110.28 116.77 -6.49 1.55e+00 4.16e-01 1.75e+01 ... (remaining 41573 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.79: 17911 34.79 - 69.58: 320 69.58 - 104.37: 69 104.37 - 139.16: 45 139.16 - 173.95: 9 Dihedral angle restraints: 18354 sinusoidal: 6451 harmonic: 11903 Sorted by residual: dihedral pdb=" CB CYS D1232 " pdb=" SG CYS D1232 " pdb=" SG CYS D1253 " pdb=" CB CYS D1253 " ideal model delta sinusoidal sigma weight residual -86.00 -172.05 86.05 1 1.00e+01 1.00e-02 8.94e+01 dihedral pdb=" CB CYS A1232 " pdb=" SG CYS A1232 " pdb=" SG CYS A1253 " pdb=" CB CYS A1253 " ideal model delta sinusoidal sigma weight residual -86.00 -172.02 86.02 1 1.00e+01 1.00e-02 8.93e+01 dihedral pdb=" CB CYS C1232 " pdb=" SG CYS C1232 " pdb=" SG CYS C1253 " pdb=" CB CYS C1253 " ideal model delta sinusoidal sigma weight residual -86.00 -171.31 85.31 1 1.00e+01 1.00e-02 8.81e+01 ... (remaining 18351 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 4493 0.080 - 0.159: 428 0.159 - 0.238: 25 0.238 - 0.318: 5 0.318 - 0.397: 6 Chirality restraints: 4957 Sorted by residual: chirality pdb=" C6 PLX A2602 " pdb=" C7 PLX A2602 " pdb=" O6 PLX A2602 " pdb=" O7 PLX A2602 " both_signs ideal model delta sigma weight residual False 2.01 2.41 -0.40 2.00e-01 2.50e+01 3.95e+00 chirality pdb=" C6 PLX D2602 " pdb=" C7 PLX D2602 " pdb=" O6 PLX D2602 " pdb=" O7 PLX D2602 " both_signs ideal model delta sigma weight residual False 2.01 2.41 -0.40 2.00e-01 2.50e+01 3.93e+00 chirality pdb=" C6 PLX C2602 " pdb=" C7 PLX C2602 " pdb=" O6 PLX C2602 " pdb=" O7 PLX C2602 " both_signs ideal model delta sigma weight residual False 2.01 2.41 -0.40 2.00e-01 2.50e+01 3.93e+00 ... (remaining 4954 not shown) Planarity restraints: 5196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 836 " -0.018 2.00e-02 2.50e+03 2.07e-02 1.07e+01 pdb=" CG TRP D 836 " 0.055 2.00e-02 2.50e+03 pdb=" CD1 TRP D 836 " -0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP D 836 " 0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP D 836 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP D 836 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 836 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 836 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 836 " -0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 836 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A2321 " -0.017 2.00e-02 2.50e+03 2.06e-02 1.06e+01 pdb=" CG TRP A2321 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A2321 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP A2321 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A2321 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP A2321 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A2321 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A2321 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A2321 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A2321 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D2321 " 0.016 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP D2321 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP D2321 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 TRP D2321 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D2321 " -0.007 2.00e-02 2.50e+03 pdb=" CE2 TRP D2321 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D2321 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP D2321 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP D2321 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP D2321 " 0.000 2.00e-02 2.50e+03 ... (remaining 5193 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2939 2.74 - 3.28: 32812 3.28 - 3.82: 51143 3.82 - 4.36: 53749 4.36 - 4.90: 89817 Nonbonded interactions: 230460 Sorted by model distance: nonbonded pdb=" O ALA D1019 " pdb=" OG1 THR D1022 " model vdw 2.202 3.040 nonbonded pdb=" OG SER A1148 " pdb=" OD2 ASP A1151 " model vdw 2.204 3.040 nonbonded pdb=" O ALA A1019 " pdb=" OG1 THR A1022 " model vdw 2.212 3.040 nonbonded pdb=" OG SER C1148 " pdb=" OD2 ASP C1151 " model vdw 2.222 3.040 nonbonded pdb=" O ALA C1019 " pdb=" OG1 THR C1022 " model vdw 2.226 3.040 ... (remaining 230455 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 576 through 1049 or (resid 1050 through 1052 and (name N o \ r name CA or name C or name O or name CB )) or resid 1055 or (resid 1056 through \ 1060 and (name N or name CA or name C or name O or name CB )) or resid 1061 thr \ ough 1790 or (resid 1791 through 1792 and (name N or name CA or name C or name O \ or name CB )) or resid 1793 through 1976 or (resid 1977 through 1978 and (name \ N or name CA or name C or name O or name CB )) or resid 1979 through 2142 or (re \ sid 2143 and (name N or name CA or name C or name O or name CB )) or resid 2144 \ through 2182 or (resid 2183 and (name N or name CA or name C or name O or name C \ B )) or resid 2184 through 2515 or (resid 2516 and (name N or name CA or name C \ or name O or name CB )) or resid 2517 through 2547 or resid 2601 through 2604)) selection = (chain 'C' and (resid 576 through 1055 or (resid 1056 through 1060 and (name N o \ r name CA or name C or name O or name CB )) or resid 1061 through 1697 or (resid \ 1698 through 1699 and (name N or name CA or name C or name O or name CB )) or r \ esid 1700 through 1976 or (resid 1977 through 1978 and (name N or name CA or nam \ e C or name O or name CB )) or resid 1979 through 2137 or (resid 2138 and (name \ N or name CA or name C or name O or name CB )) or resid 2139 through 2182 or (re \ sid 2183 and (name N or name CA or name C or name O or name CB )) or resid 2184 \ through 2266 or (resid 2267 and (name N or name CA or name C or name O or name C \ B )) or resid 2268 through 2297 or (resid 2298 and (name N or name CA or name C \ or name O or name CB )) or resid 2299 through 2515 or (resid 2516 and (name N or \ name CA or name C or name O or name CB )) or resid 2517 through 2547 or resid 2 \ 601 through 2604)) selection = (chain 'D' and (resid 576 through 1049 or (resid 1050 through 1052 and (name N o \ r name CA or name C or name O or name CB )) or resid 1055 through 1197 or (resid \ 1198 and (name N or name CA or name C or name O or name CB )) or resid 1199 thr \ ough 1205 or (resid 1206 and (name N or name CA or name C or name O or name CB ) \ ) or resid 1207 through 1697 or (resid 1698 through 1699 and (name N or name CA \ or name C or name O or name CB )) or resid 1700 through 1790 or (resid 1791 thro \ ugh 1792 and (name N or name CA or name C or name O or name CB )) or resid 1793 \ through 2108 or (resid 2109 through 2110 and (name N or name CA or name C or nam \ e O or name CB )) or resid 2111 through 2137 or (resid 2138 and (name N or name \ CA or name C or name O or name CB )) or resid 2139 through 2142 or (resid 2143 a \ nd (name N or name CA or name C or name O or name CB )) or resid 2144 through 22 \ 66 or (resid 2267 and (name N or name CA or name C or name O or name CB )) or re \ sid 2268 through 2297 or (resid 2298 and (name N or name CA or name C or name O \ or name CB )) or resid 2299 through 2547 or resid 2601 through 2604)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 6.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 1.270 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 65.720 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 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 : 0.005 0.071 30589 Z= 0.230 Angle : 0.914 11.322 41584 Z= 0.449 Chirality : 0.049 0.397 4957 Planarity : 0.005 0.070 5196 Dihedral : 17.893 173.947 10551 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 20.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.18 % Favored : 94.69 % Rotamer: Outliers : 0.04 % Allowed : 0.50 % Favored : 99.46 % 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: 0.19 (0.14), residues: 3936 helix: 1.28 (0.10), residues: 2712 sheet: -1.78 (0.39), residues: 153 loop : -2.67 (0.18), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.003 TRP D 836 HIS 0.014 0.002 HIS C1013 PHE 0.052 0.002 PHE C1008 TYR 0.030 0.002 TYR A1977 ARG 0.008 0.001 ARG A2135 Details of bonding type rmsd hydrogen bonds : bond 0.12430 ( 2125) hydrogen bonds : angle 5.66722 ( 6240) SS BOND : bond 0.00114 ( 3) SS BOND : angle 1.16921 ( 6) covalent geometry : bond 0.00454 (30586) covalent geometry : angle 0.91366 (41578) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 340 time to evaluate : 3.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 2023 MET cc_start: 0.8094 (mpp) cc_final: 0.7831 (mmm) REVERT: C 2031 MET cc_start: 0.7678 (mtt) cc_final: 0.7418 (mtp) REVERT: C 2230 LEU cc_start: 0.9016 (tt) cc_final: 0.8678 (tp) REVERT: A 1012 LEU cc_start: 0.9020 (tp) cc_final: 0.8765 (tp) REVERT: A 1097 ASP cc_start: 0.8421 (t70) cc_final: 0.8006 (t70) REVERT: A 1182 LEU cc_start: 0.7701 (mt) cc_final: 0.6727 (pt) REVERT: A 1226 MET cc_start: 0.8616 (ppp) cc_final: 0.8180 (ppp) REVERT: A 2031 MET cc_start: 0.7469 (mtp) cc_final: 0.7203 (mtp) REVERT: A 2304 MET cc_start: 0.8667 (mmm) cc_final: 0.8319 (mmm) REVERT: A 2335 TYR cc_start: 0.9074 (m-10) cc_final: 0.8843 (m-80) REVERT: D 2241 MET cc_start: 0.8632 (tpp) cc_final: 0.8336 (tpt) REVERT: D 2270 MET cc_start: 0.7507 (mmp) cc_final: 0.7265 (mmm) REVERT: D 2370 HIS cc_start: 0.7805 (m-70) cc_final: 0.7381 (m90) outliers start: 1 outliers final: 0 residues processed: 341 average time/residue: 0.3333 time to fit residues: 198.5966 Evaluate side-chains 257 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 3.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 341 optimal weight: 6.9990 chunk 306 optimal weight: 7.9990 chunk 170 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 207 optimal weight: 0.6980 chunk 163 optimal weight: 10.0000 chunk 317 optimal weight: 0.9990 chunk 122 optimal weight: 0.8980 chunk 193 optimal weight: 0.9980 chunk 236 optimal weight: 6.9990 chunk 367 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1200 GLN ** C1356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2151 ASN C2222 GLN ** C2271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2380 ASN A1200 GLN A1789 GLN A2151 ASN A2380 ASN A2391 GLN ** D1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2151 ASN ** D2271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2380 ASN ** D2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.057298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.049446 restraints weight = 282747.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.050203 restraints weight = 201117.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.050724 restraints weight = 152755.500| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 30589 Z= 0.134 Angle : 0.637 8.428 41584 Z= 0.324 Chirality : 0.041 0.237 4957 Planarity : 0.004 0.053 5196 Dihedral : 16.476 163.927 4907 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 0.04 % Allowed : 4.52 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.14), residues: 3936 helix: 1.63 (0.10), residues: 2745 sheet: -1.69 (0.34), residues: 177 loop : -2.50 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C2321 HIS 0.008 0.002 HIS C1013 PHE 0.027 0.001 PHE A1039 TYR 0.017 0.001 TYR C2533 ARG 0.008 0.000 ARG A2534 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 2125) hydrogen bonds : angle 4.19454 ( 6240) SS BOND : bond 0.00189 ( 3) SS BOND : angle 0.57760 ( 6) covalent geometry : bond 0.00281 (30586) covalent geometry : angle 0.63741 (41578) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 319 time to evaluate : 3.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1287 PHE cc_start: 0.8139 (t80) cc_final: 0.7688 (t80) REVERT: C 1730 TRP cc_start: 0.6640 (m100) cc_final: 0.6224 (m100) REVERT: C 2023 MET cc_start: 0.7914 (mpp) cc_final: 0.7686 (mmm) REVERT: C 2031 MET cc_start: 0.8184 (mtt) cc_final: 0.7781 (mtp) REVERT: C 2156 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8367 (mm-30) REVERT: C 2270 MET cc_start: 0.8859 (mmt) cc_final: 0.8369 (mmm) REVERT: A 1097 ASP cc_start: 0.8585 (t0) cc_final: 0.8098 (t70) REVERT: A 1182 LEU cc_start: 0.7814 (mt) cc_final: 0.6757 (pt) REVERT: A 1226 MET cc_start: 0.8619 (ppp) cc_final: 0.8190 (ppp) REVERT: A 1786 ASP cc_start: 0.8020 (m-30) cc_final: 0.7759 (m-30) REVERT: A 2023 MET cc_start: 0.8100 (mtm) cc_final: 0.7191 (ptp) REVERT: A 2335 TYR cc_start: 0.9356 (m-10) cc_final: 0.9130 (m-80) REVERT: D 1170 PHE cc_start: 0.8912 (t80) cc_final: 0.8591 (t80) REVERT: D 2138 MET cc_start: 0.9075 (tpt) cc_final: 0.8683 (tpp) REVERT: D 2241 MET cc_start: 0.8849 (tpp) cc_final: 0.8276 (tpt) REVERT: D 2270 MET cc_start: 0.7368 (mmp) cc_final: 0.7015 (mmm) REVERT: D 2370 HIS cc_start: 0.7902 (m-70) cc_final: 0.7434 (m90) REVERT: D 2446 MET cc_start: 0.7725 (mmp) cc_final: 0.7281 (mmp) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.3400 time to fit residues: 190.4550 Evaluate side-chains 250 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 250 time to evaluate : 3.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 255 optimal weight: 10.0000 chunk 373 optimal weight: 6.9990 chunk 289 optimal weight: 2.9990 chunk 321 optimal weight: 1.9990 chunk 8 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 292 optimal weight: 2.9990 chunk 280 optimal weight: 9.9990 chunk 63 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1225 ASN C1300 HIS ** C1356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1217 ASN A1300 HIS A2123 GLN A2285 GLN D1300 HIS D1315 GLN ** D1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.053264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.045389 restraints weight = 290147.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.046057 restraints weight = 197031.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.046654 restraints weight = 148755.512| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 30589 Z= 0.181 Angle : 0.693 10.512 41584 Z= 0.358 Chirality : 0.044 0.212 4957 Planarity : 0.005 0.057 5196 Dihedral : 15.313 165.723 4907 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 0.19 % Allowed : 7.35 % Favored : 92.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.14), residues: 3936 helix: 1.56 (0.10), residues: 2745 sheet: -1.54 (0.36), residues: 177 loop : -2.49 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP C2321 HIS 0.010 0.002 HIS C2340 PHE 0.038 0.002 PHE D1794 TYR 0.023 0.002 TYR A2256 ARG 0.008 0.001 ARG C2534 Details of bonding type rmsd hydrogen bonds : bond 0.04435 ( 2125) hydrogen bonds : angle 4.14788 ( 6240) SS BOND : bond 0.00181 ( 3) SS BOND : angle 0.61210 ( 6) covalent geometry : bond 0.00390 (30586) covalent geometry : angle 0.69334 (41578) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 295 time to evaluate : 3.203 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1098 PHE cc_start: 0.8545 (t80) cc_final: 0.8331 (t80) REVERT: C 1226 MET cc_start: 0.9021 (ppp) cc_final: 0.8820 (ppp) REVERT: C 2023 MET cc_start: 0.8170 (mpp) cc_final: 0.7814 (mmm) REVERT: C 2270 MET cc_start: 0.8830 (mmt) cc_final: 0.8625 (mmp) REVERT: A 1097 ASP cc_start: 0.8908 (t70) cc_final: 0.8389 (t70) REVERT: A 1530 MET cc_start: 0.9165 (mtm) cc_final: 0.8850 (mtp) REVERT: A 1713 LEU cc_start: 0.9316 (mm) cc_final: 0.9111 (mm) REVERT: A 1791 MET cc_start: 0.8233 (ptm) cc_final: 0.7784 (ptt) REVERT: A 2270 MET cc_start: 0.8396 (mmm) cc_final: 0.8125 (mmm) REVERT: A 2335 TYR cc_start: 0.9332 (m-10) cc_final: 0.9116 (m-80) REVERT: A 2448 ILE cc_start: 0.9326 (mm) cc_final: 0.9124 (tp) REVERT: A 2495 GLU cc_start: 0.8898 (mp0) cc_final: 0.8679 (mp0) REVERT: A 2522 GLU cc_start: 0.8617 (tt0) cc_final: 0.8117 (mp0) REVERT: D 1170 PHE cc_start: 0.8909 (t80) cc_final: 0.8604 (t80) REVERT: D 1219 THR cc_start: 0.9236 (t) cc_final: 0.9033 (p) REVERT: D 2138 MET cc_start: 0.9000 (mmm) cc_final: 0.8589 (tpp) REVERT: D 2241 MET cc_start: 0.8913 (tpp) cc_final: 0.8172 (tpt) REVERT: D 2270 MET cc_start: 0.7618 (mmp) cc_final: 0.7104 (mmm) REVERT: D 2446 MET cc_start: 0.7947 (mmp) cc_final: 0.7183 (mmm) outliers start: 5 outliers final: 2 residues processed: 299 average time/residue: 0.3195 time to fit residues: 169.3881 Evaluate side-chains 228 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 226 time to evaluate : 3.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 236 optimal weight: 3.9990 chunk 368 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 258 optimal weight: 20.0000 chunk 223 optimal weight: 0.0170 chunk 347 optimal weight: 0.9990 chunk 120 optimal weight: 0.0060 chunk 369 optimal weight: 4.9990 chunk 319 optimal weight: 5.9990 chunk 403 optimal weight: 0.7980 chunk 321 optimal weight: 4.9990 overall best weight: 1.1638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1225 ASN ** C1356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2151 ASN C2391 GLN A2123 GLN ** D1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2285 GLN D2391 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.054103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.046268 restraints weight = 284287.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.047050 restraints weight = 193645.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.047564 restraints weight = 144162.581| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30589 Z= 0.122 Angle : 0.594 8.599 41584 Z= 0.303 Chirality : 0.041 0.237 4957 Planarity : 0.004 0.050 5196 Dihedral : 14.721 177.117 4907 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 0.08 % Allowed : 3.06 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.14), residues: 3936 helix: 1.75 (0.10), residues: 2775 sheet: -1.47 (0.36), residues: 177 loop : -2.45 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP C 836 HIS 0.007 0.001 HIS C2058 PHE 0.031 0.001 PHE A 800 TYR 0.019 0.001 TYR D2533 ARG 0.010 0.000 ARG A1353 Details of bonding type rmsd hydrogen bonds : bond 0.03779 ( 2125) hydrogen bonds : angle 3.90757 ( 6240) SS BOND : bond 0.00160 ( 3) SS BOND : angle 0.62535 ( 6) covalent geometry : bond 0.00256 (30586) covalent geometry : angle 0.59379 (41578) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 290 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 836 TRP cc_start: 0.8304 (m100) cc_final: 0.8003 (m100) REVERT: C 1045 LEU cc_start: 0.9133 (tp) cc_final: 0.8925 (tt) REVERT: C 1098 PHE cc_start: 0.8568 (t80) cc_final: 0.8309 (t80) REVERT: C 2023 MET cc_start: 0.8176 (mpp) cc_final: 0.7944 (mmm) REVERT: C 2270 MET cc_start: 0.8841 (mmt) cc_final: 0.8268 (mmm) REVERT: A 1097 ASP cc_start: 0.8963 (t70) cc_final: 0.8453 (t70) REVERT: A 1182 LEU cc_start: 0.8353 (mt) cc_final: 0.8111 (mp) REVERT: A 1349 MET cc_start: 0.8508 (tpp) cc_final: 0.8295 (tpp) REVERT: A 1713 LEU cc_start: 0.9334 (mm) cc_final: 0.9099 (mm) REVERT: A 1719 MET cc_start: 0.8109 (pmm) cc_final: 0.7875 (pmm) REVERT: A 1791 MET cc_start: 0.8316 (ptm) cc_final: 0.8082 (ptt) REVERT: A 2023 MET cc_start: 0.8047 (mtt) cc_final: 0.7590 (mmt) REVERT: A 2197 LEU cc_start: 0.9284 (mm) cc_final: 0.9081 (tt) REVERT: A 2270 MET cc_start: 0.8369 (mmm) cc_final: 0.8095 (mmm) REVERT: A 2304 MET cc_start: 0.8927 (mmm) cc_final: 0.8476 (mmm) REVERT: A 2335 TYR cc_start: 0.9253 (m-10) cc_final: 0.9039 (m-80) REVERT: D 1219 THR cc_start: 0.9185 (t) cc_final: 0.8912 (p) REVERT: D 1223 SER cc_start: 0.8955 (p) cc_final: 0.8695 (p) REVERT: D 1700 MET cc_start: 0.8601 (ptm) cc_final: 0.8239 (ppp) REVERT: D 2138 MET cc_start: 0.9121 (mmm) cc_final: 0.8726 (tpp) REVERT: D 2241 MET cc_start: 0.8863 (tpp) cc_final: 0.8010 (tpt) REVERT: D 2270 MET cc_start: 0.7599 (mmp) cc_final: 0.7016 (mmm) REVERT: D 2446 MET cc_start: 0.7803 (mmp) cc_final: 0.7185 (mmm) outliers start: 2 outliers final: 0 residues processed: 292 average time/residue: 0.3217 time to fit residues: 164.7667 Evaluate side-chains 228 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 3.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 186 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 339 optimal weight: 0.8980 chunk 327 optimal weight: 0.8980 chunk 256 optimal weight: 6.9990 chunk 209 optimal weight: 6.9990 chunk 343 optimal weight: 8.9990 chunk 288 optimal weight: 8.9990 chunk 374 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1293 GLN ** C1356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2391 GLN ** D1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.053757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.045997 restraints weight = 285714.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.046660 restraints weight = 192215.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.047270 restraints weight = 144396.826| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 30589 Z= 0.117 Angle : 0.578 9.752 41584 Z= 0.295 Chirality : 0.041 0.246 4957 Planarity : 0.004 0.048 5196 Dihedral : 14.175 175.787 4907 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.11 % Allowed : 2.80 % Favored : 97.09 % 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: 1.05 (0.14), residues: 3936 helix: 1.84 (0.10), residues: 2775 sheet: -1.44 (0.35), residues: 177 loop : -2.31 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D2321 HIS 0.005 0.001 HIS C2058 PHE 0.052 0.001 PHE A1297 TYR 0.013 0.001 TYR D2256 ARG 0.004 0.000 ARG A1353 Details of bonding type rmsd hydrogen bonds : bond 0.03635 ( 2125) hydrogen bonds : angle 3.82835 ( 6240) SS BOND : bond 0.00170 ( 3) SS BOND : angle 0.53062 ( 6) covalent geometry : bond 0.00243 (30586) covalent geometry : angle 0.57836 (41578) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 277 time to evaluate : 3.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 836 TRP cc_start: 0.8277 (m100) cc_final: 0.7894 (m100) REVERT: C 1098 PHE cc_start: 0.8593 (t80) cc_final: 0.8292 (t80) REVERT: C 2156 GLU cc_start: 0.8963 (mm-30) cc_final: 0.8705 (mm-30) REVERT: C 2270 MET cc_start: 0.8919 (tpp) cc_final: 0.8694 (mmp) REVERT: A 1049 LEU cc_start: 0.9421 (tp) cc_final: 0.9134 (pp) REVERT: A 1097 ASP cc_start: 0.9014 (t70) cc_final: 0.8522 (t70) REVERT: A 1182 LEU cc_start: 0.8387 (mt) cc_final: 0.8165 (mp) REVERT: A 1719 MET cc_start: 0.8137 (pmm) cc_final: 0.7923 (pmm) REVERT: A 1791 MET cc_start: 0.8318 (ptm) cc_final: 0.8094 (ptt) REVERT: A 2023 MET cc_start: 0.8045 (mtt) cc_final: 0.7595 (mmt) REVERT: A 2270 MET cc_start: 0.8348 (mmm) cc_final: 0.8091 (mmm) REVERT: A 2304 MET cc_start: 0.8943 (mmm) cc_final: 0.8546 (mmp) REVERT: A 2335 TYR cc_start: 0.9311 (m-10) cc_final: 0.9083 (m-80) REVERT: A 2375 TYR cc_start: 0.9099 (m-10) cc_final: 0.8895 (m-80) REVERT: D 1219 THR cc_start: 0.9180 (t) cc_final: 0.8897 (p) REVERT: D 1700 MET cc_start: 0.8548 (ptm) cc_final: 0.8208 (ppp) REVERT: D 2138 MET cc_start: 0.9134 (mmm) cc_final: 0.8706 (tpp) REVERT: D 2241 MET cc_start: 0.8795 (tpp) cc_final: 0.7952 (tpt) REVERT: D 2270 MET cc_start: 0.7662 (mmp) cc_final: 0.7045 (mmm) outliers start: 3 outliers final: 1 residues processed: 280 average time/residue: 0.3243 time to fit residues: 161.6357 Evaluate side-chains 221 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 220 time to evaluate : 3.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 59 optimal weight: 0.9990 chunk 133 optimal weight: 0.0770 chunk 249 optimal weight: 3.9990 chunk 290 optimal weight: 0.8980 chunk 265 optimal weight: 0.7980 chunk 177 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 223 optimal weight: 0.0270 chunk 349 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 253 optimal weight: 7.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1698 ASN C1789 GLN A2151 ASN ** D1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1293 GLN ** D1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2340 HIS ** D2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.054024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.046279 restraints weight = 284392.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.047066 restraints weight = 191684.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.047580 restraints weight = 142146.940| |-----------------------------------------------------------------------------| r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 30589 Z= 0.108 Angle : 0.579 8.468 41584 Z= 0.291 Chirality : 0.040 0.263 4957 Planarity : 0.003 0.048 5196 Dihedral : 13.770 171.675 4907 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: 1.15 (0.14), residues: 3936 helix: 1.89 (0.10), residues: 2775 sheet: -1.31 (0.36), residues: 177 loop : -2.23 (0.20), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP C2321 HIS 0.005 0.001 HIS C1304 PHE 0.039 0.001 PHE D1297 TYR 0.013 0.001 TYR A2526 ARG 0.003 0.000 ARG A1353 Details of bonding type rmsd hydrogen bonds : bond 0.03477 ( 2125) hydrogen bonds : angle 3.75654 ( 6240) SS BOND : bond 0.00200 ( 3) SS BOND : angle 0.58650 ( 6) covalent geometry : bond 0.00217 (30586) covalent geometry : angle 0.57940 (41578) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 279 time to evaluate : 3.387 Fit side-chains revert: symmetry clash REVERT: C 836 TRP cc_start: 0.8265 (m100) cc_final: 0.8004 (m100) REVERT: C 1098 PHE cc_start: 0.8581 (t80) cc_final: 0.8305 (t80) REVERT: C 1226 MET cc_start: 0.9133 (ppp) cc_final: 0.8884 (ppp) REVERT: C 1740 MET cc_start: 0.8811 (tmm) cc_final: 0.8040 (tmm) REVERT: C 2156 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8700 (mm-30) REVERT: C 2270 MET cc_start: 0.8908 (tpp) cc_final: 0.8672 (mmp) REVERT: A 1049 LEU cc_start: 0.9435 (tp) cc_final: 0.9155 (pp) REVERT: A 1097 ASP cc_start: 0.8951 (t70) cc_final: 0.8461 (t70) REVERT: A 1182 LEU cc_start: 0.8460 (mt) cc_final: 0.8240 (mp) REVERT: A 1713 LEU cc_start: 0.9331 (mm) cc_final: 0.9107 (mm) REVERT: A 1791 MET cc_start: 0.8293 (ptm) cc_final: 0.8073 (ptt) REVERT: A 2023 MET cc_start: 0.8047 (mtt) cc_final: 0.7586 (mmt) REVERT: A 2270 MET cc_start: 0.8339 (mmm) cc_final: 0.8078 (mmm) REVERT: A 2304 MET cc_start: 0.8930 (mmm) cc_final: 0.8571 (mmp) REVERT: A 2485 PHE cc_start: 0.8903 (t80) cc_final: 0.8657 (t80) REVERT: D 1219 THR cc_start: 0.9216 (t) cc_final: 0.8974 (p) REVERT: D 1223 SER cc_start: 0.8932 (p) cc_final: 0.8709 (p) REVERT: D 1690 LEU cc_start: 0.8751 (pt) cc_final: 0.8435 (tt) REVERT: D 1700 MET cc_start: 0.8524 (ptm) cc_final: 0.8130 (ppp) REVERT: D 2138 MET cc_start: 0.9162 (mmm) cc_final: 0.8707 (tpp) REVERT: D 2241 MET cc_start: 0.8703 (tpp) cc_final: 0.7891 (tpt) REVERT: D 2270 MET cc_start: 0.7651 (mmp) cc_final: 0.7109 (mmm) REVERT: D 2446 MET cc_start: 0.7736 (mmp) cc_final: 0.7411 (mpp) outliers start: 0 outliers final: 0 residues processed: 279 average time/residue: 0.3306 time to fit residues: 164.5324 Evaluate side-chains 216 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 3.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 274 optimal weight: 8.9990 chunk 195 optimal weight: 4.9990 chunk 257 optimal weight: 0.9990 chunk 377 optimal weight: 8.9990 chunk 379 optimal weight: 2.9990 chunk 306 optimal weight: 10.0000 chunk 202 optimal weight: 30.0000 chunk 209 optimal weight: 0.9990 chunk 158 optimal weight: 20.0000 chunk 187 optimal weight: 1.9990 chunk 165 optimal weight: 4.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2151 ASN ** C2244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2244 GLN ** A2340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2244 GLN ** D2385 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2391 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.052087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.044238 restraints weight = 290150.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.044893 restraints weight = 191361.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.045497 restraints weight = 142578.179| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 30589 Z= 0.151 Angle : 0.615 8.899 41584 Z= 0.314 Chirality : 0.042 0.300 4957 Planarity : 0.004 0.043 5196 Dihedral : 13.487 178.022 4907 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % 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: 1.13 (0.14), residues: 3936 helix: 1.88 (0.10), residues: 2766 sheet: -1.32 (0.36), residues: 177 loop : -2.22 (0.20), residues: 993 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP D1210 HIS 0.006 0.001 HIS C1304 PHE 0.025 0.001 PHE A2198 TYR 0.020 0.001 TYR D1184 ARG 0.014 0.001 ARG C2377 Details of bonding type rmsd hydrogen bonds : bond 0.03768 ( 2125) hydrogen bonds : angle 3.87609 ( 6240) SS BOND : bond 0.00153 ( 3) SS BOND : angle 0.72924 ( 6) covalent geometry : bond 0.00332 (30586) covalent geometry : angle 0.61495 (41578) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 3.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 836 TRP cc_start: 0.8509 (m100) cc_final: 0.8097 (m100) REVERT: C 1095 ILE cc_start: 0.8206 (tt) cc_final: 0.7970 (tp) REVERT: C 1098 PHE cc_start: 0.8673 (t80) cc_final: 0.8361 (t80) REVERT: C 2156 GLU cc_start: 0.9106 (mm-30) cc_final: 0.8895 (mm-30) REVERT: C 2270 MET cc_start: 0.8947 (tpp) cc_final: 0.8653 (mmp) REVERT: C 2485 PHE cc_start: 0.9069 (t80) cc_final: 0.8737 (t80) REVERT: A 1097 ASP cc_start: 0.8932 (t70) cc_final: 0.8503 (t70) REVERT: A 1791 MET cc_start: 0.8181 (ptm) cc_final: 0.7963 (ptt) REVERT: A 2023 MET cc_start: 0.8195 (mtt) cc_final: 0.7784 (mmt) REVERT: A 2058 HIS cc_start: 0.8431 (m90) cc_final: 0.8153 (m170) REVERT: A 2087 CYS cc_start: 0.9270 (m) cc_final: 0.9070 (m) REVERT: A 2270 MET cc_start: 0.8301 (mmm) cc_final: 0.8049 (mmm) REVERT: D 1219 THR cc_start: 0.9260 (t) cc_final: 0.9016 (p) REVERT: D 1700 MET cc_start: 0.8547 (ptm) cc_final: 0.8100 (ppp) REVERT: D 1731 MET cc_start: 0.8798 (mmm) cc_final: 0.8514 (ptm) REVERT: D 2138 MET cc_start: 0.9145 (mmm) cc_final: 0.8747 (tpp) REVERT: D 2241 MET cc_start: 0.8801 (tpp) cc_final: 0.7946 (tpt) REVERT: D 2270 MET cc_start: 0.7801 (mmp) cc_final: 0.7267 (mmm) REVERT: D 2446 MET cc_start: 0.7702 (mmp) cc_final: 0.7389 (mpp) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.3115 time to fit residues: 136.7936 Evaluate side-chains 200 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 3.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 317 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 174 optimal weight: 10.0000 chunk 233 optimal weight: 20.0000 chunk 120 optimal weight: 0.2980 chunk 248 optimal weight: 0.9990 chunk 186 optimal weight: 4.9990 chunk 151 optimal weight: 0.0980 chunk 222 optimal weight: 0.9990 chunk 62 optimal weight: 9.9990 chunk 249 optimal weight: 1.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C1356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2340 HIS A2385 ASN A2391 GLN ** D1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2285 GLN D2385 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.052980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.045252 restraints weight = 286483.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.045910 restraints weight = 189398.581| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.046521 restraints weight = 140254.229| |-----------------------------------------------------------------------------| r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30589 Z= 0.108 Angle : 0.588 9.602 41584 Z= 0.292 Chirality : 0.040 0.283 4957 Planarity : 0.003 0.046 5196 Dihedral : 12.838 178.226 4907 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.08 % Allowed : 1.00 % Favored : 98.93 % 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: 1.27 (0.14), residues: 3936 helix: 2.00 (0.10), residues: 2763 sheet: -1.39 (0.38), residues: 147 loop : -2.15 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP C2321 HIS 0.006 0.001 HIS C1304 PHE 0.023 0.001 PHE C1504 TYR 0.017 0.001 TYR C 842 ARG 0.008 0.000 ARG C 844 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 2125) hydrogen bonds : angle 3.68722 ( 6240) SS BOND : bond 0.00168 ( 3) SS BOND : angle 0.48513 ( 6) covalent geometry : bond 0.00217 (30586) covalent geometry : angle 0.58814 (41578) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 256 time to evaluate : 3.483 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 817 THR cc_start: 0.9320 (t) cc_final: 0.9110 (p) REVERT: C 836 TRP cc_start: 0.8361 (m100) cc_final: 0.7998 (m100) REVERT: C 1095 ILE cc_start: 0.8194 (tt) cc_final: 0.7924 (tp) REVERT: C 1098 PHE cc_start: 0.8695 (t80) cc_final: 0.8328 (t80) REVERT: C 2023 MET cc_start: 0.7670 (mmt) cc_final: 0.6290 (mtt) REVERT: C 2156 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8863 (mm-30) REVERT: C 2270 MET cc_start: 0.8953 (tpp) cc_final: 0.8634 (mmp) REVERT: C 2304 MET cc_start: 0.8437 (mmm) cc_final: 0.8205 (mmm) REVERT: C 2485 PHE cc_start: 0.9103 (t80) cc_final: 0.8789 (t80) REVERT: A 1097 ASP cc_start: 0.8916 (t70) cc_final: 0.8477 (t70) REVERT: A 1719 MET cc_start: 0.8152 (pmm) cc_final: 0.7807 (pmm) REVERT: A 1791 MET cc_start: 0.8162 (ptm) cc_final: 0.7940 (ptt) REVERT: A 2023 MET cc_start: 0.8231 (mtt) cc_final: 0.7792 (mmt) REVERT: A 2270 MET cc_start: 0.8347 (mmm) cc_final: 0.8087 (mmm) REVERT: A 2304 MET cc_start: 0.8991 (mmm) cc_final: 0.8622 (mmm) REVERT: A 2446 MET cc_start: 0.6666 (mmp) cc_final: 0.6325 (mmp) REVERT: A 2485 PHE cc_start: 0.8938 (t80) cc_final: 0.8725 (t80) REVERT: D 1170 PHE cc_start: 0.8902 (t80) cc_final: 0.8631 (t80) REVERT: D 1219 THR cc_start: 0.9129 (t) cc_final: 0.8895 (p) REVERT: D 1223 SER cc_start: 0.8940 (p) cc_final: 0.8727 (p) REVERT: D 1690 LEU cc_start: 0.8666 (pt) cc_final: 0.8372 (tt) REVERT: D 1700 MET cc_start: 0.8522 (ptm) cc_final: 0.8026 (ppp) REVERT: D 2138 MET cc_start: 0.9141 (mmm) cc_final: 0.8708 (tpp) REVERT: D 2241 MET cc_start: 0.8608 (tpp) cc_final: 0.7782 (tpt) REVERT: D 2270 MET cc_start: 0.7853 (mmp) cc_final: 0.7312 (mmm) REVERT: D 2446 MET cc_start: 0.7767 (mmp) cc_final: 0.7408 (mpp) REVERT: D 2487 GLU cc_start: 0.8774 (tp30) cc_final: 0.8422 (tp30) outliers start: 2 outliers final: 0 residues processed: 258 average time/residue: 0.3251 time to fit residues: 151.3659 Evaluate side-chains 206 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 3.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 61 optimal weight: 20.0000 chunk 401 optimal weight: 9.9990 chunk 375 optimal weight: 6.9990 chunk 257 optimal weight: 0.4980 chunk 385 optimal weight: 30.0000 chunk 240 optimal weight: 8.9990 chunk 337 optimal weight: 5.9990 chunk 79 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 chunk 132 optimal weight: 0.7980 overall best weight: 3.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2244 GLN ** C2285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 983 ASN ** D1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2285 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.050328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.042497 restraints weight = 293475.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.043157 restraints weight = 190075.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.043714 restraints weight = 139959.532| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 30589 Z= 0.206 Angle : 0.685 9.758 41584 Z= 0.354 Chirality : 0.044 0.324 4957 Planarity : 0.004 0.041 5196 Dihedral : 12.991 175.496 4907 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.14), residues: 3936 helix: 1.74 (0.10), residues: 2739 sheet: -1.53 (0.36), residues: 183 loop : -2.25 (0.19), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP D1210 HIS 0.009 0.001 HIS C2340 PHE 0.027 0.002 PHE D2319 TYR 0.021 0.002 TYR D2533 ARG 0.011 0.001 ARG D2377 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 2125) hydrogen bonds : angle 4.11871 ( 6240) SS BOND : bond 0.00199 ( 3) SS BOND : angle 0.46414 ( 6) covalent geometry : bond 0.00449 (30586) covalent geometry : angle 0.68499 (41578) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 3.360 Fit side-chains revert: symmetry clash REVERT: C 1098 PHE cc_start: 0.8691 (t80) cc_final: 0.8319 (t80) REVERT: C 1161 LEU cc_start: 0.9491 (tp) cc_final: 0.9227 (tt) REVERT: C 1219 THR cc_start: 0.9098 (t) cc_final: 0.8838 (p) REVERT: C 1786 ASP cc_start: 0.8342 (m-30) cc_final: 0.8141 (m-30) REVERT: C 2270 MET cc_start: 0.8933 (tpp) cc_final: 0.8589 (mmp) REVERT: A 1041 THR cc_start: 0.9124 (m) cc_final: 0.8876 (p) REVERT: A 1097 ASP cc_start: 0.8964 (t70) cc_final: 0.8594 (t70) REVERT: A 1226 MET cc_start: 0.8704 (ppp) cc_final: 0.8172 (ppp) REVERT: A 1719 MET cc_start: 0.8239 (pmm) cc_final: 0.7971 (pmm) REVERT: A 1791 MET cc_start: 0.8239 (ptm) cc_final: 0.8036 (ptt) REVERT: A 2023 MET cc_start: 0.8439 (mtt) cc_final: 0.7937 (mtp) REVERT: A 2061 MET cc_start: 0.7573 (mmp) cc_final: 0.7330 (mmp) REVERT: A 2270 MET cc_start: 0.8313 (mmm) cc_final: 0.8032 (tpp) REVERT: D 1170 PHE cc_start: 0.8914 (t80) cc_final: 0.8649 (t80) REVERT: D 1219 THR cc_start: 0.9344 (t) cc_final: 0.9121 (p) REVERT: D 1530 MET cc_start: 0.8687 (ptp) cc_final: 0.8191 (ttm) REVERT: D 1700 MET cc_start: 0.8565 (ptm) cc_final: 0.8103 (ppp) REVERT: D 2138 MET cc_start: 0.9002 (mmm) cc_final: 0.8682 (tpp) REVERT: D 2241 MET cc_start: 0.8797 (tpp) cc_final: 0.8045 (tpt) REVERT: D 2270 MET cc_start: 0.7698 (mmp) cc_final: 0.7134 (mmm) REVERT: D 2446 MET cc_start: 0.7790 (mmp) cc_final: 0.7573 (mpp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.3275 time to fit residues: 134.2719 Evaluate side-chains 183 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 183 time to evaluate : 3.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 24 optimal weight: 9.9990 chunk 328 optimal weight: 1.9990 chunk 133 optimal weight: 0.5980 chunk 97 optimal weight: 0.9980 chunk 268 optimal weight: 0.8980 chunk 231 optimal weight: 1.9990 chunk 225 optimal weight: 5.9990 chunk 91 optimal weight: 0.5980 chunk 397 optimal weight: 5.9990 chunk 403 optimal weight: 0.9980 chunk 236 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2340 HIS ** A2027 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 983 ASN ** D1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.051775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.044066 restraints weight = 288500.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.044697 restraints weight = 185609.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.045309 restraints weight = 138027.101| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.5757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 30589 Z= 0.113 Angle : 0.604 8.854 41584 Z= 0.301 Chirality : 0.041 0.296 4957 Planarity : 0.004 0.047 5196 Dihedral : 12.470 173.212 4907 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % 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: 1.20 (0.14), residues: 3936 helix: 1.92 (0.10), residues: 2760 sheet: -0.93 (0.39), residues: 162 loop : -2.16 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP C1210 HIS 0.007 0.001 HIS D1304 PHE 0.041 0.001 PHE C1297 TYR 0.012 0.001 TYR C 842 ARG 0.005 0.000 ARG D2534 Details of bonding type rmsd hydrogen bonds : bond 0.03610 ( 2125) hydrogen bonds : angle 3.81250 ( 6240) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.40551 ( 6) covalent geometry : bond 0.00232 (30586) covalent geometry : angle 0.60435 (41578) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7872 Ramachandran restraints generated. 3936 Oldfield, 0 Emsley, 3936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 3.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 1219 THR cc_start: 0.9033 (t) cc_final: 0.8789 (p) REVERT: C 1719 MET cc_start: 0.8276 (pmm) cc_final: 0.7911 (pmm) REVERT: C 2023 MET cc_start: 0.7734 (mmt) cc_final: 0.6269 (mtt) REVERT: C 2270 MET cc_start: 0.8918 (tpp) cc_final: 0.8613 (mmm) REVERT: C 2304 MET cc_start: 0.8404 (mmm) cc_final: 0.8203 (mmm) REVERT: A 1097 ASP cc_start: 0.8968 (t70) cc_final: 0.8572 (t70) REVERT: A 1719 MET cc_start: 0.8183 (pmm) cc_final: 0.7868 (pmm) REVERT: A 1791 MET cc_start: 0.8157 (ptm) cc_final: 0.7941 (ptt) REVERT: A 1980 MET cc_start: 0.8535 (pmm) cc_final: 0.7777 (ptp) REVERT: A 2023 MET cc_start: 0.8551 (mtt) cc_final: 0.8111 (mtp) REVERT: A 2270 MET cc_start: 0.8359 (mmm) cc_final: 0.8100 (mmm) REVERT: A 2495 GLU cc_start: 0.8934 (mp0) cc_final: 0.8728 (mp0) REVERT: D 1170 PHE cc_start: 0.8956 (t80) cc_final: 0.8685 (t80) REVERT: D 1219 THR cc_start: 0.9245 (t) cc_final: 0.8998 (p) REVERT: D 1530 MET cc_start: 0.8689 (ptp) cc_final: 0.8283 (ttm) REVERT: D 1690 LEU cc_start: 0.8777 (pt) cc_final: 0.8460 (tt) REVERT: D 1700 MET cc_start: 0.8531 (ptm) cc_final: 0.8016 (ppp) REVERT: D 2138 MET cc_start: 0.9120 (mmm) cc_final: 0.8662 (tpp) REVERT: D 2241 MET cc_start: 0.8495 (tpp) cc_final: 0.7750 (tpt) REVERT: D 2270 MET cc_start: 0.7909 (mmp) cc_final: 0.7547 (mmm) REVERT: D 2446 MET cc_start: 0.7719 (mmp) cc_final: 0.7482 (mpp) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.3166 time to fit residues: 131.6009 Evaluate side-chains 193 residues out of total 3639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 3.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 405 random chunks: chunk 146 optimal weight: 8.9990 chunk 73 optimal weight: 0.0570 chunk 11 optimal weight: 7.9990 chunk 255 optimal weight: 0.0040 chunk 395 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 157 optimal weight: 4.9990 chunk 364 optimal weight: 4.9990 chunk 397 optimal weight: 5.9990 chunk 347 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 overall best weight: 2.6116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2364 GLN C2391 GLN ** D1200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D2285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.050506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.042746 restraints weight = 293502.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.043372 restraints weight = 187096.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.043865 restraints weight = 138523.289| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.6203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 30589 Z= 0.156 Angle : 0.635 11.687 41584 Z= 0.323 Chirality : 0.042 0.300 4957 Planarity : 0.004 0.044 5196 Dihedral : 12.361 175.779 4907 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.04 % Allowed : 0.46 % Favored : 99.50 % 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: 1.16 (0.14), residues: 3936 helix: 1.91 (0.10), residues: 2745 sheet: -1.00 (0.39), residues: 162 loop : -2.18 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D1210 HIS 0.006 0.001 HIS C2058 PHE 0.051 0.002 PHE C1297 TYR 0.018 0.001 TYR C2533 ARG 0.006 0.001 ARG D2534 Details of bonding type rmsd hydrogen bonds : bond 0.03885 ( 2125) hydrogen bonds : angle 3.96562 ( 6240) SS BOND : bond 0.00211 ( 3) SS BOND : angle 0.44627 ( 6) covalent geometry : bond 0.00336 (30586) covalent geometry : angle 0.63487 (41578) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7872.89 seconds wall clock time: 139 minutes 7.51 seconds (8347.51 seconds total)