Starting phenix.real_space_refine on Sat Mar 23 05:05:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3r_7042/03_2024/6b3r_7042.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3r_7042/03_2024/6b3r_7042.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3r_7042/03_2024/6b3r_7042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3r_7042/03_2024/6b3r_7042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3r_7042/03_2024/6b3r_7042.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3r_7042/03_2024/6b3r_7042.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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: 4 Type Number sf(0) Gaussians S 210 5.16 5 C 23361 2.51 5 N 6060 2.21 5 O 6087 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 2272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 2533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 2272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 2533": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1062": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 2272": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 2533": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 35718 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1502, 11826 Classifications: {'peptide': 1502} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 1433} Chain breaks: 11 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 608 Unresolved non-hydrogen angles: 803 Unresolved non-hydrogen dihedrals: 525 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 12, 'ASN:plan1': 1, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 16, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 350 Chain: "B" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 11826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1502, 11826 Classifications: {'peptide': 1502} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 1433} Chain breaks: 11 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 608 Unresolved non-hydrogen angles: 803 Unresolved non-hydrogen dihedrals: 525 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 12, 'ASN:plan1': 1, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 16, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 350 Chain: "E" Number of atoms: 11826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1502, 11826 Classifications: {'peptide': 1502} Incomplete info: {'truncation_to_alanine': 149} Link IDs: {'PCIS': 1, 'PTRANS': 67, 'TRANS': 1433} Chain breaks: 11 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 608 Unresolved non-hydrogen angles: 803 Unresolved non-hydrogen dihedrals: 525 Unresolved non-hydrogen chiralities: 64 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 2, 'TYR:plan': 12, 'ASN:plan1': 1, 'TRP:plan': 5, 'ASP:plan': 7, 'PHE:plan': 16, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 350 Chain: "D" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 80 Classifications: {'peptide': 16} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'TRANS': 15} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 18.84, per 1000 atoms: 0.53 Number of scatterers: 35718 At special positions: 0 Unit cell: (204.1, 214.5, 153.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 210 16.00 O 6087 8.00 N 6060 7.00 C 23361 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 881 " - pdb=" SG CYS A1059 " distance=2.03 Simple disulfide: pdb=" SG CYS C 881 " - pdb=" SG CYS C1059 " distance=2.03 Simple disulfide: pdb=" SG CYS E 881 " - pdb=" SG CYS E1059 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 12.64 Conformation dependent library (CDL) restraints added in 6.6 seconds 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8730 Finding SS restraints... Secondary structure from input PDB file: 198 helices and 18 sheets defined 64.6% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.50 Creating SS restraints... Processing helix chain 'A' and resid 587 through 599 removed outlier: 3.752A pdb=" N PHE A 594 " --> pdb=" O CYS A 590 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 625 removed outlier: 3.889A pdb=" N LEU A 613 " --> pdb=" O VAL A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 652 removed outlier: 3.659A pdb=" N THR A 652 " --> pdb=" O ILE A 648 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 Processing helix chain 'A' and resid 684 through 706 Proline residue: A 693 - end of helix removed outlier: 3.810A pdb=" N PHE A 696 " --> pdb=" O ILE A 692 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A 698 " --> pdb=" O GLY A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 709 through 714 removed outlier: 3.776A pdb=" N GLN A 713 " --> pdb=" O ARG A 709 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 805 Processing helix chain 'A' and resid 809 through 824 Processing helix chain 'A' and resid 829 through 840 Processing helix chain 'A' and resid 845 through 866 removed outlier: 3.516A pdb=" N CYS A 851 " --> pdb=" O PRO A 847 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS A 858 " --> pdb=" O THR A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 895 through 899 removed outlier: 4.078A pdb=" N SER A 899 " --> pdb=" O ILE A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 949 removed outlier: 3.637A pdb=" N TYR A 941 " --> pdb=" O GLU A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 972 Processing helix chain 'A' and resid 973 through 984 Processing helix chain 'A' and resid 984 through 989 Processing helix chain 'A' and resid 989 through 1005 removed outlier: 3.521A pdb=" N ILE A 993 " --> pdb=" O PHE A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1022 Processing helix chain 'A' and resid 1025 through 1031 Processing helix chain 'A' and resid 1032 through 1050 Processing helix chain 'A' and resid 1066 through 1070 removed outlier: 3.881A pdb=" N ALA A1069 " --> pdb=" O TRP A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1080 Processing helix chain 'A' and resid 1094 through 1116 removed outlier: 4.050A pdb=" N GLN A1109 " --> pdb=" O SER A1105 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A1114 " --> pdb=" O VAL A1110 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG A1115 " --> pdb=" O PHE A1111 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1161 Processing helix chain 'A' and resid 1162 through 1175 removed outlier: 3.521A pdb=" N LEU A1166 " --> pdb=" O PHE A1162 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1199 removed outlier: 5.715A pdb=" N THR A1196 " --> pdb=" O LEU A1192 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR A1197 " --> pdb=" O LEU A1193 " (cutoff:3.500A) Processing helix chain 'A' and resid 1205 through 1228 Processing helix chain 'A' and resid 1229 through 1232 removed outlier: 3.613A pdb=" N CYS A1232 " --> pdb=" O LEU A1229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1229 through 1232' Processing helix chain 'A' and resid 1245 through 1250 removed outlier: 3.806A pdb=" N PHE A1249 " --> pdb=" O VAL A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1267 removed outlier: 4.098A pdb=" N THR A1266 " --> pdb=" O GLU A1263 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG A1267 " --> pdb=" O MET A1264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1263 through 1267' Processing helix chain 'A' and resid 1279 through 1298 removed outlier: 3.590A pdb=" N ASP A1283 " --> pdb=" O GLY A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1299 through 1315 removed outlier: 3.559A pdb=" N LEU A1303 " --> pdb=" O SER A1299 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA A1307 " --> pdb=" O LEU A1303 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A1311 " --> pdb=" O ALA A1307 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR A1312 " --> pdb=" O ASP A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1315 through 1365 Processing helix chain 'A' and resid 1494 through 1499 Processing helix chain 'A' and resid 1499 through 1504 Processing helix chain 'A' and resid 1506 through 1524 Processing helix chain 'A' and resid 1524 through 1546 removed outlier: 4.609A pdb=" N MET A1530 " --> pdb=" O HIS A1526 " (cutoff:3.500A) Processing helix chain 'A' and resid 1554 through 1563 removed outlier: 3.877A pdb=" N GLN A1558 " --> pdb=" O GLY A1554 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A1559 " --> pdb=" O VAL A1555 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N TYR A1560 " --> pdb=" O LEU A1556 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL A1561 " --> pdb=" O ASP A1557 " (cutoff:3.500A) Processing helix chain 'A' and resid 1565 through 1570 removed outlier: 4.238A pdb=" N SER A1569 " --> pdb=" O GLU A1565 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY A1570 " --> pdb=" O ALA A1566 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1565 through 1570' Processing helix chain 'A' and resid 1656 through 1667 removed outlier: 3.585A pdb=" N GLU A1660 " --> pdb=" O ILE A1656 " (cutoff:3.500A) Processing helix chain 'A' and resid 1673 through 1686 Processing helix chain 'A' and resid 1687 through 1702 removed outlier: 3.746A pdb=" N HIS A1699 " --> pdb=" O ILE A1695 " (cutoff:3.500A) Processing helix chain 'A' and resid 1708 through 1718 removed outlier: 3.522A pdb=" N VAL A1712 " --> pdb=" O LEU A1708 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A1713 " --> pdb=" O VAL A1709 " (cutoff:3.500A) Processing helix chain 'A' and resid 1726 through 1746 removed outlier: 3.901A pdb=" N TRP A1730 " --> pdb=" O SER A1726 " (cutoff:3.500A) Processing helix chain 'A' and resid 1752 through 1755 Processing helix chain 'A' and resid 1756 through 1763 Processing helix chain 'A' and resid 1769 through 1775 Processing helix chain 'A' and resid 1785 through 1803 Processing helix chain 'A' and resid 1955 through 1967 removed outlier: 4.279A pdb=" N PHE A1961 " --> pdb=" O PRO A1957 " (cutoff:3.500A) Processing helix chain 'A' and resid 1976 through 1995 Processing helix chain 'A' and resid 2016 through 2041 removed outlier: 3.775A pdb=" N PHE A2020 " --> pdb=" O VAL A2016 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU A2021 " --> pdb=" O PRO A2017 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE A2022 " --> pdb=" O GLN A2018 " (cutoff:3.500A) Processing helix chain 'A' and resid 2042 through 2063 removed outlier: 3.790A pdb=" N PHE A2062 " --> pdb=" O HIS A2058 " (cutoff:3.500A) Processing helix chain 'A' and resid 2076 through 2098 Processing helix chain 'A' and resid 2115 through 2128 removed outlier: 3.830A pdb=" N VAL A2128 " --> pdb=" O GLY A2124 " (cutoff:3.500A) Processing helix chain 'A' and resid 2131 through 2143 Processing helix chain 'A' and resid 2148 through 2175 Processing helix chain 'A' and resid 2186 through 2205 removed outlier: 3.717A pdb=" N GLY A2193 " --> pdb=" O TYR A2189 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A2194 " --> pdb=" O GLY A2190 " (cutoff:3.500A) Processing helix chain 'A' and resid 2205 through 2212 Processing helix chain 'A' and resid 2252 through 2263 removed outlier: 3.522A pdb=" N TYR A2256 " --> pdb=" O THR A2252 " (cutoff:3.500A) Processing helix chain 'A' and resid 2266 through 2275 removed outlier: 3.557A pdb=" N MET A2270 " --> pdb=" O TYR A2266 " (cutoff:3.500A) Processing helix chain 'A' and resid 2297 through 2310 Processing helix chain 'A' and resid 2348 through 2360 Processing helix chain 'A' and resid 2466 through 2485 removed outlier: 4.026A pdb=" N PHE A2484 " --> pdb=" O PHE A2480 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE A2485 " --> pdb=" O VAL A2481 " (cutoff:3.500A) Processing helix chain 'A' and resid 2491 through 2496 Processing helix chain 'A' and resid 2500 through 2517 Processing helix chain 'A' and resid 2518 through 2533 removed outlier: 3.595A pdb=" N GLU A2522 " --> pdb=" O GLU A2518 " (cutoff:3.500A) Processing helix chain 'A' and resid 2535 through 2543 Processing helix chain 'C' and resid 587 through 599 removed outlier: 3.752A pdb=" N PHE C 594 " --> pdb=" O CYS C 590 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ILE C 595 " --> pdb=" O ALA C 591 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 625 removed outlier: 3.890A pdb=" N LEU C 613 " --> pdb=" O VAL C 609 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 652 removed outlier: 3.659A pdb=" N THR C 652 " --> pdb=" O ILE C 648 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 664 Processing helix chain 'C' and resid 684 through 706 Proline residue: C 693 - end of helix removed outlier: 3.810A pdb=" N PHE C 696 " --> pdb=" O ILE C 692 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 698 " --> pdb=" O GLY C 694 " (cutoff:3.500A) Processing helix chain 'C' and resid 709 through 714 removed outlier: 3.776A pdb=" N GLN C 713 " --> pdb=" O ARG C 709 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 805 Processing helix chain 'C' and resid 809 through 824 Processing helix chain 'C' and resid 829 through 840 Processing helix chain 'C' and resid 845 through 866 removed outlier: 3.516A pdb=" N CYS C 851 " --> pdb=" O PRO C 847 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N CYS C 858 " --> pdb=" O THR C 854 " (cutoff:3.500A) Processing helix chain 'C' and resid 895 through 899 removed outlier: 4.078A pdb=" N SER C 899 " --> pdb=" O ILE C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 924 through 949 removed outlier: 3.639A pdb=" N TYR C 941 " --> pdb=" O GLU C 937 " (cutoff:3.500A) Processing helix chain 'C' and resid 968 through 972 Processing helix chain 'C' and resid 973 through 984 Processing helix chain 'C' and resid 984 through 989 Processing helix chain 'C' and resid 989 through 1005 removed outlier: 3.521A pdb=" N ILE C 993 " --> pdb=" O PHE C 989 " (cutoff:3.500A) Processing helix chain 'C' and resid 1010 through 1022 Processing helix chain 'C' and resid 1025 through 1031 Processing helix chain 'C' and resid 1032 through 1050 Processing helix chain 'C' and resid 1066 through 1070 removed outlier: 3.882A pdb=" N ALA C1069 " --> pdb=" O TRP C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1075 through 1080 Processing helix chain 'C' and resid 1094 through 1116 removed outlier: 4.050A pdb=" N GLN C1109 " --> pdb=" O SER C1105 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU C1114 " --> pdb=" O VAL C1110 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG C1115 " --> pdb=" O PHE C1111 " (cutoff:3.500A) Processing helix chain 'C' and resid 1149 through 1161 Processing helix chain 'C' and resid 1162 through 1175 removed outlier: 3.520A pdb=" N LEU C1166 " --> pdb=" O PHE C1162 " (cutoff:3.500A) Processing helix chain 'C' and resid 1178 through 1199 removed outlier: 5.715A pdb=" N THR C1196 " --> pdb=" O LEU C1192 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N THR C1197 " --> pdb=" O LEU C1193 " (cutoff:3.500A) Processing helix chain 'C' and resid 1205 through 1228 Processing helix chain 'C' and resid 1229 through 1232 removed outlier: 3.614A pdb=" N CYS C1232 " --> pdb=" O LEU C1229 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1229 through 1232' Processing helix chain 'C' and resid 1245 through 1250 removed outlier: 3.805A pdb=" N PHE C1249 " --> pdb=" O VAL C1245 " (cutoff:3.500A) Processing helix chain 'C' and resid 1263 through 1267 removed outlier: 4.099A pdb=" N THR C1266 " --> pdb=" O GLU C1263 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ARG C1267 " --> pdb=" O MET C1264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1263 through 1267' Processing helix chain 'C' and resid 1279 through 1298 removed outlier: 3.590A pdb=" N ASP C1283 " --> pdb=" O GLY C1279 " (cutoff:3.500A) Processing helix chain 'C' and resid 1299 through 1315 removed outlier: 3.558A pdb=" N LEU C1303 " --> pdb=" O SER C1299 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA C1307 " --> pdb=" O LEU C1303 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA C1311 " --> pdb=" O ALA C1307 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR C1312 " --> pdb=" O ASP C1308 " (cutoff:3.500A) Processing helix chain 'C' and resid 1315 through 1365 Processing helix chain 'C' and resid 1494 through 1499 Processing helix chain 'C' and resid 1499 through 1504 Processing helix chain 'C' and resid 1506 through 1524 Processing helix chain 'C' and resid 1524 through 1546 removed outlier: 4.609A pdb=" N MET C1530 " --> pdb=" O HIS C1526 " (cutoff:3.500A) Processing helix chain 'C' and resid 1554 through 1563 removed outlier: 3.877A pdb=" N GLN C1558 " --> pdb=" O GLY C1554 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU C1559 " --> pdb=" O VAL C1555 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR C1560 " --> pdb=" O LEU C1556 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL C1561 " --> pdb=" O ASP C1557 " (cutoff:3.500A) Processing helix chain 'C' and resid 1565 through 1570 removed outlier: 4.238A pdb=" N SER C1569 " --> pdb=" O GLU C1565 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY C1570 " --> pdb=" O ALA C1566 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1565 through 1570' Processing helix chain 'C' and resid 1656 through 1667 removed outlier: 3.585A pdb=" N GLU C1660 " --> pdb=" O ILE C1656 " (cutoff:3.500A) Processing helix chain 'C' and resid 1673 through 1686 Processing helix chain 'C' and resid 1687 through 1702 removed outlier: 3.746A pdb=" N HIS C1699 " --> pdb=" O ILE C1695 " (cutoff:3.500A) Processing helix chain 'C' and resid 1708 through 1718 removed outlier: 3.522A pdb=" N VAL C1712 " --> pdb=" O LEU C1708 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU C1713 " --> pdb=" O VAL C1709 " (cutoff:3.500A) Processing helix chain 'C' and resid 1726 through 1746 removed outlier: 3.901A pdb=" N TRP C1730 " --> pdb=" O SER C1726 " (cutoff:3.500A) Processing helix chain 'C' and resid 1752 through 1755 Processing helix chain 'C' and resid 1756 through 1763 Processing helix chain 'C' and resid 1769 through 1775 Processing helix chain 'C' and resid 1785 through 1803 Processing helix chain 'C' and resid 1955 through 1967 removed outlier: 4.280A pdb=" N PHE C1961 " --> pdb=" O PRO C1957 " (cutoff:3.500A) Processing helix chain 'C' and resid 1976 through 1995 Processing helix chain 'C' and resid 2016 through 2041 removed outlier: 3.775A pdb=" N PHE C2020 " --> pdb=" O VAL C2016 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C2021 " --> pdb=" O PRO C2017 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N PHE C2022 " --> pdb=" O GLN C2018 " (cutoff:3.500A) Processing helix chain 'C' and resid 2042 through 2063 removed outlier: 3.790A pdb=" N PHE C2062 " --> pdb=" O HIS C2058 " (cutoff:3.500A) Processing helix chain 'C' and resid 2076 through 2098 Processing helix chain 'C' and resid 2115 through 2128 removed outlier: 3.830A pdb=" N VAL C2128 " --> pdb=" O GLY C2124 " (cutoff:3.500A) Processing helix chain 'C' and resid 2131 through 2143 Processing helix chain 'C' and resid 2148 through 2175 Processing helix chain 'C' and resid 2186 through 2205 removed outlier: 3.717A pdb=" N GLY C2193 " --> pdb=" O TYR C2189 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU C2194 " --> pdb=" O GLY C2190 " (cutoff:3.500A) Processing helix chain 'C' and resid 2205 through 2212 Processing helix chain 'C' and resid 2252 through 2263 removed outlier: 3.521A pdb=" N TYR C2256 " --> pdb=" O THR C2252 " (cutoff:3.500A) Processing helix chain 'C' and resid 2266 through 2275 removed outlier: 3.558A pdb=" N MET C2270 " --> pdb=" O TYR C2266 " (cutoff:3.500A) Processing helix chain 'C' and resid 2297 through 2310 Processing helix chain 'C' and resid 2348 through 2360 Processing helix chain 'C' and resid 2466 through 2485 removed outlier: 4.026A pdb=" N PHE C2484 " --> pdb=" O PHE C2480 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE C2485 " --> pdb=" O VAL C2481 " (cutoff:3.500A) Processing helix chain 'C' and resid 2491 through 2496 Processing helix chain 'C' and resid 2500 through 2517 Processing helix chain 'C' and resid 2518 through 2533 removed outlier: 3.596A pdb=" N GLU C2522 " --> pdb=" O GLU C2518 " (cutoff:3.500A) Processing helix chain 'C' and resid 2535 through 2543 Processing helix chain 'E' and resid 587 through 599 removed outlier: 3.753A pdb=" N PHE E 594 " --> pdb=" O CYS E 590 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE E 595 " --> pdb=" O ALA E 591 " (cutoff:3.500A) Processing helix chain 'E' and resid 609 through 625 removed outlier: 3.890A pdb=" N LEU E 613 " --> pdb=" O VAL E 609 " (cutoff:3.500A) Processing helix chain 'E' and resid 630 through 652 removed outlier: 3.660A pdb=" N THR E 652 " --> pdb=" O ILE E 648 " (cutoff:3.500A) Processing helix chain 'E' and resid 656 through 664 Processing helix chain 'E' and resid 684 through 706 Proline residue: E 693 - end of helix removed outlier: 3.810A pdb=" N PHE E 696 " --> pdb=" O ILE E 692 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 698 " --> pdb=" O GLY E 694 " (cutoff:3.500A) Processing helix chain 'E' and resid 709 through 714 removed outlier: 3.776A pdb=" N GLN E 713 " --> pdb=" O ARG E 709 " (cutoff:3.500A) Processing helix chain 'E' and resid 783 through 805 Processing helix chain 'E' and resid 809 through 824 Processing helix chain 'E' and resid 829 through 840 Processing helix chain 'E' and resid 845 through 866 removed outlier: 3.516A pdb=" N CYS E 851 " --> pdb=" O PRO E 847 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N CYS E 858 " --> pdb=" O THR E 854 " (cutoff:3.500A) Processing helix chain 'E' and resid 895 through 899 removed outlier: 4.078A pdb=" N SER E 899 " --> pdb=" O ILE E 896 " (cutoff:3.500A) Processing helix chain 'E' and resid 924 through 949 removed outlier: 3.638A pdb=" N TYR E 941 " --> pdb=" O GLU E 937 " (cutoff:3.500A) Processing helix chain 'E' and resid 968 through 972 Processing helix chain 'E' and resid 973 through 984 Processing helix chain 'E' and resid 984 through 989 Processing helix chain 'E' and resid 989 through 1005 removed outlier: 3.521A pdb=" N ILE E 993 " --> pdb=" O PHE E 989 " (cutoff:3.500A) Processing helix chain 'E' and resid 1010 through 1022 Processing helix chain 'E' and resid 1025 through 1031 Processing helix chain 'E' and resid 1032 through 1050 Processing helix chain 'E' and resid 1066 through 1070 removed outlier: 3.882A pdb=" N ALA E1069 " --> pdb=" O TRP E1066 " (cutoff:3.500A) Processing helix chain 'E' and resid 1075 through 1080 Processing helix chain 'E' and resid 1094 through 1116 removed outlier: 4.050A pdb=" N GLN E1109 " --> pdb=" O SER E1105 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU E1114 " --> pdb=" O VAL E1110 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ARG E1115 " --> pdb=" O PHE E1111 " (cutoff:3.500A) Processing helix chain 'E' and resid 1149 through 1161 Processing helix chain 'E' and resid 1162 through 1175 removed outlier: 3.519A pdb=" N LEU E1166 " --> pdb=" O PHE E1162 " (cutoff:3.500A) Processing helix chain 'E' and resid 1178 through 1199 removed outlier: 5.716A pdb=" N THR E1196 " --> pdb=" O LEU E1192 " (cutoff:3.500A) removed outlier: 5.800A pdb=" N THR E1197 " --> pdb=" O LEU E1193 " (cutoff:3.500A) Processing helix chain 'E' and resid 1205 through 1228 Processing helix chain 'E' and resid 1229 through 1232 removed outlier: 3.613A pdb=" N CYS E1232 " --> pdb=" O LEU E1229 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1229 through 1232' Processing helix chain 'E' and resid 1245 through 1250 removed outlier: 3.806A pdb=" N PHE E1249 " --> pdb=" O VAL E1245 " (cutoff:3.500A) Processing helix chain 'E' and resid 1263 through 1267 removed outlier: 4.099A pdb=" N THR E1266 " --> pdb=" O GLU E1263 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG E1267 " --> pdb=" O MET E1264 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1263 through 1267' Processing helix chain 'E' and resid 1279 through 1298 removed outlier: 3.591A pdb=" N ASP E1283 " --> pdb=" O GLY E1279 " (cutoff:3.500A) Processing helix chain 'E' and resid 1299 through 1315 removed outlier: 3.558A pdb=" N LEU E1303 " --> pdb=" O SER E1299 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA E1307 " --> pdb=" O LEU E1303 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA E1311 " --> pdb=" O ALA E1307 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR E1312 " --> pdb=" O ASP E1308 " (cutoff:3.500A) Processing helix chain 'E' and resid 1315 through 1365 Processing helix chain 'E' and resid 1494 through 1499 Processing helix chain 'E' and resid 1499 through 1504 Processing helix chain 'E' and resid 1506 through 1524 Processing helix chain 'E' and resid 1524 through 1546 removed outlier: 4.609A pdb=" N MET E1530 " --> pdb=" O HIS E1526 " (cutoff:3.500A) Processing helix chain 'E' and resid 1554 through 1563 removed outlier: 3.877A pdb=" N GLN E1558 " --> pdb=" O GLY E1554 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU E1559 " --> pdb=" O VAL E1555 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N TYR E1560 " --> pdb=" O LEU E1556 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL E1561 " --> pdb=" O ASP E1557 " (cutoff:3.500A) Processing helix chain 'E' and resid 1565 through 1570 removed outlier: 4.238A pdb=" N SER E1569 " --> pdb=" O GLU E1565 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY E1570 " --> pdb=" O ALA E1566 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1565 through 1570' Processing helix chain 'E' and resid 1656 through 1667 removed outlier: 3.586A pdb=" N GLU E1660 " --> pdb=" O ILE E1656 " (cutoff:3.500A) Processing helix chain 'E' and resid 1673 through 1686 Processing helix chain 'E' and resid 1687 through 1702 removed outlier: 3.747A pdb=" N HIS E1699 " --> pdb=" O ILE E1695 " (cutoff:3.500A) Processing helix chain 'E' and resid 1708 through 1718 removed outlier: 3.522A pdb=" N VAL E1712 " --> pdb=" O LEU E1708 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU E1713 " --> pdb=" O VAL E1709 " (cutoff:3.500A) Processing helix chain 'E' and resid 1726 through 1746 removed outlier: 3.900A pdb=" N TRP E1730 " --> pdb=" O SER E1726 " (cutoff:3.500A) Processing helix chain 'E' and resid 1752 through 1755 Processing helix chain 'E' and resid 1756 through 1763 Processing helix chain 'E' and resid 1769 through 1775 Processing helix chain 'E' and resid 1785 through 1803 Processing helix chain 'E' and resid 1955 through 1967 removed outlier: 4.280A pdb=" N PHE E1961 " --> pdb=" O PRO E1957 " (cutoff:3.500A) Processing helix chain 'E' and resid 1976 through 1995 Processing helix chain 'E' and resid 2016 through 2041 removed outlier: 3.775A pdb=" N PHE E2020 " --> pdb=" O VAL E2016 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E2021 " --> pdb=" O PRO E2017 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N PHE E2022 " --> pdb=" O GLN E2018 " (cutoff:3.500A) Processing helix chain 'E' and resid 2042 through 2063 removed outlier: 3.791A pdb=" N PHE E2062 " --> pdb=" O HIS E2058 " (cutoff:3.500A) Processing helix chain 'E' and resid 2076 through 2098 Processing helix chain 'E' and resid 2115 through 2128 removed outlier: 3.830A pdb=" N VAL E2128 " --> pdb=" O GLY E2124 " (cutoff:3.500A) Processing helix chain 'E' and resid 2131 through 2143 Processing helix chain 'E' and resid 2148 through 2175 Processing helix chain 'E' and resid 2186 through 2205 removed outlier: 3.717A pdb=" N GLY E2193 " --> pdb=" O TYR E2189 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU E2194 " --> pdb=" O GLY E2190 " (cutoff:3.500A) Processing helix chain 'E' and resid 2205 through 2212 Processing helix chain 'E' and resid 2252 through 2263 removed outlier: 3.522A pdb=" N TYR E2256 " --> pdb=" O THR E2252 " (cutoff:3.500A) Processing helix chain 'E' and resid 2266 through 2275 removed outlier: 3.557A pdb=" N MET E2270 " --> pdb=" O TYR E2266 " (cutoff:3.500A) Processing helix chain 'E' and resid 2297 through 2310 Processing helix chain 'E' and resid 2348 through 2360 Processing helix chain 'E' and resid 2466 through 2485 removed outlier: 4.027A pdb=" N PHE E2484 " --> pdb=" O PHE E2480 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHE E2485 " --> pdb=" O VAL E2481 " (cutoff:3.500A) Processing helix chain 'E' and resid 2491 through 2496 Processing helix chain 'E' and resid 2500 through 2517 Processing helix chain 'E' and resid 2518 through 2533 removed outlier: 3.595A pdb=" N GLU E2522 " --> pdb=" O GLU E2518 " (cutoff:3.500A) Processing helix chain 'E' and resid 2535 through 2543 Processing sheet with id=AA1, first strand: chain 'A' and resid 2219 through 2220 removed outlier: 4.124A pdb=" N VAL A2219 " --> pdb=" O VAL A2453 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2229 through 2231 removed outlier: 6.402A pdb=" N LEU A2230 " --> pdb=" O LEU A2238 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 2281 through 2282 Processing sheet with id=AA4, first strand: chain 'A' and resid 2286 through 2287 Processing sheet with id=AA5, first strand: chain 'A' and resid 2315 through 2317 Processing sheet with id=AA6, first strand: chain 'A' and resid 2366 through 2372 removed outlier: 5.604A pdb=" N VAL A2367 " --> pdb=" O ILE A2403 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE A2403 " --> pdb=" O VAL A2367 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL A2401 " --> pdb=" O PRO A2369 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU A2399 " --> pdb=" O LEU A2371 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A2406 " --> pdb=" O TRP A2429 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2219 through 2220 removed outlier: 4.125A pdb=" N VAL C2219 " --> pdb=" O VAL C2453 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 2229 through 2231 removed outlier: 6.401A pdb=" N LEU C2230 " --> pdb=" O LEU C2238 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2281 through 2282 Processing sheet with id=AB1, first strand: chain 'C' and resid 2286 through 2287 Processing sheet with id=AB2, first strand: chain 'C' and resid 2315 through 2317 Processing sheet with id=AB3, first strand: chain 'C' and resid 2366 through 2372 removed outlier: 5.604A pdb=" N VAL C2367 " --> pdb=" O ILE C2403 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE C2403 " --> pdb=" O VAL C2367 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL C2401 " --> pdb=" O PRO C2369 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N LEU C2399 " --> pdb=" O LEU C2371 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG C2406 " --> pdb=" O TRP C2429 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 2219 through 2220 removed outlier: 4.124A pdb=" N VAL E2219 " --> pdb=" O VAL E2453 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 2229 through 2231 removed outlier: 6.402A pdb=" N LEU E2230 " --> pdb=" O LEU E2238 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 2281 through 2282 Processing sheet with id=AB7, first strand: chain 'E' and resid 2286 through 2287 Processing sheet with id=AB8, first strand: chain 'E' and resid 2315 through 2317 Processing sheet with id=AB9, first strand: chain 'E' and resid 2366 through 2372 removed outlier: 5.605A pdb=" N VAL E2367 " --> pdb=" O ILE E2403 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N ILE E2403 " --> pdb=" O VAL E2367 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N VAL E2401 " --> pdb=" O PRO E2369 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N LEU E2399 " --> pdb=" O LEU E2371 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG E2406 " --> pdb=" O TRP E2429 " (cutoff:3.500A) 2028 hydrogen bonds defined for protein. 6003 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: 13.08 Time building geometry restraints manager: 13.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 11094 1.34 - 1.46: 8886 1.46 - 1.58: 16284 1.58 - 1.71: 0 1.71 - 1.83: 324 Bond restraints: 36588 Sorted by residual: bond pdb=" CG1 ILE A2162 " pdb=" CD1 ILE A2162 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.34e+00 bond pdb=" CG1 ILE E2162 " pdb=" CD1 ILE E2162 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.32e+00 bond pdb=" CG1 ILE C2162 " pdb=" CD1 ILE C2162 " ideal model delta sigma weight residual 1.513 1.423 0.090 3.90e-02 6.57e+02 5.30e+00 bond pdb=" C PHE A1751 " pdb=" N PHE A1752 " ideal model delta sigma weight residual 1.331 1.293 0.038 2.07e-02 2.33e+03 3.34e+00 bond pdb=" C PHE E1751 " pdb=" N PHE E1752 " ideal model delta sigma weight residual 1.331 1.293 0.038 2.07e-02 2.33e+03 3.34e+00 ... (remaining 36583 not shown) Histogram of bond angle deviations from ideal: 94.19 - 102.83: 161 102.83 - 111.47: 15423 111.47 - 120.12: 18697 120.12 - 128.76: 15117 128.76 - 137.40: 348 Bond angle restraints: 49746 Sorted by residual: angle pdb=" C VAL A 827 " pdb=" N MET A 828 " pdb=" CA MET A 828 " ideal model delta sigma weight residual 126.32 134.08 -7.76 1.74e+00 3.30e-01 1.99e+01 angle pdb=" C VAL E 827 " pdb=" N MET E 828 " pdb=" CA MET E 828 " ideal model delta sigma weight residual 126.32 134.00 -7.68 1.74e+00 3.30e-01 1.95e+01 angle pdb=" C VAL C 827 " pdb=" N MET C 828 " pdb=" CA MET C 828 " ideal model delta sigma weight residual 126.32 133.98 -7.66 1.74e+00 3.30e-01 1.94e+01 angle pdb=" N PHE E2205 " pdb=" CA PHE E2205 " pdb=" C PHE E2205 " ideal model delta sigma weight residual 109.81 119.29 -9.48 2.21e+00 2.05e-01 1.84e+01 angle pdb=" N PHE C2205 " pdb=" CA PHE C2205 " pdb=" C PHE C2205 " ideal model delta sigma weight residual 109.81 119.26 -9.45 2.21e+00 2.05e-01 1.83e+01 ... (remaining 49741 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.62: 20426 15.62 - 31.24: 1033 31.24 - 46.86: 165 46.86 - 62.47: 6 62.47 - 78.09: 21 Dihedral angle restraints: 21651 sinusoidal: 8229 harmonic: 13422 Sorted by residual: dihedral pdb=" CA TRP E1506 " pdb=" C TRP E1506 " pdb=" N VAL E1507 " pdb=" CA VAL E1507 " ideal model delta harmonic sigma weight residual -180.00 -151.56 -28.44 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA TRP C1506 " pdb=" C TRP C1506 " pdb=" N VAL C1507 " pdb=" CA VAL C1507 " ideal model delta harmonic sigma weight residual -180.00 -151.58 -28.42 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA TRP A1506 " pdb=" C TRP A1506 " pdb=" N VAL A1507 " pdb=" CA VAL A1507 " ideal model delta harmonic sigma weight residual -180.00 -151.59 -28.41 0 5.00e+00 4.00e-02 3.23e+01 ... (remaining 21648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 3898 0.054 - 0.109: 1415 0.109 - 0.163: 288 0.163 - 0.218: 54 0.218 - 0.272: 12 Chirality restraints: 5667 Sorted by residual: chirality pdb=" CA PHE E2205 " pdb=" N PHE E2205 " pdb=" C PHE E2205 " pdb=" CB PHE E2205 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" CA PHE A2205 " pdb=" N PHE A2205 " pdb=" C PHE A2205 " pdb=" CB PHE A2205 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 chirality pdb=" CA PHE C2205 " pdb=" N PHE C2205 " pdb=" C PHE C2205 " pdb=" CB PHE C2205 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 5664 not shown) Planarity restraints: 6246 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C2455 " -0.062 5.00e-02 4.00e+02 9.35e-02 1.40e+01 pdb=" N PRO C2456 " 0.161 5.00e-02 4.00e+02 pdb=" CA PRO C2456 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO C2456 " -0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A2455 " 0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO A2456 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO A2456 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A2456 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO E2455 " 0.062 5.00e-02 4.00e+02 9.31e-02 1.39e+01 pdb=" N PRO E2456 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO E2456 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E2456 " 0.057 5.00e-02 4.00e+02 ... (remaining 6243 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 7665 2.78 - 3.31: 33127 3.31 - 3.84: 58159 3.84 - 4.37: 66494 4.37 - 4.90: 111107 Nonbonded interactions: 276552 Sorted by model distance: nonbonded pdb=" OG SER C2535 " pdb=" OG1 THR C2538 " model vdw 2.247 2.440 nonbonded pdb=" OG SER A2535 " pdb=" OG1 THR A2538 " model vdw 2.247 2.440 nonbonded pdb=" OG SER E2535 " pdb=" OG1 THR E2538 " model vdw 2.247 2.440 nonbonded pdb=" O LEU C1161 " pdb=" NE2 GLN C1293 " model vdw 2.292 2.520 nonbonded pdb=" O LEU A1161 " pdb=" NE2 GLN A1293 " model vdw 2.292 2.520 ... (remaining 276547 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 15.910 Check model and map are aligned: 0.540 Set scattering table: 0.340 Process input model: 89.690 Find NCS groups from input model: 2.060 Set up NCS constraints: 0.210 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5245 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 : 0.006 0.090 36588 Z= 0.396 Angle : 1.042 13.441 49746 Z= 0.526 Chirality : 0.058 0.272 5667 Planarity : 0.007 0.093 6246 Dihedral : 10.173 78.092 12912 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.25 % Allowed : 4.59 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -4.41 (0.09), residues: 4434 helix: -2.45 (0.07), residues: 2586 sheet: -3.56 (0.29), residues: 168 loop : -3.48 (0.13), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP A2542 HIS 0.012 0.002 HIS A2340 PHE 0.031 0.003 PHE E2205 TYR 0.029 0.003 TYR C1184 ARG 0.009 0.001 ARG E 846 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1060 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1051 time to evaluate : 3.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 844 ARG cc_start: 0.6083 (mtt180) cc_final: 0.5802 (ptt-90) REVERT: A 858 CYS cc_start: 0.8729 (m) cc_final: 0.8432 (m) REVERT: A 870 LYS cc_start: 0.2274 (mttt) cc_final: 0.2013 (mptt) REVERT: A 910 ASN cc_start: 0.7957 (t0) cc_final: 0.7532 (m-40) REVERT: A 975 LEU cc_start: 0.7678 (tm) cc_final: 0.7466 (mm) REVERT: A 1054 MET cc_start: 0.4192 (mmm) cc_final: 0.3756 (mpp) REVERT: A 1093 ASN cc_start: 0.7360 (m110) cc_final: 0.7108 (m-40) REVERT: A 1320 PHE cc_start: 0.7556 (t80) cc_final: 0.7299 (t80) REVERT: A 1342 LEU cc_start: 0.8826 (mt) cc_final: 0.8584 (tp) REVERT: A 1348 GLN cc_start: 0.8123 (mt0) cc_final: 0.7281 (mt0) REVERT: A 1349 MET cc_start: 0.8509 (mmm) cc_final: 0.8030 (mmm) REVERT: A 1495 MET cc_start: 0.3677 (ptt) cc_final: 0.2793 (ptm) REVERT: A 1544 GLU cc_start: 0.7635 (tt0) cc_final: 0.7167 (tm-30) REVERT: A 1716 LEU cc_start: 0.7738 (mt) cc_final: 0.7497 (mp) REVERT: A 1740 MET cc_start: 0.7978 (tpt) cc_final: 0.6361 (ttm) REVERT: A 1755 ASN cc_start: 0.5017 (m-40) cc_final: 0.4520 (m-40) REVERT: A 1791 MET cc_start: 0.6486 (ptp) cc_final: 0.6030 (ptm) REVERT: A 1952 GLN cc_start: 0.1783 (pt0) cc_final: 0.1309 (mp10) REVERT: A 1980 MET cc_start: 0.6350 (mtp) cc_final: 0.6119 (mtp) REVERT: A 1984 ASP cc_start: 0.7677 (m-30) cc_final: 0.7128 (m-30) REVERT: A 1996 TRP cc_start: 0.4566 (t-100) cc_final: 0.4221 (t-100) REVERT: A 2062 PHE cc_start: 0.6664 (m-80) cc_final: 0.6008 (m-80) REVERT: A 2191 MET cc_start: 0.5081 (ptt) cc_final: 0.4093 (ttm) REVERT: A 2222 GLN cc_start: 0.6020 (mt0) cc_final: 0.5600 (pp30) REVERT: A 2231 LYS cc_start: 0.7926 (mttt) cc_final: 0.7543 (mtmm) REVERT: A 2276 TYR cc_start: 0.6652 (m-80) cc_final: 0.6304 (m-10) REVERT: A 2285 GLN cc_start: 0.6290 (mt0) cc_final: 0.6053 (mm110) REVERT: A 2314 ASP cc_start: 0.7692 (m-30) cc_final: 0.7351 (p0) REVERT: A 2323 PHE cc_start: 0.6832 (m-80) cc_final: 0.6428 (m-80) REVERT: A 2333 VAL cc_start: 0.6156 (t) cc_final: 0.5766 (p) REVERT: A 2352 ARG cc_start: 0.7938 (mtt180) cc_final: 0.7460 (tpm170) REVERT: A 2353 GLN cc_start: 0.7638 (mt0) cc_final: 0.7397 (tt0) REVERT: A 2365 SER cc_start: 0.8469 (p) cc_final: 0.8160 (m) REVERT: A 2430 TRP cc_start: 0.5754 (m100) cc_final: 0.5158 (m100) REVERT: A 2434 LEU cc_start: 0.6610 (mt) cc_final: 0.6275 (mt) REVERT: A 2451 ASP cc_start: 0.5684 (m-30) cc_final: 0.5138 (t70) REVERT: A 2485 PHE cc_start: 0.6442 (m-10) cc_final: 0.6133 (m-10) REVERT: A 2492 ILE cc_start: 0.7849 (mt) cc_final: 0.7556 (mt) REVERT: A 2505 LYS cc_start: 0.7389 (mttt) cc_final: 0.7181 (mtpp) REVERT: A 2520 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7327 (mt-10) REVERT: C 860 ILE cc_start: 0.2684 (mt) cc_final: 0.2203 (mt) REVERT: C 946 HIS cc_start: -0.2913 (m90) cc_final: -0.3469 (m170) REVERT: C 1031 ARG cc_start: 0.3468 (mtt180) cc_final: 0.3178 (ptm160) REVERT: C 1094 LEU cc_start: 0.2455 (tp) cc_final: 0.2170 (mp) REVERT: C 1210 TRP cc_start: 0.3676 (t-100) cc_final: 0.3284 (t-100) REVERT: C 1261 PRO cc_start: 0.4263 (Cg_endo) cc_final: 0.3759 (Cg_exo) REVERT: C 1347 ARG cc_start: 0.6159 (mtt180) cc_final: 0.5671 (ttp80) REVERT: C 1495 MET cc_start: 0.2876 (ptt) cc_final: 0.2528 (mmp) REVERT: C 1668 GLN cc_start: 0.5242 (mp-120) cc_final: 0.4927 (pt0) REVERT: C 1695 ILE cc_start: 0.3907 (mt) cc_final: 0.3383 (tt) REVERT: C 1740 MET cc_start: 0.2909 (tpt) cc_final: 0.2698 (mmm) REVERT: C 1976 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.8135 (m) REVERT: C 1977 TYR cc_start: 0.7659 (t80) cc_final: 0.7315 (t80) REVERT: C 1980 MET cc_start: 0.6562 (mtp) cc_final: 0.6327 (mtp) REVERT: C 1984 ASP cc_start: 0.7934 (m-30) cc_final: 0.7713 (m-30) REVERT: C 2083 TYR cc_start: 0.6016 (t80) cc_final: 0.5663 (t80) REVERT: C 2120 PHE cc_start: 0.7982 (m-80) cc_final: 0.7349 (m-80) REVERT: C 2197 LEU cc_start: 0.8633 (tm) cc_final: 0.8344 (mp) REVERT: C 2268 LEU cc_start: 0.8092 (mt) cc_final: 0.7742 (mt) REVERT: C 2324 GLN cc_start: 0.6299 (mt0) cc_final: 0.5071 (tp40) REVERT: C 2356 GLN cc_start: 0.6432 (mt0) cc_final: 0.6050 (mt0) REVERT: C 2357 LEU cc_start: 0.7282 (mt) cc_final: 0.6992 (mt) REVERT: C 2385 ASN cc_start: 0.6747 (m-40) cc_final: 0.5827 (m-40) REVERT: C 2387 VAL cc_start: 0.5067 (t) cc_final: 0.4483 (m) REVERT: C 2391 GLN cc_start: 0.6475 (mt0) cc_final: 0.6005 (mp-120) REVERT: C 2395 GLU cc_start: 0.7749 (mt-10) cc_final: 0.6835 (tp30) REVERT: C 2431 VAL cc_start: 0.7198 (t) cc_final: 0.6075 (t) REVERT: C 2443 LEU cc_start: 0.7642 (mt) cc_final: 0.7383 (mp) REVERT: C 2499 CYS cc_start: 0.7109 (m) cc_final: 0.5783 (m) REVERT: C 2528 LYS cc_start: 0.6741 (mtpm) cc_final: 0.6280 (tptt) REVERT: C 2539 MET cc_start: 0.7589 (tpp) cc_final: 0.6764 (tpp) REVERT: C 2541 LYS cc_start: 0.5098 (mttt) cc_final: 0.4398 (tttm) REVERT: E 782 ARG cc_start: 0.1643 (mtt180) cc_final: 0.1329 (mtp-110) REVERT: E 843 PRO cc_start: 0.3729 (Cg_endo) cc_final: 0.3196 (Cg_exo) REVERT: E 925 GLN cc_start: -0.0011 (mt0) cc_final: -0.0271 (pp30) REVERT: E 1038 LEU cc_start: 0.1423 (mt) cc_final: 0.1216 (tt) REVERT: E 1147 ARG cc_start: 0.3143 (ptt-90) cc_final: 0.2814 (ptp90) REVERT: E 1264 MET cc_start: 0.1089 (ptm) cc_final: 0.0247 (ttm) REVERT: E 1358 LYS cc_start: 0.8033 (mttt) cc_final: 0.7707 (ttmm) REVERT: E 1502 MET cc_start: 0.1164 (tpt) cc_final: 0.0829 (ptm) REVERT: E 1731 MET cc_start: 0.4282 (mmm) cc_final: 0.3925 (mtm) REVERT: E 1774 LEU cc_start: 0.3101 (tt) cc_final: 0.2733 (mm) REVERT: E 1791 MET cc_start: 0.4398 (ptp) cc_final: 0.4102 (ppp) REVERT: E 1980 MET cc_start: 0.6004 (mtp) cc_final: 0.5560 (mpp) REVERT: E 1996 TRP cc_start: 0.3200 (t-100) cc_final: 0.2513 (m-10) REVERT: E 2133 GLU cc_start: 0.7105 (mp0) cc_final: 0.6459 (mp0) REVERT: E 2134 LEU cc_start: 0.7529 (mt) cc_final: 0.7230 (mt) REVERT: E 2170 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6990 (mm-30) REVERT: E 2182 LYS cc_start: 0.7858 (tttt) cc_final: 0.6974 (pttp) REVERT: E 2230 LEU cc_start: 0.8043 (mt) cc_final: 0.7777 (tp) REVERT: E 2256 TYR cc_start: 0.4812 (m-80) cc_final: 0.4459 (t80) REVERT: E 2258 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7026 (mm-30) REVERT: E 2270 MET cc_start: 0.5052 (mmm) cc_final: 0.4174 (mtp) REVERT: E 2279 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6143 (mm-30) REVERT: E 2287 GLU cc_start: 0.5017 (mt-10) cc_final: 0.4530 (tt0) REVERT: E 2304 MET cc_start: 0.6095 (mmm) cc_final: 0.5662 (ttt) REVERT: E 2341 THR cc_start: 0.4483 (p) cc_final: 0.4193 (m) REVERT: E 2375 TYR cc_start: 0.4630 (m-80) cc_final: 0.4343 (m-80) REVERT: E 2390 LEU cc_start: 0.4135 (mt) cc_final: 0.3740 (mt) REVERT: E 2520 GLU cc_start: 0.8043 (mt-10) cc_final: 0.7599 (pt0) REVERT: E 2523 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7396 (mt-10) REVERT: E 2528 LYS cc_start: 0.6937 (mtpm) cc_final: 0.6585 (tptt) REVERT: E 2545 GLU cc_start: 0.7716 (tt0) cc_final: 0.7500 (tp30) outliers start: 9 outliers final: 2 residues processed: 1057 average time/residue: 0.5385 time to fit residues: 901.6216 Evaluate side-chains 611 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 608 time to evaluate : 3.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 1976 VAL Chi-restraints excluded: chain C residue 2500 VAL Chi-restraints excluded: chain E residue 2500 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 382 optimal weight: 2.9990 chunk 343 optimal weight: 10.0000 chunk 190 optimal weight: 0.8980 chunk 117 optimal weight: 0.9990 chunk 231 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 355 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 215 optimal weight: 0.9980 chunk 264 optimal weight: 0.7980 chunk 411 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 808 HIS ** A 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 946 HIS ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 GLN A1145 HIS A1206 GLN A1510 GLN A1543 GLN A2177 GLN A2244 GLN A2262 GLN A2322 ASN ** A2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 798 GLN C1013 HIS C1138 ASN C1503 GLN C1543 GLN C1698 ASN ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2435 GLN E 798 GLN E1013 HIS E1047 GLN ** E1145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E2050 GLN E2096 GLN E2116 HIS E2181 GLN E2261 GLN ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5331 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 36588 Z= 0.206 Angle : 0.711 12.031 49746 Z= 0.355 Chirality : 0.044 0.276 5667 Planarity : 0.005 0.062 6246 Dihedral : 5.909 53.384 4944 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.22 % Favored : 92.76 % Rotamer: Outliers : 3.39 % Allowed : 11.02 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.12), residues: 4434 helix: -0.31 (0.09), residues: 2691 sheet: -2.83 (0.31), residues: 180 loop : -3.22 (0.14), residues: 1563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C2542 HIS 0.009 0.001 HIS A1145 PHE 0.021 0.002 PHE A1769 TYR 0.023 0.002 TYR C 923 ARG 0.010 0.001 ARG C2546 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 806 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 684 time to evaluate : 4.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6385 (mm) REVERT: A 816 TYR cc_start: 0.7564 (t80) cc_final: 0.7146 (t80) REVERT: A 858 CYS cc_start: 0.8526 (m) cc_final: 0.8190 (m) REVERT: A 869 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6989 (pp) REVERT: A 910 ASN cc_start: 0.8035 (t0) cc_final: 0.7596 (m-40) REVERT: A 925 GLN cc_start: 0.7638 (mm-40) cc_final: 0.7142 (pt0) REVERT: A 997 MET cc_start: 0.8419 (mmm) cc_final: 0.7902 (mmm) REVERT: A 1054 MET cc_start: 0.4002 (mmm) cc_final: 0.3662 (mpp) REVERT: A 1060 ILE cc_start: 0.6401 (tp) cc_final: 0.6172 (mm) REVERT: A 1093 ASN cc_start: 0.7534 (m110) cc_final: 0.7160 (m-40) REVERT: A 1160 TYR cc_start: 0.7466 (m-10) cc_final: 0.7120 (m-10) REVERT: A 1238 MET cc_start: 0.6331 (ttm) cc_final: 0.6107 (ttt) REVERT: A 1293 GLN cc_start: 0.6563 (mm-40) cc_final: 0.6316 (tp40) REVERT: A 1323 TYR cc_start: 0.7686 (OUTLIER) cc_final: 0.6988 (t80) REVERT: A 1347 ARG cc_start: 0.7879 (ttp-110) cc_final: 0.7365 (mmt-90) REVERT: A 1348 GLN cc_start: 0.8034 (mt0) cc_final: 0.7577 (mt0) REVERT: A 1349 MET cc_start: 0.8319 (mmm) cc_final: 0.8034 (mmm) REVERT: A 1356 GLN cc_start: 0.8018 (mt0) cc_final: 0.7654 (pp30) REVERT: A 1544 GLU cc_start: 0.7580 (tt0) cc_final: 0.7304 (tm-30) REVERT: A 1716 LEU cc_start: 0.7722 (mt) cc_final: 0.7519 (mp) REVERT: A 1745 TYR cc_start: 0.8058 (t80) cc_final: 0.7697 (t80) REVERT: A 1754 TRP cc_start: 0.6950 (p-90) cc_final: 0.6637 (p-90) REVERT: A 1791 MET cc_start: 0.5932 (ptp) cc_final: 0.5526 (ptm) REVERT: A 1952 GLN cc_start: 0.1778 (pt0) cc_final: 0.1162 (mp10) REVERT: A 1984 ASP cc_start: 0.7462 (m-30) cc_final: 0.6978 (m-30) REVERT: A 1996 TRP cc_start: 0.4856 (t-100) cc_final: 0.4565 (t-100) REVERT: A 2062 PHE cc_start: 0.6833 (m-80) cc_final: 0.5940 (m-80) REVERT: A 2133 GLU cc_start: 0.6967 (mp0) cc_final: 0.6659 (mp0) REVERT: A 2222 GLN cc_start: 0.5828 (mt0) cc_final: 0.5341 (pp30) REVERT: A 2244 GLN cc_start: 0.5236 (OUTLIER) cc_final: 0.5000 (mt0) REVERT: A 2285 GLN cc_start: 0.6531 (mt0) cc_final: 0.5936 (mm110) REVERT: A 2303 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7291 (mp10) REVERT: A 2307 GLU cc_start: 0.7642 (mt-10) cc_final: 0.7419 (mt-10) REVERT: A 2352 ARG cc_start: 0.7796 (mtt180) cc_final: 0.7588 (tpm170) REVERT: A 2385 ASN cc_start: 0.7045 (m-40) cc_final: 0.6580 (m-40) REVERT: A 2405 LEU cc_start: 0.7169 (mm) cc_final: 0.6727 (pp) REVERT: A 2430 TRP cc_start: 0.5568 (m100) cc_final: 0.4840 (m100) REVERT: A 2432 ILE cc_start: 0.7598 (tt) cc_final: 0.7244 (mm) REVERT: A 2448 ILE cc_start: 0.8055 (OUTLIER) cc_final: 0.7786 (pt) REVERT: A 2451 ASP cc_start: 0.5678 (m-30) cc_final: 0.5030 (t70) REVERT: A 2492 ILE cc_start: 0.7936 (mt) cc_final: 0.7724 (mt) REVERT: A 2505 LYS cc_start: 0.7384 (mttt) cc_final: 0.7156 (mtpt) REVERT: C 846 ARG cc_start: 0.2010 (mtm-85) cc_final: 0.1728 (tpt170) REVERT: C 923 TYR cc_start: 0.1159 (t80) cc_final: 0.0895 (t80) REVERT: C 928 LEU cc_start: 0.2393 (OUTLIER) cc_final: 0.2157 (mt) REVERT: C 1005 ARG cc_start: 0.0706 (mmm-85) cc_final: -0.0042 (mmm-85) REVERT: C 1031 ARG cc_start: 0.3381 (mtt180) cc_final: 0.3120 (ptm160) REVERT: C 1129 HIS cc_start: 0.1637 (m90) cc_final: 0.1302 (t70) REVERT: C 1238 MET cc_start: -0.0086 (ptp) cc_final: -0.0735 (tpp) REVERT: C 1347 ARG cc_start: 0.6219 (mtt180) cc_final: 0.5802 (ttp80) REVERT: C 1495 MET cc_start: 0.2998 (ptt) cc_final: 0.2779 (mmp) REVERT: C 1668 GLN cc_start: 0.4801 (mp-120) cc_final: 0.4486 (pt0) REVERT: C 1754 TRP cc_start: 0.2267 (p90) cc_final: 0.0914 (m-10) REVERT: C 1977 TYR cc_start: 0.6830 (t80) cc_final: 0.6613 (t80) REVERT: C 1980 MET cc_start: 0.6287 (mtp) cc_final: 0.5897 (mtp) REVERT: C 1984 ASP cc_start: 0.8035 (m-30) cc_final: 0.7774 (m-30) REVERT: C 2035 ARG cc_start: 0.6147 (mmm160) cc_final: 0.5882 (mmt180) REVERT: C 2041 LYS cc_start: 0.6540 (mttt) cc_final: 0.5666 (tmmt) REVERT: C 2116 HIS cc_start: 0.7739 (t-90) cc_final: 0.7041 (t70) REVERT: C 2120 PHE cc_start: 0.7786 (m-80) cc_final: 0.6911 (m-80) REVERT: C 2149 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6248 (tp) REVERT: C 2153 MET cc_start: 0.8575 (mmt) cc_final: 0.7372 (mtm) REVERT: C 2241 MET cc_start: 0.6802 (tpp) cc_final: 0.6072 (tpt) REVERT: C 2287 GLU cc_start: 0.8131 (tt0) cc_final: 0.7917 (tp30) REVERT: C 2329 LYS cc_start: 0.6662 (mttt) cc_final: 0.6158 (mtmt) REVERT: C 2387 VAL cc_start: 0.4432 (t) cc_final: 0.4107 (m) REVERT: C 2391 GLN cc_start: 0.6737 (mt0) cc_final: 0.6373 (mp10) REVERT: C 2395 GLU cc_start: 0.7775 (mt-10) cc_final: 0.6638 (tp30) REVERT: C 2450 SER cc_start: 0.4792 (p) cc_final: 0.4435 (t) REVERT: C 2528 LYS cc_start: 0.6900 (mtpm) cc_final: 0.6586 (tppt) REVERT: C 2541 LYS cc_start: 0.5487 (mttt) cc_final: 0.4769 (tptp) REVERT: E 782 ARG cc_start: 0.1610 (mtt180) cc_final: 0.1252 (mtp-110) REVERT: E 928 LEU cc_start: 0.0028 (OUTLIER) cc_final: -0.0312 (mt) REVERT: E 1016 TRP cc_start: 0.1985 (m100) cc_final: 0.1686 (p-90) REVERT: E 1143 PHE cc_start: 0.3200 (p90) cc_final: 0.2527 (m-80) REVERT: E 1159 ARG cc_start: 0.3377 (ttt180) cc_final: 0.2957 (tpt90) REVERT: E 1264 MET cc_start: 0.0769 (ptm) cc_final: 0.0032 (ttm) REVERT: E 1349 MET cc_start: 0.7546 (mmm) cc_final: 0.7280 (mmm) REVERT: E 1502 MET cc_start: 0.1135 (tpt) cc_final: 0.0726 (ptm) REVERT: E 1731 MET cc_start: 0.4178 (mmm) cc_final: 0.3827 (mtm) REVERT: E 1791 MET cc_start: 0.4260 (ptp) cc_final: 0.4038 (ppp) REVERT: E 1980 MET cc_start: 0.5801 (mtp) cc_final: 0.5449 (mpp) REVERT: E 1996 TRP cc_start: 0.2964 (t-100) cc_final: 0.2555 (m-10) REVERT: E 2031 MET cc_start: 0.7115 (mmm) cc_final: 0.6915 (mmm) REVERT: E 2034 ASP cc_start: 0.8106 (m-30) cc_final: 0.7760 (m-30) REVERT: E 2046 LYS cc_start: 0.7819 (tptp) cc_final: 0.7479 (tptp) REVERT: E 2181 GLN cc_start: 0.6568 (tt0) cc_final: 0.6031 (tt0) REVERT: E 2182 LYS cc_start: 0.7893 (tttt) cc_final: 0.6873 (pttp) REVERT: E 2241 MET cc_start: 0.6417 (mmm) cc_final: 0.5635 (tpt) REVERT: E 2245 GLN cc_start: 0.7583 (mt0) cc_final: 0.6963 (tp40) REVERT: E 2258 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7413 (mm-30) REVERT: E 2279 GLU cc_start: 0.6777 (mt-10) cc_final: 0.6217 (mm-30) REVERT: E 2285 GLN cc_start: 0.7582 (mt0) cc_final: 0.7095 (mp10) REVERT: E 2304 MET cc_start: 0.6337 (mmm) cc_final: 0.6034 (ttt) REVERT: E 2429 TRP cc_start: 0.3857 (m-90) cc_final: 0.2429 (m-90) REVERT: E 2520 GLU cc_start: 0.7986 (mt-10) cc_final: 0.7530 (pt0) REVERT: E 2523 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7283 (mt-10) outliers start: 122 outliers final: 56 residues processed: 768 average time/residue: 0.4689 time to fit residues: 582.8773 Evaluate side-chains 616 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 551 time to evaluate : 3.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 827 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 869 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1121 ARG Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1323 TYR Chi-restraints excluded: chain A residue 1525 LYS Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2119 LEU Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2229 THR Chi-restraints excluded: chain A residue 2244 GLN Chi-restraints excluded: chain A residue 2303 GLN Chi-restraints excluded: chain A residue 2448 ILE Chi-restraints excluded: chain A residue 2474 VAL Chi-restraints excluded: chain C residue 827 VAL Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2127 LEU Chi-restraints excluded: chain C residue 2149 LEU Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2264 ASP Chi-restraints excluded: chain C residue 2295 ARG Chi-restraints excluded: chain C residue 2339 LYS Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2380 ASN Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain E residue 827 VAL Chi-restraints excluded: chain E residue 928 LEU Chi-restraints excluded: chain E residue 1661 GLU Chi-restraints excluded: chain E residue 1734 ILE Chi-restraints excluded: chain E residue 2044 LEU Chi-restraints excluded: chain E residue 2119 LEU Chi-restraints excluded: chain E residue 2146 THR Chi-restraints excluded: chain E residue 2149 LEU Chi-restraints excluded: chain E residue 2186 ILE Chi-restraints excluded: chain E residue 2197 LEU Chi-restraints excluded: chain E residue 2207 LEU Chi-restraints excluded: chain E residue 2248 ILE Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2364 GLN Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2432 ILE Chi-restraints excluded: chain E residue 2440 ASP Chi-restraints excluded: chain E residue 2447 VAL Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2530 ILE Chi-restraints excluded: chain E residue 2532 LEU Chi-restraints excluded: chain E residue 2540 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 228 optimal weight: 0.0010 chunk 127 optimal weight: 9.9990 chunk 342 optimal weight: 10.0000 chunk 280 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 412 optimal weight: 3.9990 chunk 445 optimal weight: 2.9990 chunk 367 optimal weight: 8.9990 chunk 408 optimal weight: 0.1980 chunk 140 optimal weight: 9.9990 chunk 330 optimal weight: 8.9990 overall best weight: 1.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 927 HIS ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1138 ASN A1200 GLN A1206 GLN A1225 ASN A1315 GLN A1655 HIS A2244 GLN ** A2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 808 HIS C 927 HIS ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 808 HIS E1200 GLN ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5389 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 36588 Z= 0.238 Angle : 0.698 13.720 49746 Z= 0.346 Chirality : 0.044 0.234 5667 Planarity : 0.005 0.070 6246 Dihedral : 5.479 33.231 4941 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.44 % Favored : 92.53 % Rotamer: Outliers : 4.31 % Allowed : 12.55 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.35 (0.12), residues: 4434 helix: 0.36 (0.10), residues: 2718 sheet: -2.69 (0.31), residues: 180 loop : -3.01 (0.14), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C2542 HIS 0.006 0.001 HIS E2340 PHE 0.021 0.002 PHE C2163 TYR 0.021 0.002 TYR A1970 ARG 0.009 0.001 ARG E1147 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 579 time to evaluate : 3.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 845 PHE cc_start: 0.7227 (t80) cc_final: 0.6241 (t80) REVERT: A 858 CYS cc_start: 0.8520 (m) cc_final: 0.8183 (m) REVERT: A 865 MET cc_start: 0.8270 (mtm) cc_final: 0.8064 (mtm) REVERT: A 869 LEU cc_start: 0.7438 (tp) cc_final: 0.6969 (pp) REVERT: A 911 TRP cc_start: 0.7521 (t60) cc_final: 0.7270 (t60) REVERT: A 914 VAL cc_start: 0.7627 (t) cc_final: 0.7426 (t) REVERT: A 925 GLN cc_start: 0.7396 (mm-40) cc_final: 0.7084 (pt0) REVERT: A 941 TYR cc_start: 0.7740 (m-80) cc_final: 0.7500 (m-80) REVERT: A 1045 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.8010 (mm) REVERT: A 1062 TYR cc_start: 0.5067 (p90) cc_final: 0.4626 (p90) REVERT: A 1093 ASN cc_start: 0.7567 (m110) cc_final: 0.7095 (m-40) REVERT: A 1160 TYR cc_start: 0.7690 (m-10) cc_final: 0.7413 (m-10) REVERT: A 1323 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.7196 (t80) REVERT: A 1348 GLN cc_start: 0.7873 (mt0) cc_final: 0.7448 (mt0) REVERT: A 1349 MET cc_start: 0.8304 (mmm) cc_final: 0.7923 (mmm) REVERT: A 1355 LYS cc_start: 0.7481 (tppt) cc_final: 0.6963 (tppt) REVERT: A 1356 GLN cc_start: 0.8144 (mt0) cc_final: 0.7595 (tm-30) REVERT: A 1537 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: A 1545 LEU cc_start: 0.8419 (mm) cc_final: 0.8156 (mm) REVERT: A 1655 HIS cc_start: 0.5257 (OUTLIER) cc_final: 0.4748 (t70) REVERT: A 1661 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8305 (pm20) REVERT: A 1754 TRP cc_start: 0.7122 (p-90) cc_final: 0.6781 (p-90) REVERT: A 1791 MET cc_start: 0.6009 (ptp) cc_final: 0.5505 (ptm) REVERT: A 1952 GLN cc_start: 0.1769 (pt0) cc_final: 0.1094 (mp10) REVERT: A 1984 ASP cc_start: 0.7156 (m-30) cc_final: 0.6639 (m-30) REVERT: A 1996 TRP cc_start: 0.4924 (t-100) cc_final: 0.4696 (t-100) REVERT: A 2062 PHE cc_start: 0.6828 (m-80) cc_final: 0.5960 (m-80) REVERT: A 2285 GLN cc_start: 0.6392 (mt0) cc_final: 0.6036 (mm110) REVERT: A 2352 ARG cc_start: 0.7876 (mtt180) cc_final: 0.7651 (tpm170) REVERT: A 2353 GLN cc_start: 0.7792 (tt0) cc_final: 0.7484 (tt0) REVERT: A 2428 GLU cc_start: 0.7383 (mt-10) cc_final: 0.7170 (mt-10) REVERT: A 2430 TRP cc_start: 0.5892 (m100) cc_final: 0.5601 (m100) REVERT: A 2432 ILE cc_start: 0.7756 (tt) cc_final: 0.7440 (mm) REVERT: A 2506 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6388 (tt) REVERT: C 794 LEU cc_start: 0.0007 (OUTLIER) cc_final: -0.0344 (mp) REVERT: C 846 ARG cc_start: 0.2281 (mtm-85) cc_final: 0.2019 (tpt170) REVERT: C 959 GLN cc_start: -0.1454 (pm20) cc_final: -0.1859 (mm110) REVERT: C 1005 ARG cc_start: 0.0743 (mmm-85) cc_final: -0.0080 (mmm-85) REVERT: C 1031 ARG cc_start: 0.3646 (mtt180) cc_final: 0.3411 (ptm160) REVERT: C 1101 LEU cc_start: 0.3161 (OUTLIER) cc_final: 0.2631 (mm) REVERT: C 1129 HIS cc_start: 0.1667 (m90) cc_final: 0.1331 (t70) REVERT: C 1238 MET cc_start: -0.0479 (ptp) cc_final: -0.0845 (tpp) REVERT: C 1347 ARG cc_start: 0.5922 (mtt180) cc_final: 0.5516 (ttp80) REVERT: C 1668 GLN cc_start: 0.4959 (mp-120) cc_final: 0.4717 (pt0) REVERT: C 1754 TRP cc_start: 0.1518 (p90) cc_final: 0.0517 (m-10) REVERT: C 1980 MET cc_start: 0.6124 (mtp) cc_final: 0.5891 (mtp) REVERT: C 1984 ASP cc_start: 0.8087 (m-30) cc_final: 0.7603 (m-30) REVERT: C 2120 PHE cc_start: 0.7701 (m-80) cc_final: 0.6935 (m-80) REVERT: C 2149 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6446 (tp) REVERT: C 2153 MET cc_start: 0.8476 (mmt) cc_final: 0.7445 (mtm) REVERT: C 2241 MET cc_start: 0.7192 (tpp) cc_final: 0.6314 (tpp) REVERT: C 2266 TYR cc_start: 0.6832 (t80) cc_final: 0.6475 (t80) REVERT: C 2287 GLU cc_start: 0.8153 (tt0) cc_final: 0.7851 (tp30) REVERT: C 2376 ILE cc_start: 0.7477 (mt) cc_final: 0.7272 (mp) REVERT: C 2395 GLU cc_start: 0.7817 (mt-10) cc_final: 0.6767 (tp30) REVERT: C 2497 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.5323 (mp) REVERT: C 2528 LYS cc_start: 0.6802 (mtpm) cc_final: 0.6590 (tppt) REVERT: C 2541 LYS cc_start: 0.5349 (mttt) cc_final: 0.4720 (tmtt) REVERT: E 782 ARG cc_start: 0.1562 (mtt180) cc_final: 0.1048 (mtp-110) REVERT: E 856 TRP cc_start: 0.2975 (m100) cc_final: 0.2511 (m-90) REVERT: E 928 LEU cc_start: -0.0207 (OUTLIER) cc_final: -0.0478 (mt) REVERT: E 1143 PHE cc_start: 0.3053 (p90) cc_final: 0.2305 (m-80) REVERT: E 1150 LEU cc_start: 0.4959 (pt) cc_final: 0.4644 (tp) REVERT: E 1264 MET cc_start: 0.0627 (ptm) cc_final: -0.0096 (ttm) REVERT: E 1304 HIS cc_start: 0.3545 (m90) cc_final: 0.3268 (m170) REVERT: E 1349 MET cc_start: 0.7751 (mmm) cc_final: 0.7400 (mmm) REVERT: E 1502 MET cc_start: 0.0670 (tpt) cc_final: 0.0282 (ptm) REVERT: E 1791 MET cc_start: 0.4221 (ptp) cc_final: 0.4018 (ppp) REVERT: E 1980 MET cc_start: 0.5300 (mtp) cc_final: 0.4829 (mpp) REVERT: E 2017 PRO cc_start: 0.4497 (Cg_endo) cc_final: 0.4132 (Cg_exo) REVERT: E 2031 MET cc_start: 0.7136 (mmm) cc_final: 0.6876 (mmm) REVERT: E 2034 ASP cc_start: 0.8145 (m-30) cc_final: 0.7669 (m-30) REVERT: E 2046 LYS cc_start: 0.7172 (tptp) cc_final: 0.6872 (tptp) REVERT: E 2182 LYS cc_start: 0.7855 (tttt) cc_final: 0.6803 (pttp) REVERT: E 2231 LYS cc_start: 0.7864 (mttt) cc_final: 0.7592 (mtpt) REVERT: E 2245 GLN cc_start: 0.7556 (mt0) cc_final: 0.7036 (tp40) REVERT: E 2258 GLU cc_start: 0.7721 (mt-10) cc_final: 0.7429 (mm-30) REVERT: E 2272 PHE cc_start: 0.5526 (t80) cc_final: 0.5202 (t80) REVERT: E 2279 GLU cc_start: 0.6718 (mt-10) cc_final: 0.6274 (mm-30) REVERT: E 2285 GLN cc_start: 0.7437 (mt0) cc_final: 0.6916 (mp10) REVERT: E 2321 TRP cc_start: 0.6169 (m-10) cc_final: 0.5415 (m-90) REVERT: E 2324 GLN cc_start: 0.4247 (OUTLIER) cc_final: 0.4035 (tt0) REVERT: E 2375 TYR cc_start: 0.4896 (m-80) cc_final: 0.4531 (m-80) REVERT: E 2520 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7476 (pt0) REVERT: E 2523 GLU cc_start: 0.7659 (mt-10) cc_final: 0.7195 (mt-10) outliers start: 155 outliers final: 79 residues processed: 693 average time/residue: 0.4357 time to fit residues: 500.7449 Evaluate side-chains 609 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 518 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1323 TYR Chi-restraints excluded: chain A residue 1537 GLU Chi-restraints excluded: chain A residue 1655 HIS Chi-restraints excluded: chain A residue 1661 GLU Chi-restraints excluded: chain A residue 1683 VAL Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2042 THR Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2281 ILE Chi-restraints excluded: chain A residue 2322 ASN Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2431 VAL Chi-restraints excluded: chain A residue 2474 VAL Chi-restraints excluded: chain A residue 2499 CYS Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1695 ILE Chi-restraints excluded: chain C residue 1783 ILE Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2054 VAL Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2097 ILE Chi-restraints excluded: chain C residue 2127 LEU Chi-restraints excluded: chain C residue 2149 LEU Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2264 ASP Chi-restraints excluded: chain C residue 2339 LYS Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2380 ASN Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2506 LEU Chi-restraints excluded: chain E residue 928 LEU Chi-restraints excluded: chain E residue 1182 LEU Chi-restraints excluded: chain E residue 1361 GLN Chi-restraints excluded: chain E residue 1661 GLU Chi-restraints excluded: chain E residue 1701 VAL Chi-restraints excluded: chain E residue 1734 ILE Chi-restraints excluded: chain E residue 1759 VAL Chi-restraints excluded: chain E residue 1805 LEU Chi-restraints excluded: chain E residue 2044 LEU Chi-restraints excluded: chain E residue 2146 THR Chi-restraints excluded: chain E residue 2186 ILE Chi-restraints excluded: chain E residue 2197 LEU Chi-restraints excluded: chain E residue 2203 ILE Chi-restraints excluded: chain E residue 2281 ILE Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2324 GLN Chi-restraints excluded: chain E residue 2347 ASN Chi-restraints excluded: chain E residue 2401 VAL Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2440 ASP Chi-restraints excluded: chain E residue 2447 VAL Chi-restraints excluded: chain E residue 2488 ILE Chi-restraints excluded: chain E residue 2497 LEU Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2530 ILE Chi-restraints excluded: chain E residue 2532 LEU Chi-restraints excluded: chain E residue 2540 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 407 optimal weight: 1.9990 chunk 309 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 196 optimal weight: 5.9990 chunk 276 optimal weight: 9.9990 chunk 413 optimal weight: 5.9990 chunk 437 optimal weight: 2.9990 chunk 216 optimal weight: 0.9980 chunk 391 optimal weight: 5.9990 chunk 118 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1000 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 GLN A1324 ASN A1655 HIS A2181 GLN A2244 GLN A2322 ASN ** A2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1145 HIS E1543 GLN ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5408 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 36588 Z= 0.232 Angle : 0.677 12.054 49746 Z= 0.332 Chirality : 0.043 0.250 5667 Planarity : 0.005 0.045 6246 Dihedral : 5.258 26.326 4941 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.58 % Favored : 92.40 % Rotamer: Outliers : 4.23 % Allowed : 14.00 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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 (0.13), residues: 4434 helix: 0.75 (0.10), residues: 2718 sheet: -2.44 (0.32), residues: 180 loop : -2.92 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C2542 HIS 0.031 0.001 HIS A1655 PHE 0.020 0.002 PHE E2531 TYR 0.020 0.002 TYR C 923 ARG 0.006 0.001 ARG A1347 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 559 time to evaluate : 3.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 844 ARG cc_start: 0.4510 (ptt-90) cc_final: 0.4299 (ptt180) REVERT: A 845 PHE cc_start: 0.7383 (t80) cc_final: 0.6441 (t80) REVERT: A 858 CYS cc_start: 0.8504 (m) cc_final: 0.8168 (m) REVERT: A 911 TRP cc_start: 0.7619 (t60) cc_final: 0.7293 (t60) REVERT: A 937 GLU cc_start: 0.8622 (tm-30) cc_final: 0.8319 (tm-30) REVERT: A 941 TYR cc_start: 0.7793 (m-80) cc_final: 0.7504 (m-80) REVERT: A 1045 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7978 (mm) REVERT: A 1093 ASN cc_start: 0.7665 (m110) cc_final: 0.7142 (m-40) REVERT: A 1323 TYR cc_start: 0.7771 (OUTLIER) cc_final: 0.7171 (t80) REVERT: A 1347 ARG cc_start: 0.7763 (ttp80) cc_final: 0.7540 (ttp-110) REVERT: A 1348 GLN cc_start: 0.7897 (mt0) cc_final: 0.7616 (mt0) REVERT: A 1349 MET cc_start: 0.8312 (mmm) cc_final: 0.7932 (mmm) REVERT: A 1355 LYS cc_start: 0.7561 (tppt) cc_final: 0.7052 (tppt) REVERT: A 1356 GLN cc_start: 0.8084 (mt0) cc_final: 0.7578 (tm-30) REVERT: A 1530 MET cc_start: 0.8444 (ttp) cc_final: 0.8210 (ttt) REVERT: A 1661 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8287 (pm20) REVERT: A 1754 TRP cc_start: 0.7182 (p-90) cc_final: 0.6710 (p-90) REVERT: A 1952 GLN cc_start: 0.2419 (pt0) cc_final: 0.1462 (mp10) REVERT: A 1984 ASP cc_start: 0.7046 (m-30) cc_final: 0.6337 (m-30) REVERT: A 2062 PHE cc_start: 0.6597 (m-80) cc_final: 0.5783 (m-80) REVERT: A 2153 MET cc_start: 0.6478 (mmm) cc_final: 0.6164 (mtm) REVERT: A 2285 GLN cc_start: 0.6012 (mt0) cc_final: 0.5791 (mm110) REVERT: A 2353 GLN cc_start: 0.7798 (tt0) cc_final: 0.7323 (tt0) REVERT: A 2430 TRP cc_start: 0.6338 (m100) cc_final: 0.6069 (m100) REVERT: A 2432 ILE cc_start: 0.7679 (tt) cc_final: 0.7382 (mm) REVERT: A 2506 LEU cc_start: 0.6950 (OUTLIER) cc_final: 0.6388 (tt) REVERT: C 794 LEU cc_start: 0.0120 (OUTLIER) cc_final: -0.0210 (mp) REVERT: C 846 ARG cc_start: 0.1991 (mtm-85) cc_final: 0.1742 (tpt170) REVERT: C 928 LEU cc_start: 0.2389 (OUTLIER) cc_final: 0.2180 (mt) REVERT: C 959 GLN cc_start: -0.1611 (pm20) cc_final: -0.2037 (mm110) REVERT: C 1031 ARG cc_start: 0.4032 (mtt180) cc_final: 0.3756 (ptm160) REVERT: C 1101 LEU cc_start: 0.3614 (OUTLIER) cc_final: 0.2915 (mm) REVERT: C 1129 HIS cc_start: 0.1682 (m90) cc_final: 0.1342 (t70) REVERT: C 1238 MET cc_start: 0.0497 (ptp) cc_final: 0.0126 (tpp) REVERT: C 1347 ARG cc_start: 0.5950 (mtt180) cc_final: 0.5533 (ttp80) REVERT: C 1668 GLN cc_start: 0.5041 (mp-120) cc_final: 0.4696 (pt0) REVERT: C 1754 TRP cc_start: 0.1374 (p90) cc_final: 0.0435 (m-10) REVERT: C 1969 LYS cc_start: 0.4634 (ttmt) cc_final: 0.4432 (ttmt) REVERT: C 1984 ASP cc_start: 0.7885 (m-30) cc_final: 0.7510 (m-30) REVERT: C 2120 PHE cc_start: 0.7812 (m-80) cc_final: 0.6995 (m-80) REVERT: C 2149 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6612 (tp) REVERT: C 2153 MET cc_start: 0.8584 (mmt) cc_final: 0.7753 (mtt) REVERT: C 2232 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8029 (mp) REVERT: C 2241 MET cc_start: 0.7414 (tpp) cc_final: 0.6616 (tpp) REVERT: C 2264 ASP cc_start: 0.6025 (OUTLIER) cc_final: 0.5821 (p0) REVERT: C 2266 TYR cc_start: 0.6743 (t80) cc_final: 0.6268 (t80) REVERT: C 2287 GLU cc_start: 0.8111 (tt0) cc_final: 0.7882 (tp30) REVERT: C 2293 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6456 (mt) REVERT: C 2395 GLU cc_start: 0.7846 (mt-10) cc_final: 0.6899 (tp30) REVERT: C 2473 ILE cc_start: 0.6086 (tt) cc_final: 0.5787 (mt) REVERT: C 2497 LEU cc_start: 0.7345 (OUTLIER) cc_final: 0.5323 (mp) REVERT: C 2528 LYS cc_start: 0.6863 (mtpm) cc_final: 0.6642 (tppt) REVERT: C 2541 LYS cc_start: 0.5495 (mttt) cc_final: 0.4940 (tmtt) REVERT: E 782 ARG cc_start: 0.1473 (mtt180) cc_final: 0.0967 (mtp-110) REVERT: E 856 TRP cc_start: 0.2972 (m100) cc_final: 0.2494 (m-90) REVERT: E 1143 PHE cc_start: 0.2931 (p90) cc_final: 0.2227 (m-80) REVERT: E 1264 MET cc_start: 0.1478 (ptm) cc_final: 0.0719 (ttm) REVERT: E 1349 MET cc_start: 0.7829 (mmm) cc_final: 0.7426 (mmm) REVERT: E 1498 VAL cc_start: 0.0543 (t) cc_final: 0.0326 (t) REVERT: E 1502 MET cc_start: 0.0541 (tpt) cc_final: 0.0196 (ptm) REVERT: E 1734 ILE cc_start: 0.3075 (OUTLIER) cc_final: 0.2419 (pt) REVERT: E 1960 ARG cc_start: 0.4146 (mtt180) cc_final: 0.3032 (tpp80) REVERT: E 1980 MET cc_start: 0.5267 (mtp) cc_final: 0.4792 (mpp) REVERT: E 2031 MET cc_start: 0.6960 (mmm) cc_final: 0.6583 (mmm) REVERT: E 2034 ASP cc_start: 0.8246 (m-30) cc_final: 0.7767 (m-30) REVERT: E 2046 LYS cc_start: 0.6967 (tptp) cc_final: 0.6716 (tptp) REVERT: E 2258 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7403 (mm-30) REVERT: E 2279 GLU cc_start: 0.6755 (mt-10) cc_final: 0.6266 (mm-30) REVERT: E 2285 GLN cc_start: 0.7417 (mt0) cc_final: 0.6898 (mp10) REVERT: E 2321 TRP cc_start: 0.6120 (m-10) cc_final: 0.3934 (m100) REVERT: E 2375 TYR cc_start: 0.4905 (m-80) cc_final: 0.4450 (m-80) REVERT: E 2429 TRP cc_start: 0.4135 (m-90) cc_final: 0.2581 (m-90) REVERT: E 2485 PHE cc_start: 0.5818 (m-10) cc_final: 0.5260 (m-80) REVERT: E 2487 GLU cc_start: 0.5153 (mt-10) cc_final: 0.4735 (tt0) REVERT: E 2520 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7647 (pt0) REVERT: E 2523 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7313 (mt-10) outliers start: 152 outliers final: 88 residues processed: 669 average time/residue: 0.4228 time to fit residues: 474.0181 Evaluate side-chains 612 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 511 time to evaluate : 3.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1323 TYR Chi-restraints excluded: chain A residue 1661 GLU Chi-restraints excluded: chain A residue 1683 VAL Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2042 THR Chi-restraints excluded: chain A residue 2106 LEU Chi-restraints excluded: chain A residue 2119 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain A residue 2133 GLU Chi-restraints excluded: chain A residue 2216 VAL Chi-restraints excluded: chain A residue 2281 ILE Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2320 THR Chi-restraints excluded: chain A residue 2321 TRP Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2431 VAL Chi-restraints excluded: chain A residue 2474 VAL Chi-restraints excluded: chain A residue 2499 CYS Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1702 THR Chi-restraints excluded: chain C residue 1783 ILE Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 1976 VAL Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2097 ILE Chi-restraints excluded: chain C residue 2127 LEU Chi-restraints excluded: chain C residue 2149 LEU Chi-restraints excluded: chain C residue 2203 ILE Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2232 LEU Chi-restraints excluded: chain C residue 2264 ASP Chi-restraints excluded: chain C residue 2286 ILE Chi-restraints excluded: chain C residue 2293 LEU Chi-restraints excluded: chain C residue 2339 LYS Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2380 ASN Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2530 ILE Chi-restraints excluded: chain E residue 827 VAL Chi-restraints excluded: chain E residue 1038 LEU Chi-restraints excluded: chain E residue 1182 LEU Chi-restraints excluded: chain E residue 1245 VAL Chi-restraints excluded: chain E residue 1361 GLN Chi-restraints excluded: chain E residue 1542 THR Chi-restraints excluded: chain E residue 1734 ILE Chi-restraints excluded: chain E residue 1759 VAL Chi-restraints excluded: chain E residue 2111 THR Chi-restraints excluded: chain E residue 2119 LEU Chi-restraints excluded: chain E residue 2146 THR Chi-restraints excluded: chain E residue 2186 ILE Chi-restraints excluded: chain E residue 2197 LEU Chi-restraints excluded: chain E residue 2207 LEU Chi-restraints excluded: chain E residue 2270 MET Chi-restraints excluded: chain E residue 2281 ILE Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2347 ASN Chi-restraints excluded: chain E residue 2401 VAL Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2440 ASP Chi-restraints excluded: chain E residue 2447 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2488 ILE Chi-restraints excluded: chain E residue 2497 LEU Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2512 LEU Chi-restraints excluded: chain E residue 2532 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 364 optimal weight: 9.9990 chunk 248 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 326 optimal weight: 10.0000 chunk 180 optimal weight: 10.0000 chunk 373 optimal weight: 9.9990 chunk 302 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 223 optimal weight: 5.9990 chunk 393 optimal weight: 7.9990 chunk 110 optimal weight: 1.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1225 ASN A1324 ASN A2340 HIS A2370 HIS A2385 ASN C 798 GLN C1004 GLN C1047 GLN C1107 GLN ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1356 GLN C1796 HIS E1004 GLN E1200 GLN E1304 HIS ** E1668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5495 moved from start: 0.5368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 36588 Z= 0.516 Angle : 0.933 15.165 49746 Z= 0.463 Chirality : 0.051 0.375 5667 Planarity : 0.007 0.076 6246 Dihedral : 6.033 29.238 4941 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 9.68 % Favored : 90.30 % Rotamer: Outliers : 5.40 % Allowed : 14.75 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -1.78 (0.12), residues: 4434 helix: -0.03 (0.10), residues: 2748 sheet: -2.75 (0.34), residues: 162 loop : -3.15 (0.14), residues: 1524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP E1066 HIS 0.012 0.002 HIS E1526 PHE 0.037 0.003 PHE C2494 TYR 0.036 0.003 TYR C1323 ARG 0.021 0.001 ARG A2301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 709 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 515 time to evaluate : 4.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 812 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8057 (tt) REVERT: A 941 TYR cc_start: 0.8098 (m-80) cc_final: 0.7730 (m-80) REVERT: A 1045 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8011 (mm) REVERT: A 1093 ASN cc_start: 0.7695 (m110) cc_final: 0.7340 (m-40) REVERT: A 1241 ASN cc_start: 0.3371 (OUTLIER) cc_final: 0.2750 (m-40) REVERT: A 1323 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.7209 (t80) REVERT: A 1348 GLN cc_start: 0.7882 (mt0) cc_final: 0.7461 (mt0) REVERT: A 1356 GLN cc_start: 0.8064 (mt0) cc_final: 0.7569 (pp30) REVERT: A 1530 MET cc_start: 0.8433 (ttp) cc_final: 0.8166 (ttt) REVERT: A 1661 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8289 (pm20) REVERT: A 1754 TRP cc_start: 0.7483 (p-90) cc_final: 0.6837 (p-90) REVERT: A 1791 MET cc_start: 0.5927 (ptt) cc_final: 0.5616 (ptm) REVERT: A 1984 ASP cc_start: 0.6880 (m-30) cc_final: 0.6410 (m-30) REVERT: A 2021 LEU cc_start: 0.7450 (mt) cc_final: 0.7172 (mt) REVERT: A 2047 LEU cc_start: 0.7563 (OUTLIER) cc_final: 0.7236 (mt) REVERT: A 2061 MET cc_start: 0.8228 (ttm) cc_final: 0.8011 (ttt) REVERT: A 2153 MET cc_start: 0.6566 (mmm) cc_final: 0.5987 (mtp) REVERT: A 2174 LYS cc_start: 0.6567 (tptt) cc_final: 0.6362 (tttm) REVERT: A 2231 LYS cc_start: 0.7701 (mtmm) cc_final: 0.7270 (mtpp) REVERT: A 2271 GLN cc_start: 0.6495 (pp30) cc_final: 0.5696 (pp30) REVERT: A 2285 GLN cc_start: 0.6081 (mt0) cc_final: 0.5650 (mm110) REVERT: A 2388 LYS cc_start: 0.8191 (ttpt) cc_final: 0.7784 (ttpt) REVERT: A 2398 TYR cc_start: 0.6394 (m-80) cc_final: 0.5832 (m-80) REVERT: A 2430 TRP cc_start: 0.6272 (m100) cc_final: 0.5999 (m100) REVERT: A 2436 ASP cc_start: 0.7830 (m-30) cc_final: 0.7255 (p0) REVERT: A 2447 VAL cc_start: 0.7824 (t) cc_final: 0.7505 (t) REVERT: A 2506 LEU cc_start: 0.7134 (OUTLIER) cc_final: 0.6569 (tt) REVERT: A 2523 GLU cc_start: 0.6264 (mt-10) cc_final: 0.6049 (mt-10) REVERT: C 928 LEU cc_start: 0.1908 (OUTLIER) cc_final: 0.1704 (mt) REVERT: C 959 GLN cc_start: -0.1370 (pm20) cc_final: -0.1703 (tp40) REVERT: C 1031 ARG cc_start: 0.4042 (mtt180) cc_final: 0.3814 (ptt180) REVERT: C 1101 LEU cc_start: 0.2939 (OUTLIER) cc_final: 0.2386 (mp) REVERT: C 1129 HIS cc_start: 0.2234 (m90) cc_final: 0.1587 (t70) REVERT: C 1347 ARG cc_start: 0.6200 (mtt180) cc_final: 0.5653 (ttp80) REVERT: C 1668 GLN cc_start: 0.4886 (mp-120) cc_final: 0.4470 (pt0) REVERT: C 1700 MET cc_start: 0.5387 (ttp) cc_final: 0.5129 (mtp) REVERT: C 1754 TRP cc_start: 0.1640 (p90) cc_final: 0.0638 (m-10) REVERT: C 1984 ASP cc_start: 0.7682 (m-30) cc_final: 0.7396 (m-30) REVERT: C 2049 PHE cc_start: 0.7176 (t80) cc_final: 0.6932 (t80) REVERT: C 2053 LEU cc_start: 0.7149 (mp) cc_final: 0.6923 (mp) REVERT: C 2120 PHE cc_start: 0.7746 (m-80) cc_final: 0.6892 (m-80) REVERT: C 2239 PHE cc_start: 0.3852 (OUTLIER) cc_final: 0.2609 (m-80) REVERT: C 2241 MET cc_start: 0.7675 (tpp) cc_final: 0.6337 (tpp) REVERT: C 2266 TYR cc_start: 0.6534 (t80) cc_final: 0.6313 (t80) REVERT: C 2270 MET cc_start: 0.5432 (mmm) cc_final: 0.4752 (mpp) REVERT: C 2287 GLU cc_start: 0.8226 (tt0) cc_final: 0.7872 (tp30) REVERT: C 2395 GLU cc_start: 0.7941 (mt-10) cc_final: 0.6955 (tp30) REVERT: C 2488 ILE cc_start: 0.7968 (OUTLIER) cc_final: 0.7494 (tt) REVERT: C 2526 TYR cc_start: 0.7570 (t80) cc_final: 0.7193 (t80) REVERT: C 2528 LYS cc_start: 0.6974 (mtpm) cc_final: 0.6568 (tppt) REVERT: C 2541 LYS cc_start: 0.5189 (mttt) cc_final: 0.4550 (tmtt) REVERT: E 782 ARG cc_start: 0.1471 (mtt180) cc_final: 0.0878 (mtp-110) REVERT: E 928 LEU cc_start: -0.0251 (OUTLIER) cc_final: -0.0572 (mt) REVERT: E 1264 MET cc_start: 0.1196 (ptm) cc_final: 0.0453 (ttm) REVERT: E 1349 MET cc_start: 0.7827 (mmm) cc_final: 0.7473 (mmm) REVERT: E 1498 VAL cc_start: 0.1135 (t) cc_final: 0.0912 (t) REVERT: E 1502 MET cc_start: 0.0484 (tpt) cc_final: 0.0182 (ptt) REVERT: E 1734 ILE cc_start: 0.2868 (OUTLIER) cc_final: 0.2312 (pt) REVERT: E 1791 MET cc_start: 0.4591 (OUTLIER) cc_final: 0.3908 (ppp) REVERT: E 1960 ARG cc_start: 0.3645 (mtt180) cc_final: 0.2870 (ptp-170) REVERT: E 1980 MET cc_start: 0.5533 (mtp) cc_final: 0.5313 (mtp) REVERT: E 2031 MET cc_start: 0.6728 (mmm) cc_final: 0.6373 (mmm) REVERT: E 2034 ASP cc_start: 0.8214 (m-30) cc_final: 0.7751 (m-30) REVERT: E 2046 LYS cc_start: 0.6963 (tptp) cc_final: 0.6737 (tptt) REVERT: E 2231 LYS cc_start: 0.7744 (mttt) cc_final: 0.7238 (mtpt) REVERT: E 2258 GLU cc_start: 0.7648 (mt-10) cc_final: 0.6890 (mm-30) REVERT: E 2279 GLU cc_start: 0.6720 (mt-10) cc_final: 0.6312 (mm-30) REVERT: E 2285 GLN cc_start: 0.7376 (mt0) cc_final: 0.6870 (mp10) REVERT: E 2321 TRP cc_start: 0.6346 (m-10) cc_final: 0.3910 (m100) REVERT: E 2375 TYR cc_start: 0.5111 (m-80) cc_final: 0.4871 (m-10) REVERT: E 2446 MET cc_start: 0.6585 (tpp) cc_final: 0.6223 (tpp) REVERT: E 2479 LYS cc_start: 0.5338 (OUTLIER) cc_final: 0.5106 (ttmm) REVERT: E 2520 GLU cc_start: 0.8260 (mt-10) cc_final: 0.7673 (pt0) REVERT: E 2523 GLU cc_start: 0.7777 (mt-10) cc_final: 0.7347 (mt-10) outliers start: 194 outliers final: 125 residues processed: 656 average time/residue: 0.4301 time to fit residues: 476.9095 Evaluate side-chains 608 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 468 time to evaluate : 3.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 795 THR Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 812 LEU Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 854 THR Chi-restraints excluded: chain A residue 862 VAL Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 961 VAL Chi-restraints excluded: chain A residue 1040 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1058 LEU Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain A residue 1082 LEU Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1144 ILE Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1155 VAL Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1182 LEU Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1219 THR Chi-restraints excluded: chain A residue 1241 ASN Chi-restraints excluded: chain A residue 1273 LEU Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1323 TYR Chi-restraints excluded: chain A residue 1661 GLU Chi-restraints excluded: chain A residue 1683 VAL Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1732 THR Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2016 VAL Chi-restraints excluded: chain A residue 2037 LEU Chi-restraints excluded: chain A residue 2042 THR Chi-restraints excluded: chain A residue 2047 LEU Chi-restraints excluded: chain A residue 2053 LEU Chi-restraints excluded: chain A residue 2119 LEU Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain A residue 2133 GLU Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2244 GLN Chi-restraints excluded: chain A residue 2281 ILE Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2318 ARG Chi-restraints excluded: chain A residue 2320 THR Chi-restraints excluded: chain A residue 2321 TRP Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2431 VAL Chi-restraints excluded: chain A residue 2474 VAL Chi-restraints excluded: chain A residue 2488 ILE Chi-restraints excluded: chain A residue 2493 MET Chi-restraints excluded: chain A residue 2499 CYS Chi-restraints excluded: chain A residue 2500 VAL Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 827 VAL Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 923 TYR Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1032 LEU Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1337 ILE Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1702 THR Chi-restraints excluded: chain C residue 1776 LEU Chi-restraints excluded: chain C residue 1783 ILE Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2047 LEU Chi-restraints excluded: chain C residue 2052 VAL Chi-restraints excluded: chain C residue 2078 VAL Chi-restraints excluded: chain C residue 2097 ILE Chi-restraints excluded: chain C residue 2127 LEU Chi-restraints excluded: chain C residue 2203 ILE Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2239 PHE Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2286 ILE Chi-restraints excluded: chain C residue 2322 ASN Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2380 ASN Chi-restraints excluded: chain C residue 2431 VAL Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2488 ILE Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2530 ILE Chi-restraints excluded: chain E residue 928 LEU Chi-restraints excluded: chain E residue 1038 LEU Chi-restraints excluded: chain E residue 1144 ILE Chi-restraints excluded: chain E residue 1245 VAL Chi-restraints excluded: chain E residue 1361 GLN Chi-restraints excluded: chain E residue 1542 THR Chi-restraints excluded: chain E residue 1701 VAL Chi-restraints excluded: chain E residue 1734 ILE Chi-restraints excluded: chain E residue 1759 VAL Chi-restraints excluded: chain E residue 1788 VAL Chi-restraints excluded: chain E residue 1791 MET Chi-restraints excluded: chain E residue 1793 LEU Chi-restraints excluded: chain E residue 1800 LEU Chi-restraints excluded: chain E residue 1976 VAL Chi-restraints excluded: chain E residue 2103 THR Chi-restraints excluded: chain E residue 2111 THR Chi-restraints excluded: chain E residue 2119 LEU Chi-restraints excluded: chain E residue 2146 THR Chi-restraints excluded: chain E residue 2171 THR Chi-restraints excluded: chain E residue 2203 ILE Chi-restraints excluded: chain E residue 2207 LEU Chi-restraints excluded: chain E residue 2211 SER Chi-restraints excluded: chain E residue 2248 ILE Chi-restraints excluded: chain E residue 2270 MET Chi-restraints excluded: chain E residue 2281 ILE Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2324 GLN Chi-restraints excluded: chain E residue 2336 THR Chi-restraints excluded: chain E residue 2399 LEU Chi-restraints excluded: chain E residue 2401 VAL Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2441 CYS Chi-restraints excluded: chain E residue 2447 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2474 VAL Chi-restraints excluded: chain E residue 2479 LYS Chi-restraints excluded: chain E residue 2488 ILE Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2512 LEU Chi-restraints excluded: chain E residue 2532 LEU Chi-restraints excluded: chain E residue 2540 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 147 optimal weight: 0.5980 chunk 394 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 257 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 438 optimal weight: 3.9990 chunk 363 optimal weight: 0.7980 chunk 202 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 144 optimal weight: 0.9980 chunk 230 optimal weight: 50.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1107 GLN A1324 ASN C 798 GLN C1200 GLN ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1304 HIS C1493 HIS C1748 GLN E1107 GLN E1200 GLN E1304 HIS ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5424 moved from start: 0.5379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 36588 Z= 0.187 Angle : 0.677 14.865 49746 Z= 0.330 Chirality : 0.043 0.244 5667 Planarity : 0.004 0.060 6246 Dihedral : 5.294 27.416 4941 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.97 % Favored : 93.01 % Rotamer: Outliers : 3.81 % Allowed : 16.97 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.94 (0.13), residues: 4434 helix: 0.67 (0.10), residues: 2769 sheet: -2.51 (0.34), residues: 186 loop : -2.93 (0.15), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E1210 HIS 0.010 0.001 HIS E1304 PHE 0.022 0.001 PHE E2205 TYR 0.026 0.001 TYR C1323 ARG 0.004 0.000 ARG C2104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 693 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 556 time to evaluate : 3.658 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6329 (mm) REVERT: A 806 GLU cc_start: 0.8242 (tt0) cc_final: 0.7989 (tt0) REVERT: A 845 PHE cc_start: 0.7210 (t80) cc_final: 0.6342 (t80) REVERT: A 858 CYS cc_start: 0.8429 (m) cc_final: 0.8074 (m) REVERT: A 861 ILE cc_start: 0.7904 (mt) cc_final: 0.7664 (mt) REVERT: A 1045 LEU cc_start: 0.8322 (OUTLIER) cc_final: 0.8017 (mm) REVERT: A 1093 ASN cc_start: 0.7923 (m110) cc_final: 0.7314 (m-40) REVERT: A 1119 TRP cc_start: 0.6775 (p90) cc_final: 0.6445 (p90) REVERT: A 1323 TYR cc_start: 0.7776 (OUTLIER) cc_final: 0.7170 (t80) REVERT: A 1348 GLN cc_start: 0.7928 (mt0) cc_final: 0.7567 (mt0) REVERT: A 1353 ARG cc_start: 0.8013 (mtt-85) cc_final: 0.7620 (mtt-85) REVERT: A 1355 LYS cc_start: 0.7510 (tppt) cc_final: 0.7016 (tppt) REVERT: A 1356 GLN cc_start: 0.7982 (mt0) cc_final: 0.7563 (pp30) REVERT: A 1530 MET cc_start: 0.8450 (ttp) cc_final: 0.8177 (ttt) REVERT: A 1537 GLU cc_start: 0.8107 (mp0) cc_final: 0.7727 (mp0) REVERT: A 1661 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8263 (pm20) REVERT: A 1984 ASP cc_start: 0.7185 (m-30) cc_final: 0.6778 (m-30) REVERT: A 2153 MET cc_start: 0.6493 (mmm) cc_final: 0.6040 (mtm) REVERT: A 2174 LYS cc_start: 0.6791 (tptt) cc_final: 0.6568 (tttm) REVERT: A 2231 LYS cc_start: 0.7606 (mtmm) cc_final: 0.7080 (mtpp) REVERT: A 2285 GLN cc_start: 0.6133 (mt0) cc_final: 0.5776 (mm110) REVERT: A 2323 PHE cc_start: 0.7085 (m-80) cc_final: 0.6709 (m-80) REVERT: A 2447 VAL cc_start: 0.7878 (t) cc_final: 0.7667 (t) REVERT: A 2485 PHE cc_start: 0.6915 (m-10) cc_final: 0.6432 (m-10) REVERT: A 2506 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6324 (tt) REVERT: A 2509 ASP cc_start: 0.8179 (m-30) cc_final: 0.7960 (m-30) REVERT: C 794 LEU cc_start: 0.0018 (OUTLIER) cc_final: -0.0231 (mp) REVERT: C 924 ILE cc_start: 0.0203 (OUTLIER) cc_final: -0.0346 (mp) REVERT: C 928 LEU cc_start: 0.2019 (OUTLIER) cc_final: 0.1812 (mt) REVERT: C 959 GLN cc_start: -0.1726 (pm20) cc_final: -0.2072 (tp40) REVERT: C 1031 ARG cc_start: 0.3900 (mtt180) cc_final: 0.3621 (ptm160) REVERT: C 1101 LEU cc_start: 0.3319 (OUTLIER) cc_final: 0.2790 (mp) REVERT: C 1129 HIS cc_start: 0.2104 (m90) cc_final: 0.1549 (t70) REVERT: C 1152 MET cc_start: 0.2652 (tmm) cc_final: 0.2042 (mtm) REVERT: C 1238 MET cc_start: -0.1619 (tpp) cc_final: -0.1862 (ptm) REVERT: C 1323 TYR cc_start: 0.3826 (m-80) cc_final: 0.3359 (m-80) REVERT: C 1347 ARG cc_start: 0.6234 (mtt180) cc_final: 0.5670 (ttp80) REVERT: C 1668 GLN cc_start: 0.5006 (mp-120) cc_final: 0.4568 (pt0) REVERT: C 1700 MET cc_start: 0.5113 (ttp) cc_final: 0.4801 (mtp) REVERT: C 1754 TRP cc_start: 0.1305 (p90) cc_final: 0.0187 (m-10) REVERT: C 2049 PHE cc_start: 0.7059 (t80) cc_final: 0.6789 (t80) REVERT: C 2120 PHE cc_start: 0.7873 (m-80) cc_final: 0.6893 (m-80) REVERT: C 2153 MET cc_start: 0.8387 (mmt) cc_final: 0.8071 (mtm) REVERT: C 2239 PHE cc_start: 0.4230 (OUTLIER) cc_final: 0.3229 (m-80) REVERT: C 2241 MET cc_start: 0.7488 (tpp) cc_final: 0.6278 (tpp) REVERT: C 2270 MET cc_start: 0.5217 (mmm) cc_final: 0.5006 (mpp) REVERT: C 2322 ASN cc_start: 0.7513 (OUTLIER) cc_final: 0.7265 (m-40) REVERT: C 2395 GLU cc_start: 0.7744 (mt-10) cc_final: 0.6795 (tp30) REVERT: C 2528 LYS cc_start: 0.6759 (mtpm) cc_final: 0.6496 (tppt) REVERT: C 2537 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: C 2541 LYS cc_start: 0.5625 (mttt) cc_final: 0.4992 (tmtt) REVERT: E 782 ARG cc_start: 0.1428 (mtt180) cc_final: 0.0788 (mtp-110) REVERT: E 928 LEU cc_start: -0.0302 (OUTLIER) cc_final: -0.0600 (mt) REVERT: E 1264 MET cc_start: 0.0984 (ptm) cc_final: 0.0460 (ttm) REVERT: E 1265 MET cc_start: 0.2529 (tpt) cc_final: 0.2071 (mtp) REVERT: E 1349 MET cc_start: 0.7919 (mmm) cc_final: 0.7486 (mmm) REVERT: E 1502 MET cc_start: 0.0413 (tpt) cc_final: 0.0155 (ptt) REVERT: E 1734 ILE cc_start: 0.2550 (OUTLIER) cc_final: 0.1958 (pt) REVERT: E 1960 ARG cc_start: 0.3619 (mtt180) cc_final: 0.2540 (tpp80) REVERT: E 1988 ILE cc_start: 0.4377 (mm) cc_final: 0.4058 (mm) REVERT: E 2027 GLN cc_start: 0.5833 (mm110) cc_final: 0.4881 (tm-30) REVERT: E 2031 MET cc_start: 0.6798 (mmm) cc_final: 0.6446 (mmm) REVERT: E 2034 ASP cc_start: 0.8256 (m-30) cc_final: 0.7662 (m-30) REVERT: E 2046 LYS cc_start: 0.6902 (tptp) cc_final: 0.6684 (tptp) REVERT: E 2258 GLU cc_start: 0.7608 (mt-10) cc_final: 0.6996 (mm-30) REVERT: E 2279 GLU cc_start: 0.7278 (mt-10) cc_final: 0.6683 (mm-30) REVERT: E 2285 GLN cc_start: 0.7207 (mt0) cc_final: 0.6791 (mp10) REVERT: E 2321 TRP cc_start: 0.6115 (m-10) cc_final: 0.5704 (m-90) REVERT: E 2485 PHE cc_start: 0.5883 (m-10) cc_final: 0.5440 (m-10) REVERT: E 2520 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7606 (pt0) REVERT: E 2523 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7278 (mt-10) outliers start: 137 outliers final: 73 residues processed: 651 average time/residue: 0.4263 time to fit residues: 466.3410 Evaluate side-chains 575 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 488 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1244 TRP Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1323 TYR Chi-restraints excluded: chain A residue 1661 GLU Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2119 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain A residue 2320 THR Chi-restraints excluded: chain A residue 2321 TRP Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2431 VAL Chi-restraints excluded: chain A residue 2488 ILE Chi-restraints excluded: chain A residue 2499 CYS Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1100 LEU Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1783 ILE Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 2031 MET Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2047 LEU Chi-restraints excluded: chain C residue 2052 VAL Chi-restraints excluded: chain C residue 2097 ILE Chi-restraints excluded: chain C residue 2200 ILE Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2239 PHE Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2322 ASN Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2380 ASN Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2474 VAL Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2537 GLU Chi-restraints excluded: chain E residue 827 VAL Chi-restraints excluded: chain E residue 928 LEU Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1161 LEU Chi-restraints excluded: chain E residue 1361 GLN Chi-restraints excluded: chain E residue 1734 ILE Chi-restraints excluded: chain E residue 1759 VAL Chi-restraints excluded: chain E residue 1800 LEU Chi-restraints excluded: chain E residue 2016 VAL Chi-restraints excluded: chain E residue 2044 LEU Chi-restraints excluded: chain E residue 2146 THR Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2186 ILE Chi-restraints excluded: chain E residue 2270 MET Chi-restraints excluded: chain E residue 2281 ILE Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2401 VAL Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2441 CYS Chi-restraints excluded: chain E residue 2447 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2488 ILE Chi-restraints excluded: chain E residue 2497 LEU Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2512 LEU Chi-restraints excluded: chain E residue 2532 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 422 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 320 optimal weight: 0.0670 chunk 247 optimal weight: 0.8980 chunk 368 optimal weight: 5.9990 chunk 244 optimal weight: 0.7980 chunk 436 optimal weight: 6.9990 chunk 273 optimal weight: 0.0570 chunk 266 optimal weight: 3.9990 chunk 201 optimal weight: 0.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 953 GLN A1324 ASN A1510 GLN A2181 GLN ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1356 GLN ** C1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 927 HIS E2075 GLN E2353 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5414 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 36588 Z= 0.174 Angle : 0.669 14.238 49746 Z= 0.321 Chirality : 0.043 0.245 5667 Planarity : 0.004 0.050 6246 Dihedral : 4.974 25.985 4941 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 3.14 % Allowed : 17.95 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.58 (0.13), residues: 4434 helix: 1.01 (0.10), residues: 2736 sheet: -2.31 (0.32), residues: 216 loop : -2.84 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP E1033 HIS 0.010 0.001 HIS E1304 PHE 0.030 0.001 PHE C2163 TYR 0.026 0.001 TYR C1323 ARG 0.009 0.000 ARG A1347 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 637 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 524 time to evaluate : 4.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 LEU cc_start: 0.7119 (OUTLIER) cc_final: 0.6466 (mm) REVERT: A 845 PHE cc_start: 0.7298 (t80) cc_final: 0.6402 (t80) REVERT: A 858 CYS cc_start: 0.8400 (m) cc_final: 0.8047 (m) REVERT: A 911 TRP cc_start: 0.7559 (t60) cc_final: 0.7349 (t60) REVERT: A 931 LEU cc_start: 0.8126 (tm) cc_final: 0.7830 (pp) REVERT: A 936 PHE cc_start: 0.7794 (t80) cc_final: 0.7484 (t80) REVERT: A 937 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7899 (tm-30) REVERT: A 941 TYR cc_start: 0.7778 (m-80) cc_final: 0.7463 (m-80) REVERT: A 1045 LEU cc_start: 0.8285 (OUTLIER) cc_final: 0.8014 (mm) REVERT: A 1054 MET cc_start: 0.4818 (mpp) cc_final: 0.4045 (mmt) REVERT: A 1093 ASN cc_start: 0.7839 (m110) cc_final: 0.7234 (m-40) REVERT: A 1118 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7165 (tm-30) REVERT: A 1323 TYR cc_start: 0.7743 (OUTLIER) cc_final: 0.7135 (t80) REVERT: A 1348 GLN cc_start: 0.7892 (mt0) cc_final: 0.7458 (mt0) REVERT: A 1356 GLN cc_start: 0.7863 (mt0) cc_final: 0.7438 (tm-30) REVERT: A 1530 MET cc_start: 0.8460 (ttp) cc_final: 0.8155 (ttt) REVERT: A 1537 GLU cc_start: 0.8021 (mp0) cc_final: 0.7668 (mp0) REVERT: A 1661 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8269 (pm20) REVERT: A 1984 ASP cc_start: 0.7259 (m-30) cc_final: 0.6860 (m-30) REVERT: A 2023 MET cc_start: 0.6182 (mtt) cc_final: 0.5859 (mtp) REVERT: A 2047 LEU cc_start: 0.7488 (OUTLIER) cc_final: 0.7228 (mt) REVERT: A 2062 PHE cc_start: 0.6852 (m-80) cc_final: 0.6014 (m-80) REVERT: A 2153 MET cc_start: 0.6519 (mmm) cc_final: 0.6017 (mtm) REVERT: A 2231 LYS cc_start: 0.7626 (mtmm) cc_final: 0.7129 (mtpp) REVERT: A 2285 GLN cc_start: 0.6060 (mt0) cc_final: 0.5741 (mm110) REVERT: A 2323 PHE cc_start: 0.7139 (m-80) cc_final: 0.6864 (m-80) REVERT: A 2407 ARG cc_start: 0.6235 (mtm180) cc_final: 0.5346 (ptm-80) REVERT: A 2447 VAL cc_start: 0.7828 (t) cc_final: 0.7612 (t) REVERT: A 2485 PHE cc_start: 0.6920 (m-10) cc_final: 0.6378 (m-10) REVERT: A 2506 LEU cc_start: 0.7103 (OUTLIER) cc_final: 0.6504 (tt) REVERT: C 794 LEU cc_start: 0.0022 (OUTLIER) cc_final: -0.0229 (mp) REVERT: C 924 ILE cc_start: 0.0267 (OUTLIER) cc_final: -0.0323 (mp) REVERT: C 928 LEU cc_start: 0.2012 (OUTLIER) cc_final: 0.1807 (mt) REVERT: C 959 GLN cc_start: -0.1370 (pm20) cc_final: -0.1770 (tp40) REVERT: C 1031 ARG cc_start: 0.3857 (mtt180) cc_final: 0.3569 (ptm160) REVERT: C 1101 LEU cc_start: 0.3390 (OUTLIER) cc_final: 0.2792 (mp) REVERT: C 1129 HIS cc_start: 0.1844 (m90) cc_final: 0.1542 (t70) REVERT: C 1191 LEU cc_start: 0.4285 (tt) cc_final: 0.3792 (mt) REVERT: C 1323 TYR cc_start: 0.3840 (m-80) cc_final: 0.3514 (m-80) REVERT: C 1347 ARG cc_start: 0.6098 (mtt180) cc_final: 0.5582 (ttp80) REVERT: C 1668 GLN cc_start: 0.4925 (mp-120) cc_final: 0.4524 (pt0) REVERT: C 1700 MET cc_start: 0.5093 (ttp) cc_final: 0.4775 (mtp) REVERT: C 1754 TRP cc_start: 0.1300 (p90) cc_final: 0.0277 (m-10) REVERT: C 2120 PHE cc_start: 0.7699 (m-80) cc_final: 0.6907 (m-80) REVERT: C 2153 MET cc_start: 0.8203 (mmt) cc_final: 0.7788 (mtm) REVERT: C 2238 LEU cc_start: 0.8497 (mt) cc_final: 0.8119 (mt) REVERT: C 2239 PHE cc_start: 0.4216 (OUTLIER) cc_final: 0.3171 (m-80) REVERT: C 2241 MET cc_start: 0.7143 (tpp) cc_final: 0.6198 (tpp) REVERT: C 2270 MET cc_start: 0.5285 (mmm) cc_final: 0.4845 (mpp) REVERT: C 2304 MET cc_start: 0.7503 (mmm) cc_final: 0.7300 (mmp) REVERT: C 2395 GLU cc_start: 0.7622 (mt-10) cc_final: 0.6651 (tp30) REVERT: C 2497 LEU cc_start: 0.7068 (OUTLIER) cc_final: 0.4810 (mp) REVERT: C 2528 LYS cc_start: 0.6963 (mtpm) cc_final: 0.6679 (tppt) REVERT: C 2537 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8081 (mm-30) REVERT: C 2541 LYS cc_start: 0.5520 (mttt) cc_final: 0.4981 (tmtt) REVERT: E 782 ARG cc_start: 0.1260 (mtt180) cc_final: 0.0702 (mtp-110) REVERT: E 856 TRP cc_start: 0.2644 (m100) cc_final: 0.2162 (m-90) REVERT: E 928 LEU cc_start: -0.0327 (OUTLIER) cc_final: -0.0607 (mt) REVERT: E 1264 MET cc_start: 0.1156 (ptm) cc_final: 0.0629 (ttm) REVERT: E 1265 MET cc_start: 0.2828 (tpt) cc_final: 0.2550 (mtp) REVERT: E 1349 MET cc_start: 0.7938 (mmm) cc_final: 0.7396 (mmm) REVERT: E 1502 MET cc_start: 0.0419 (tpt) cc_final: 0.0160 (ptt) REVERT: E 1791 MET cc_start: 0.4199 (ptp) cc_final: 0.3475 (ppp) REVERT: E 1960 ARG cc_start: 0.3585 (mtt180) cc_final: 0.2505 (tpp80) REVERT: E 1980 MET cc_start: 0.5113 (mtp) cc_final: 0.4888 (mpp) REVERT: E 2031 MET cc_start: 0.6823 (mmm) cc_final: 0.6552 (mmm) REVERT: E 2034 ASP cc_start: 0.8219 (m-30) cc_final: 0.7675 (m-30) REVERT: E 2043 VAL cc_start: 0.7694 (t) cc_final: 0.7475 (p) REVERT: E 2046 LYS cc_start: 0.6936 (tptp) cc_final: 0.5884 (pttp) REVERT: E 2230 LEU cc_start: 0.8269 (mm) cc_final: 0.7642 (mm) REVERT: E 2231 LYS cc_start: 0.7268 (mttt) cc_final: 0.6894 (mtpt) REVERT: E 2258 GLU cc_start: 0.7265 (mt-10) cc_final: 0.7003 (tp30) REVERT: E 2279 GLU cc_start: 0.7369 (mt-10) cc_final: 0.6790 (mm-30) REVERT: E 2285 GLN cc_start: 0.7198 (mt0) cc_final: 0.6806 (mp10) REVERT: E 2321 TRP cc_start: 0.6116 (m-10) cc_final: 0.5684 (m-90) REVERT: E 2353 GLN cc_start: 0.7288 (OUTLIER) cc_final: 0.6841 (tt0) REVERT: E 2390 LEU cc_start: 0.4098 (mt) cc_final: 0.3680 (mt) REVERT: E 2487 GLU cc_start: 0.5015 (mt-10) cc_final: 0.4203 (tt0) REVERT: E 2520 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7517 (pt0) REVERT: E 2523 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7227 (mt-10) outliers start: 113 outliers final: 72 residues processed: 609 average time/residue: 0.4423 time to fit residues: 452.7405 Evaluate side-chains 568 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 480 time to evaluate : 4.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1244 TRP Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1323 TYR Chi-restraints excluded: chain A residue 1661 GLU Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2047 LEU Chi-restraints excluded: chain A residue 2106 LEU Chi-restraints excluded: chain A residue 2119 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2127 LEU Chi-restraints excluded: chain A residue 2318 ARG Chi-restraints excluded: chain A residue 2320 THR Chi-restraints excluded: chain A residue 2321 TRP Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2431 VAL Chi-restraints excluded: chain A residue 2488 ILE Chi-restraints excluded: chain A residue 2499 CYS Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1039 PHE Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1783 ILE Chi-restraints excluded: chain C residue 1805 LEU Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2052 VAL Chi-restraints excluded: chain C residue 2097 ILE Chi-restraints excluded: chain C residue 2200 ILE Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2216 VAL Chi-restraints excluded: chain C residue 2239 PHE Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2264 ASP Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2380 ASN Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2474 VAL Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2537 GLU Chi-restraints excluded: chain E residue 827 VAL Chi-restraints excluded: chain E residue 928 LEU Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1144 ILE Chi-restraints excluded: chain E residue 1153 LEU Chi-restraints excluded: chain E residue 1245 VAL Chi-restraints excluded: chain E residue 1361 GLN Chi-restraints excluded: chain E residue 1533 VAL Chi-restraints excluded: chain E residue 1759 VAL Chi-restraints excluded: chain E residue 1800 LEU Chi-restraints excluded: chain E residue 2081 LEU Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2186 ILE Chi-restraints excluded: chain E residue 2252 THR Chi-restraints excluded: chain E residue 2281 ILE Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2353 GLN Chi-restraints excluded: chain E residue 2401 VAL Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2488 ILE Chi-restraints excluded: chain E residue 2497 LEU Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2512 LEU Chi-restraints excluded: chain E residue 2532 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 270 optimal weight: 0.8980 chunk 174 optimal weight: 6.9990 chunk 260 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 85 optimal weight: 0.0070 chunk 84 optimal weight: 0.9980 chunk 277 optimal weight: 6.9990 chunk 297 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 343 optimal weight: 0.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1324 ASN A2181 GLN ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 927 HIS E2353 GLN ** E2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5433 moved from start: 0.5657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 36588 Z= 0.205 Angle : 0.673 15.261 49746 Z= 0.325 Chirality : 0.043 0.243 5667 Planarity : 0.004 0.049 6246 Dihedral : 4.906 23.371 4941 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.28 % Favored : 92.69 % Rotamer: Outliers : 3.26 % Allowed : 18.31 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.51 (0.13), residues: 4434 helix: 1.07 (0.10), residues: 2748 sheet: -2.19 (0.33), residues: 213 loop : -2.84 (0.15), residues: 1473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 911 HIS 0.012 0.001 HIS E1304 PHE 0.027 0.002 PHE E2263 TYR 0.030 0.001 TYR E2375 ARG 0.007 0.000 ARG A1347 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 621 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 504 time to evaluate : 3.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 LEU cc_start: 0.7139 (OUTLIER) cc_final: 0.6540 (mm) REVERT: A 845 PHE cc_start: 0.7301 (t80) cc_final: 0.6324 (t80) REVERT: A 858 CYS cc_start: 0.8321 (m) cc_final: 0.8075 (m) REVERT: A 911 TRP cc_start: 0.7640 (t60) cc_final: 0.7378 (t60) REVERT: A 937 GLU cc_start: 0.8471 (tm-30) cc_final: 0.7962 (tm-30) REVERT: A 941 TYR cc_start: 0.7864 (m-80) cc_final: 0.7535 (m-80) REVERT: A 1045 LEU cc_start: 0.8301 (OUTLIER) cc_final: 0.7938 (mm) REVERT: A 1054 MET cc_start: 0.4919 (mpp) cc_final: 0.4469 (mmt) REVERT: A 1093 ASN cc_start: 0.7832 (m110) cc_final: 0.7210 (m-40) REVERT: A 1118 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7177 (tt0) REVERT: A 1323 TYR cc_start: 0.7777 (OUTLIER) cc_final: 0.7141 (t80) REVERT: A 1348 GLN cc_start: 0.7933 (mt0) cc_final: 0.7520 (mt0) REVERT: A 1530 MET cc_start: 0.8436 (ttp) cc_final: 0.8137 (ttt) REVERT: A 1661 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8291 (pm20) REVERT: A 1984 ASP cc_start: 0.7152 (m-30) cc_final: 0.6640 (m-30) REVERT: A 2021 LEU cc_start: 0.7277 (mt) cc_final: 0.6986 (mt) REVERT: A 2047 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7264 (mt) REVERT: A 2062 PHE cc_start: 0.6837 (m-80) cc_final: 0.6008 (m-80) REVERT: A 2153 MET cc_start: 0.6517 (mmm) cc_final: 0.5991 (mtm) REVERT: A 2174 LYS cc_start: 0.6771 (tptt) cc_final: 0.6541 (tttm) REVERT: A 2231 LYS cc_start: 0.7559 (mtmm) cc_final: 0.7070 (mtpp) REVERT: A 2270 MET cc_start: 0.5521 (mmt) cc_final: 0.5203 (mmm) REVERT: A 2285 GLN cc_start: 0.6068 (mt0) cc_final: 0.5764 (mm110) REVERT: A 2407 ARG cc_start: 0.6242 (mtm180) cc_final: 0.5391 (ptm-80) REVERT: A 2485 PHE cc_start: 0.6918 (m-10) cc_final: 0.6354 (m-10) REVERT: A 2506 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6456 (tt) REVERT: C 794 LEU cc_start: 0.0026 (OUTLIER) cc_final: -0.0223 (mp) REVERT: C 924 ILE cc_start: 0.0268 (OUTLIER) cc_final: -0.0334 (mp) REVERT: C 928 LEU cc_start: 0.2008 (OUTLIER) cc_final: 0.1805 (mt) REVERT: C 959 GLN cc_start: -0.1363 (pm20) cc_final: -0.1766 (tp40) REVERT: C 1031 ARG cc_start: 0.4118 (mtt180) cc_final: 0.3789 (ptm160) REVERT: C 1101 LEU cc_start: 0.3133 (OUTLIER) cc_final: 0.2573 (mp) REVERT: C 1129 HIS cc_start: 0.1940 (m90) cc_final: 0.1553 (t70) REVERT: C 1143 PHE cc_start: 0.1304 (p90) cc_final: 0.1096 (m-10) REVERT: C 1191 LEU cc_start: 0.4491 (tt) cc_final: 0.3995 (mt) REVERT: C 1323 TYR cc_start: 0.3751 (m-80) cc_final: 0.3413 (m-80) REVERT: C 1347 ARG cc_start: 0.6122 (mtt180) cc_final: 0.5627 (ttp80) REVERT: C 1668 GLN cc_start: 0.4932 (mp-120) cc_final: 0.4541 (pt0) REVERT: C 1700 MET cc_start: 0.5110 (ttp) cc_final: 0.4791 (mtp) REVERT: C 1754 TRP cc_start: 0.1299 (p90) cc_final: 0.0278 (m-10) REVERT: C 2120 PHE cc_start: 0.7672 (m-80) cc_final: 0.6883 (m-80) REVERT: C 2153 MET cc_start: 0.8274 (mmt) cc_final: 0.7809 (mtm) REVERT: C 2238 LEU cc_start: 0.8546 (mt) cc_final: 0.8222 (mt) REVERT: C 2239 PHE cc_start: 0.4535 (OUTLIER) cc_final: 0.3462 (m-80) REVERT: C 2241 MET cc_start: 0.7283 (tpp) cc_final: 0.6253 (tpp) REVERT: C 2266 TYR cc_start: 0.6010 (t80) cc_final: 0.5649 (t80) REVERT: C 2270 MET cc_start: 0.5238 (mmm) cc_final: 0.4758 (mpp) REVERT: C 2280 ASP cc_start: 0.5439 (OUTLIER) cc_final: 0.5174 (t0) REVERT: C 2295 ARG cc_start: 0.7283 (mmm160) cc_final: 0.7057 (mmm160) REVERT: C 2395 GLU cc_start: 0.7718 (mt-10) cc_final: 0.6687 (tp30) REVERT: C 2528 LYS cc_start: 0.6933 (mtpm) cc_final: 0.6637 (tppt) REVERT: C 2537 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8074 (mm-30) REVERT: C 2541 LYS cc_start: 0.5435 (mttt) cc_final: 0.4908 (tmtt) REVERT: E 782 ARG cc_start: 0.1332 (mtt180) cc_final: 0.0764 (mtp-110) REVERT: E 856 TRP cc_start: 0.2672 (m100) cc_final: 0.2172 (m-90) REVERT: E 928 LEU cc_start: -0.0316 (OUTLIER) cc_final: -0.0609 (mp) REVERT: E 1502 MET cc_start: 0.0430 (tpt) cc_final: 0.0129 (ptt) REVERT: E 1791 MET cc_start: 0.4361 (ptp) cc_final: 0.3584 (ppp) REVERT: E 1960 ARG cc_start: 0.3603 (mtt180) cc_final: 0.2512 (tpp80) REVERT: E 1980 MET cc_start: 0.5069 (mtp) cc_final: 0.4799 (mpp) REVERT: E 2031 MET cc_start: 0.6830 (mmm) cc_final: 0.6593 (mmm) REVERT: E 2034 ASP cc_start: 0.8207 (m-30) cc_final: 0.7590 (m-30) REVERT: E 2043 VAL cc_start: 0.7768 (t) cc_final: 0.7502 (p) REVERT: E 2046 LYS cc_start: 0.6986 (tptp) cc_final: 0.5929 (pttp) REVERT: E 2230 LEU cc_start: 0.8353 (mm) cc_final: 0.7765 (mm) REVERT: E 2231 LYS cc_start: 0.7312 (mttt) cc_final: 0.6927 (mtpt) REVERT: E 2258 GLU cc_start: 0.7339 (mt-10) cc_final: 0.7061 (tp30) REVERT: E 2279 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6665 (mm-30) REVERT: E 2285 GLN cc_start: 0.7136 (mt0) cc_final: 0.6680 (mp10) REVERT: E 2321 TRP cc_start: 0.6133 (m-10) cc_final: 0.5661 (m-90) REVERT: E 2353 GLN cc_start: 0.7860 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: E 2485 PHE cc_start: 0.5589 (m-10) cc_final: 0.5200 (m-10) REVERT: E 2487 GLU cc_start: 0.5028 (mt-10) cc_final: 0.4203 (tt0) REVERT: E 2520 GLU cc_start: 0.8061 (mt-10) cc_final: 0.7517 (pt0) REVERT: E 2523 GLU cc_start: 0.7628 (mt-10) cc_final: 0.7240 (mt-10) outliers start: 117 outliers final: 82 residues processed: 588 average time/residue: 0.4313 time to fit residues: 427.4712 Evaluate side-chains 586 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 488 time to evaluate : 3.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 825 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 928 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1244 TRP Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1323 TYR Chi-restraints excluded: chain A residue 1661 GLU Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2047 LEU Chi-restraints excluded: chain A residue 2106 LEU Chi-restraints excluded: chain A residue 2119 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2296 ILE Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2318 ARG Chi-restraints excluded: chain A residue 2320 THR Chi-restraints excluded: chain A residue 2321 TRP Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2431 VAL Chi-restraints excluded: chain A residue 2488 ILE Chi-restraints excluded: chain A residue 2499 CYS Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1039 PHE Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1783 ILE Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2047 LEU Chi-restraints excluded: chain C residue 2097 ILE Chi-restraints excluded: chain C residue 2200 ILE Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2239 PHE Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2264 ASP Chi-restraints excluded: chain C residue 2280 ASP Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2380 ASN Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2474 VAL Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2530 ILE Chi-restraints excluded: chain C residue 2537 GLU Chi-restraints excluded: chain E residue 928 LEU Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1153 LEU Chi-restraints excluded: chain E residue 1170 PHE Chi-restraints excluded: chain E residue 1245 VAL Chi-restraints excluded: chain E residue 1361 GLN Chi-restraints excluded: chain E residue 1533 VAL Chi-restraints excluded: chain E residue 1759 VAL Chi-restraints excluded: chain E residue 1800 LEU Chi-restraints excluded: chain E residue 2081 LEU Chi-restraints excluded: chain E residue 2119 LEU Chi-restraints excluded: chain E residue 2144 ASP Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2186 ILE Chi-restraints excluded: chain E residue 2252 THR Chi-restraints excluded: chain E residue 2281 ILE Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2353 GLN Chi-restraints excluded: chain E residue 2401 VAL Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2488 ILE Chi-restraints excluded: chain E residue 2497 LEU Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2512 LEU Chi-restraints excluded: chain E residue 2529 LEU Chi-restraints excluded: chain E residue 2532 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 397 optimal weight: 4.9990 chunk 418 optimal weight: 0.9980 chunk 381 optimal weight: 7.9990 chunk 406 optimal weight: 7.9990 chunk 244 optimal weight: 10.0000 chunk 177 optimal weight: 7.9990 chunk 319 optimal weight: 8.9990 chunk 124 optimal weight: 0.5980 chunk 367 optimal weight: 6.9990 chunk 384 optimal weight: 8.9990 chunk 405 optimal weight: 0.8980 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1324 ASN A1510 GLN ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1796 HIS E1655 HIS ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5476 moved from start: 0.6029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 36588 Z= 0.321 Angle : 0.756 14.886 49746 Z= 0.370 Chirality : 0.046 0.265 5667 Planarity : 0.005 0.054 6246 Dihedral : 5.236 24.851 4941 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.64 % Favored : 91.34 % Rotamer: Outliers : 3.28 % Allowed : 18.42 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % 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: -0.86 (0.13), residues: 4434 helix: 0.73 (0.10), residues: 2772 sheet: -2.20 (0.34), residues: 213 loop : -2.93 (0.15), residues: 1449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP A 911 HIS 0.012 0.001 HIS E1304 PHE 0.035 0.002 PHE A1098 TYR 0.025 0.002 TYR E2375 ARG 0.014 0.001 ARG E2351 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 610 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 492 time to evaluate : 3.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 LEU cc_start: 0.6369 (OUTLIER) cc_final: 0.5796 (mm) REVERT: A 845 PHE cc_start: 0.7321 (t80) cc_final: 0.6290 (t80) REVERT: A 911 TRP cc_start: 0.7513 (t60) cc_final: 0.7134 (t60) REVERT: A 941 TYR cc_start: 0.7927 (m-80) cc_final: 0.7623 (m-80) REVERT: A 1054 MET cc_start: 0.5214 (mpp) cc_final: 0.4563 (mmt) REVERT: A 1093 ASN cc_start: 0.7833 (m110) cc_final: 0.7192 (m-40) REVERT: A 1118 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7206 (tt0) REVERT: A 1323 TYR cc_start: 0.7867 (OUTLIER) cc_final: 0.7156 (t80) REVERT: A 1348 GLN cc_start: 0.7925 (mt0) cc_final: 0.7491 (mt0) REVERT: A 1355 LYS cc_start: 0.7664 (tppt) cc_final: 0.7301 (tppt) REVERT: A 1530 MET cc_start: 0.8441 (ttp) cc_final: 0.8155 (ttt) REVERT: A 1537 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7837 (mp0) REVERT: A 1661 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8258 (pm20) REVERT: A 1984 ASP cc_start: 0.7019 (m-30) cc_final: 0.6548 (m-30) REVERT: A 2021 LEU cc_start: 0.7269 (mt) cc_final: 0.7019 (mt) REVERT: A 2047 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7200 (mt) REVERT: A 2062 PHE cc_start: 0.6791 (m-80) cc_final: 0.5903 (m-80) REVERT: A 2153 MET cc_start: 0.6416 (mmm) cc_final: 0.5922 (mtm) REVERT: A 2174 LYS cc_start: 0.6677 (tptt) cc_final: 0.6468 (tttm) REVERT: A 2231 LYS cc_start: 0.7535 (mtmm) cc_final: 0.6991 (mmmt) REVERT: A 2285 GLN cc_start: 0.6151 (mt0) cc_final: 0.5868 (mm110) REVERT: A 2340 HIS cc_start: 0.5552 (t70) cc_final: 0.5101 (t-90) REVERT: A 2388 LYS cc_start: 0.8006 (ttpt) cc_final: 0.7699 (ttpt) REVERT: A 2485 PHE cc_start: 0.6878 (m-10) cc_final: 0.6322 (m-10) REVERT: A 2506 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6499 (tt) REVERT: A 2523 GLU cc_start: 0.6203 (mt-10) cc_final: 0.5966 (mt-10) REVERT: C 794 LEU cc_start: 0.0033 (OUTLIER) cc_final: -0.0222 (mp) REVERT: C 803 ARG cc_start: 0.1986 (tpt90) cc_final: 0.1468 (tpp80) REVERT: C 924 ILE cc_start: 0.0238 (OUTLIER) cc_final: -0.0333 (mp) REVERT: C 928 LEU cc_start: 0.1762 (OUTLIER) cc_final: 0.1539 (mt) REVERT: C 1010 VAL cc_start: 0.2823 (OUTLIER) cc_final: 0.2510 (m) REVERT: C 1031 ARG cc_start: 0.3945 (mtt180) cc_final: 0.3713 (ptt180) REVERT: C 1101 LEU cc_start: 0.3035 (OUTLIER) cc_final: 0.2549 (mp) REVERT: C 1129 HIS cc_start: 0.2348 (m90) cc_final: 0.1782 (t70) REVERT: C 1191 LEU cc_start: 0.4520 (tt) cc_final: 0.4029 (mt) REVERT: C 1323 TYR cc_start: 0.3516 (m-80) cc_final: 0.3015 (m-80) REVERT: C 1347 ARG cc_start: 0.6212 (mtt180) cc_final: 0.5661 (ttp80) REVERT: C 1668 GLN cc_start: 0.4713 (mp-120) cc_final: 0.4345 (pt0) REVERT: C 1700 MET cc_start: 0.5168 (ttp) cc_final: 0.4917 (mtp) REVERT: C 1754 TRP cc_start: 0.2129 (p90) cc_final: 0.1089 (m-10) REVERT: C 2120 PHE cc_start: 0.7625 (m-80) cc_final: 0.6882 (m-80) REVERT: C 2153 MET cc_start: 0.8393 (mmt) cc_final: 0.7950 (mtm) REVERT: C 2238 LEU cc_start: 0.8727 (mt) cc_final: 0.8416 (mt) REVERT: C 2239 PHE cc_start: 0.4579 (OUTLIER) cc_final: 0.3369 (m-80) REVERT: C 2241 MET cc_start: 0.7618 (tpp) cc_final: 0.7064 (tpp) REVERT: C 2266 TYR cc_start: 0.6367 (t80) cc_final: 0.5729 (t80) REVERT: C 2280 ASP cc_start: 0.5285 (OUTLIER) cc_final: 0.4873 (t0) REVERT: C 2295 ARG cc_start: 0.7291 (mmm160) cc_final: 0.6225 (mpp80) REVERT: C 2395 GLU cc_start: 0.7735 (mt-10) cc_final: 0.6717 (tp30) REVERT: C 2528 LYS cc_start: 0.6930 (mtpm) cc_final: 0.6589 (tppt) REVERT: C 2537 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8307 (mm-30) REVERT: C 2541 LYS cc_start: 0.5459 (mttt) cc_final: 0.4870 (tmtt) REVERT: E 782 ARG cc_start: 0.1359 (mtt180) cc_final: 0.0807 (mtp-110) REVERT: E 928 LEU cc_start: -0.0646 (OUTLIER) cc_final: -0.0908 (mp) REVERT: E 997 MET cc_start: 0.1332 (mmt) cc_final: 0.0692 (ptm) REVERT: E 1143 PHE cc_start: 0.3250 (p90) cc_final: 0.3003 (p90) REVERT: E 1349 MET cc_start: 0.7838 (mmm) cc_final: 0.7511 (mmm) REVERT: E 1502 MET cc_start: 0.0443 (tpt) cc_final: 0.0027 (ptt) REVERT: E 1960 ARG cc_start: 0.3676 (mtt180) cc_final: 0.2900 (ptp-170) REVERT: E 1980 MET cc_start: 0.5151 (mtp) cc_final: 0.4910 (mpp) REVERT: E 2031 MET cc_start: 0.6743 (mmm) cc_final: 0.6494 (mmm) REVERT: E 2034 ASP cc_start: 0.8167 (m-30) cc_final: 0.7563 (m-30) REVERT: E 2046 LYS cc_start: 0.7034 (tptp) cc_final: 0.6175 (pttp) REVERT: E 2230 LEU cc_start: 0.8419 (mm) cc_final: 0.7815 (mm) REVERT: E 2231 LYS cc_start: 0.7137 (mttt) cc_final: 0.6842 (mtpt) REVERT: E 2258 GLU cc_start: 0.7272 (mt-10) cc_final: 0.6825 (tp30) REVERT: E 2270 MET cc_start: 0.5592 (OUTLIER) cc_final: 0.5203 (tpp) REVERT: E 2279 GLU cc_start: 0.7215 (mt-10) cc_final: 0.6822 (tp30) REVERT: E 2285 GLN cc_start: 0.7190 (mt0) cc_final: 0.6445 (mp10) REVERT: E 2321 TRP cc_start: 0.6209 (m-10) cc_final: 0.5493 (m-90) REVERT: E 2431 VAL cc_start: 0.7236 (OUTLIER) cc_final: 0.6839 (p) REVERT: E 2520 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7645 (pt0) REVERT: E 2523 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7281 (mt-10) outliers start: 118 outliers final: 87 residues processed: 577 average time/residue: 0.4173 time to fit residues: 404.5156 Evaluate side-chains 574 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 470 time to evaluate : 3.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 815 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1164 LEU Chi-restraints excluded: chain A residue 1208 VAL Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1323 TYR Chi-restraints excluded: chain A residue 1349 MET Chi-restraints excluded: chain A residue 1661 GLU Chi-restraints excluded: chain A residue 1683 VAL Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2047 LEU Chi-restraints excluded: chain A residue 2053 LEU Chi-restraints excluded: chain A residue 2119 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2207 LEU Chi-restraints excluded: chain A residue 2244 GLN Chi-restraints excluded: chain A residue 2296 ILE Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2318 ARG Chi-restraints excluded: chain A residue 2320 THR Chi-restraints excluded: chain A residue 2321 TRP Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2431 VAL Chi-restraints excluded: chain A residue 2467 VAL Chi-restraints excluded: chain A residue 2488 ILE Chi-restraints excluded: chain A residue 2493 MET Chi-restraints excluded: chain A residue 2499 CYS Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1101 LEU Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1545 LEU Chi-restraints excluded: chain C residue 1783 ILE Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2047 LEU Chi-restraints excluded: chain C residue 2057 ILE Chi-restraints excluded: chain C residue 2200 ILE Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2239 PHE Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2264 ASP Chi-restraints excluded: chain C residue 2280 ASP Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2380 ASN Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2474 VAL Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2499 CYS Chi-restraints excluded: chain C residue 2530 ILE Chi-restraints excluded: chain C residue 2537 GLU Chi-restraints excluded: chain E residue 928 LEU Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1153 LEU Chi-restraints excluded: chain E residue 1170 PHE Chi-restraints excluded: chain E residue 1245 VAL Chi-restraints excluded: chain E residue 1361 GLN Chi-restraints excluded: chain E residue 1533 VAL Chi-restraints excluded: chain E residue 1759 VAL Chi-restraints excluded: chain E residue 1800 LEU Chi-restraints excluded: chain E residue 2103 THR Chi-restraints excluded: chain E residue 2119 LEU Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2186 ILE Chi-restraints excluded: chain E residue 2248 ILE Chi-restraints excluded: chain E residue 2252 THR Chi-restraints excluded: chain E residue 2270 MET Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2401 VAL Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2441 CYS Chi-restraints excluded: chain E residue 2448 ILE Chi-restraints excluded: chain E residue 2488 ILE Chi-restraints excluded: chain E residue 2497 LEU Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2512 LEU Chi-restraints excluded: chain E residue 2529 LEU Chi-restraints excluded: chain E residue 2532 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 267 optimal weight: 3.9990 chunk 430 optimal weight: 0.9980 chunk 262 optimal weight: 0.9980 chunk 204 optimal weight: 8.9990 chunk 299 optimal weight: 1.9990 chunk 451 optimal weight: 0.8980 chunk 415 optimal weight: 2.9990 chunk 359 optimal weight: 0.0970 chunk 37 optimal weight: 0.8980 chunk 277 optimal weight: 8.9990 chunk 220 optimal weight: 2.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1324 ASN A1510 GLN A2181 GLN ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5428 moved from start: 0.6076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36588 Z= 0.177 Angle : 0.672 15.428 49746 Z= 0.324 Chirality : 0.043 0.238 5667 Planarity : 0.004 0.052 6246 Dihedral : 4.893 29.839 4941 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.86 % Favored : 93.12 % Rotamer: Outliers : 2.73 % Allowed : 19.25 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.13), residues: 4434 helix: 1.07 (0.10), residues: 2769 sheet: -2.06 (0.34), residues: 213 loop : -2.78 (0.15), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A2082 HIS 0.014 0.001 HIS E1304 PHE 0.034 0.002 PHE C2198 TYR 0.031 0.001 TYR A2089 ARG 0.005 0.000 ARG A1347 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8868 Ramachandran restraints generated. 4434 Oldfield, 0 Emsley, 4434 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 616 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 518 time to evaluate : 3.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 794 LEU cc_start: 0.6321 (OUTLIER) cc_final: 0.5766 (mm) REVERT: A 845 PHE cc_start: 0.7336 (t80) cc_final: 0.6300 (t80) REVERT: A 858 CYS cc_start: 0.8269 (m) cc_final: 0.8036 (m) REVERT: A 911 TRP cc_start: 0.7595 (t60) cc_final: 0.7313 (t60) REVERT: A 937 GLU cc_start: 0.8539 (tm-30) cc_final: 0.8223 (tm-30) REVERT: A 1045 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7974 (mm) REVERT: A 1093 ASN cc_start: 0.7829 (m110) cc_final: 0.7223 (m-40) REVERT: A 1118 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.7085 (tt0) REVERT: A 1323 TYR cc_start: 0.7767 (OUTLIER) cc_final: 0.7136 (t80) REVERT: A 1348 GLN cc_start: 0.7931 (mt0) cc_final: 0.7513 (mt0) REVERT: A 1355 LYS cc_start: 0.7706 (tppt) cc_final: 0.7366 (tppt) REVERT: A 1530 MET cc_start: 0.8439 (ttp) cc_final: 0.8164 (ttt) REVERT: A 1661 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8255 (pm20) REVERT: A 1699 HIS cc_start: 0.7806 (t70) cc_final: 0.7572 (t70) REVERT: A 1984 ASP cc_start: 0.7277 (m-30) cc_final: 0.6878 (m-30) REVERT: A 2021 LEU cc_start: 0.7271 (mt) cc_final: 0.6967 (mt) REVERT: A 2023 MET cc_start: 0.5926 (mtt) cc_final: 0.5573 (mtp) REVERT: A 2047 LEU cc_start: 0.7491 (OUTLIER) cc_final: 0.7229 (mt) REVERT: A 2062 PHE cc_start: 0.6636 (m-80) cc_final: 0.5846 (m-80) REVERT: A 2153 MET cc_start: 0.6510 (mmm) cc_final: 0.6037 (mtm) REVERT: A 2174 LYS cc_start: 0.6664 (tptt) cc_final: 0.6452 (tttm) REVERT: A 2231 LYS cc_start: 0.7572 (mtmm) cc_final: 0.7145 (mtpp) REVERT: A 2285 GLN cc_start: 0.6229 (mt0) cc_final: 0.5882 (mm110) REVERT: A 2323 PHE cc_start: 0.7144 (m-80) cc_final: 0.6878 (m-80) REVERT: A 2408 GLU cc_start: 0.6736 (mt-10) cc_final: 0.5951 (mm-30) REVERT: A 2485 PHE cc_start: 0.6852 (m-10) cc_final: 0.6647 (m-10) REVERT: A 2506 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6485 (tt) REVERT: C 794 LEU cc_start: 0.0035 (OUTLIER) cc_final: -0.0216 (mp) REVERT: C 803 ARG cc_start: 0.1892 (tpt90) cc_final: 0.1411 (tpp80) REVERT: C 924 ILE cc_start: 0.0233 (OUTLIER) cc_final: -0.0399 (mp) REVERT: C 928 LEU cc_start: 0.1765 (OUTLIER) cc_final: 0.1541 (mt) REVERT: C 1010 VAL cc_start: 0.2780 (OUTLIER) cc_final: 0.2461 (m) REVERT: C 1031 ARG cc_start: 0.3864 (mtt180) cc_final: 0.3584 (ptt180) REVERT: C 1129 HIS cc_start: 0.2283 (m90) cc_final: 0.1704 (t70) REVERT: C 1191 LEU cc_start: 0.4424 (tt) cc_final: 0.4017 (mt) REVERT: C 1323 TYR cc_start: 0.3911 (m-80) cc_final: 0.3574 (m-80) REVERT: C 1347 ARG cc_start: 0.6187 (mtt180) cc_final: 0.5698 (ttp80) REVERT: C 1668 GLN cc_start: 0.5034 (mp-120) cc_final: 0.4711 (pt0) REVERT: C 1700 MET cc_start: 0.5096 (ttp) cc_final: 0.4783 (mtp) REVERT: C 1754 TRP cc_start: 0.2135 (p90) cc_final: 0.1209 (m-10) REVERT: C 2120 PHE cc_start: 0.7697 (m-80) cc_final: 0.6910 (m-80) REVERT: C 2153 MET cc_start: 0.8127 (mmt) cc_final: 0.7369 (mtm) REVERT: C 2236 GLU cc_start: 0.5449 (mt-10) cc_final: 0.5214 (mt-10) REVERT: C 2239 PHE cc_start: 0.4617 (OUTLIER) cc_final: 0.3586 (m-80) REVERT: C 2241 MET cc_start: 0.7510 (tpp) cc_final: 0.6492 (tpp) REVERT: C 2266 TYR cc_start: 0.6275 (t80) cc_final: 0.5547 (t80) REVERT: C 2280 ASP cc_start: 0.5296 (OUTLIER) cc_final: 0.5060 (t0) REVERT: C 2295 ARG cc_start: 0.7310 (mmm160) cc_final: 0.6342 (mpp80) REVERT: C 2395 GLU cc_start: 0.7635 (mt-10) cc_final: 0.6657 (tp30) REVERT: C 2537 GLU cc_start: 0.8540 (OUTLIER) cc_final: 0.8066 (mm-30) REVERT: C 2541 LYS cc_start: 0.5200 (mttt) cc_final: 0.4784 (tmtt) REVERT: E 782 ARG cc_start: 0.1398 (mtt180) cc_final: 0.0763 (mtp-110) REVERT: E 928 LEU cc_start: -0.0396 (OUTLIER) cc_final: -0.0690 (mp) REVERT: E 997 MET cc_start: 0.1943 (mmt) cc_final: 0.1394 (ptm) REVERT: E 1006 MET cc_start: 0.0725 (tpp) cc_final: 0.0465 (tpp) REVERT: E 1349 MET cc_start: 0.7772 (mmm) cc_final: 0.7356 (mmm) REVERT: E 1502 MET cc_start: 0.0309 (tpt) cc_final: -0.0106 (ptt) REVERT: E 1960 ARG cc_start: 0.4099 (mtt180) cc_final: 0.3290 (ptp-170) REVERT: E 1980 MET cc_start: 0.5154 (mtp) cc_final: 0.4893 (mpp) REVERT: E 2031 MET cc_start: 0.6825 (mmm) cc_final: 0.6578 (mmm) REVERT: E 2034 ASP cc_start: 0.8182 (m-30) cc_final: 0.7562 (m-30) REVERT: E 2043 VAL cc_start: 0.7772 (t) cc_final: 0.7501 (p) REVERT: E 2046 LYS cc_start: 0.6930 (tptp) cc_final: 0.6064 (pttp) REVERT: E 2098 ARG cc_start: 0.3201 (ptt-90) cc_final: 0.2750 (mtm110) REVERT: E 2230 LEU cc_start: 0.8457 (mm) cc_final: 0.7884 (mm) REVERT: E 2231 LYS cc_start: 0.7226 (mttt) cc_final: 0.6934 (mtpt) REVERT: E 2258 GLU cc_start: 0.7376 (mt-10) cc_final: 0.6642 (tp30) REVERT: E 2270 MET cc_start: 0.5590 (OUTLIER) cc_final: 0.4674 (mtp) REVERT: E 2279 GLU cc_start: 0.7256 (mt-10) cc_final: 0.6834 (tp30) REVERT: E 2285 GLN cc_start: 0.7083 (mt0) cc_final: 0.6399 (mp10) REVERT: E 2321 TRP cc_start: 0.5930 (m-10) cc_final: 0.5253 (m-90) REVERT: E 2431 VAL cc_start: 0.7477 (OUTLIER) cc_final: 0.7135 (p) REVERT: E 2520 GLU cc_start: 0.8024 (mt-10) cc_final: 0.7500 (pt0) REVERT: E 2523 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7243 (mt-10) outliers start: 98 outliers final: 66 residues processed: 588 average time/residue: 0.4358 time to fit residues: 430.8716 Evaluate side-chains 573 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 490 time to evaluate : 3.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 801 VAL Chi-restraints excluded: chain A residue 809 VAL Chi-restraints excluded: chain A residue 897 ASN Chi-restraints excluded: chain A residue 921 LEU Chi-restraints excluded: chain A residue 931 LEU Chi-restraints excluded: chain A residue 1038 LEU Chi-restraints excluded: chain A residue 1045 LEU Chi-restraints excluded: chain A residue 1059 CYS Chi-restraints excluded: chain A residue 1092 THR Chi-restraints excluded: chain A residue 1105 SER Chi-restraints excluded: chain A residue 1118 GLU Chi-restraints excluded: chain A residue 1153 LEU Chi-restraints excluded: chain A residue 1235 VAL Chi-restraints excluded: chain A residue 1280 ILE Chi-restraints excluded: chain A residue 1284 SER Chi-restraints excluded: chain A residue 1323 TYR Chi-restraints excluded: chain A residue 1661 GLU Chi-restraints excluded: chain A residue 1702 THR Chi-restraints excluded: chain A residue 1786 ASP Chi-restraints excluded: chain A residue 1971 ARG Chi-restraints excluded: chain A residue 2047 LEU Chi-restraints excluded: chain A residue 2119 LEU Chi-restraints excluded: chain A residue 2121 LEU Chi-restraints excluded: chain A residue 2296 ILE Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2318 ARG Chi-restraints excluded: chain A residue 2321 TRP Chi-restraints excluded: chain A residue 2426 PHE Chi-restraints excluded: chain A residue 2431 VAL Chi-restraints excluded: chain A residue 2488 ILE Chi-restraints excluded: chain A residue 2499 CYS Chi-restraints excluded: chain A residue 2506 LEU Chi-restraints excluded: chain C residue 794 LEU Chi-restraints excluded: chain C residue 830 LEU Chi-restraints excluded: chain C residue 924 ILE Chi-restraints excluded: chain C residue 928 LEU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1273 LEU Chi-restraints excluded: chain C residue 1332 ASN Chi-restraints excluded: chain C residue 1342 LEU Chi-restraints excluded: chain C residue 1526 HIS Chi-restraints excluded: chain C residue 1783 ILE Chi-restraints excluded: chain C residue 1974 THR Chi-restraints excluded: chain C residue 1982 LEU Chi-restraints excluded: chain C residue 2016 VAL Chi-restraints excluded: chain C residue 2044 LEU Chi-restraints excluded: chain C residue 2047 LEU Chi-restraints excluded: chain C residue 2057 ILE Chi-restraints excluded: chain C residue 2200 ILE Chi-restraints excluded: chain C residue 2207 LEU Chi-restraints excluded: chain C residue 2228 VAL Chi-restraints excluded: chain C residue 2239 PHE Chi-restraints excluded: chain C residue 2252 THR Chi-restraints excluded: chain C residue 2256 TYR Chi-restraints excluded: chain C residue 2280 ASP Chi-restraints excluded: chain C residue 2349 THR Chi-restraints excluded: chain C residue 2380 ASN Chi-restraints excluded: chain C residue 2466 ILE Chi-restraints excluded: chain C residue 2474 VAL Chi-restraints excluded: chain C residue 2497 LEU Chi-restraints excluded: chain C residue 2530 ILE Chi-restraints excluded: chain C residue 2537 GLU Chi-restraints excluded: chain E residue 928 LEU Chi-restraints excluded: chain E residue 1080 LEU Chi-restraints excluded: chain E residue 1153 LEU Chi-restraints excluded: chain E residue 1245 VAL Chi-restraints excluded: chain E residue 1533 VAL Chi-restraints excluded: chain E residue 1759 VAL Chi-restraints excluded: chain E residue 1800 LEU Chi-restraints excluded: chain E residue 2144 ASP Chi-restraints excluded: chain E residue 2157 ASP Chi-restraints excluded: chain E residue 2248 ILE Chi-restraints excluded: chain E residue 2252 THR Chi-restraints excluded: chain E residue 2270 MET Chi-restraints excluded: chain E residue 2320 THR Chi-restraints excluded: chain E residue 2401 VAL Chi-restraints excluded: chain E residue 2431 VAL Chi-restraints excluded: chain E residue 2441 CYS Chi-restraints excluded: chain E residue 2488 ILE Chi-restraints excluded: chain E residue 2497 LEU Chi-restraints excluded: chain E residue 2506 LEU Chi-restraints excluded: chain E residue 2529 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 285 optimal weight: 0.8980 chunk 382 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 331 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 chunk 99 optimal weight: 0.9980 chunk 359 optimal weight: 0.2980 chunk 150 optimal weight: 7.9990 chunk 369 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 66 optimal weight: 4.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1206 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1324 ASN ** A2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1698 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1304 HIS E2244 GLN ** E2391 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.222128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.218252 restraints weight = 61492.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4523 r_free = 0.4523 target = 0.217900 restraints weight = 143782.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.217246 restraints weight = 142110.708| |-----------------------------------------------------------------------------| r_work (final): 0.4516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 36588 Z= 0.173 Angle : 0.675 14.769 49746 Z= 0.324 Chirality : 0.042 0.239 5667 Planarity : 0.004 0.047 6246 Dihedral : 4.747 26.764 4941 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.13 % Favored : 92.85 % Rotamer: Outliers : 2.59 % Allowed : 19.42 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.13), residues: 4434 helix: 1.21 (0.10), residues: 2748 sheet: -1.82 (0.35), residues: 207 loop : -2.70 (0.15), residues: 1479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP C2429 HIS 0.015 0.001 HIS E1304 PHE 0.040 0.001 PHE C2198 TYR 0.031 0.001 TYR A2089 ARG 0.006 0.000 ARG A 915 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8592.37 seconds wall clock time: 154 minutes 34.89 seconds (9274.89 seconds total)