Starting phenix.real_space_refine (version: dev) on Tue May 17 02:09:50 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3r_7042/05_2022/6b3r_7042.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3r_7042/05_2022/6b3r_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_7042/05_2022/6b3r_7042.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3r_7042/05_2022/6b3r_7042.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3r_7042/05_2022/6b3r_7042.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6b3r_7042/05_2022/6b3r_7042.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral 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: 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'PTRANS': 67, 'TRANS': 1433, 'PCIS': 1} 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: {'PTRANS': 67, 'TRANS': 1433, 'PCIS': 1} 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: {'PTRANS': 67, 'TRANS': 1433, 'PCIS': 1} 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: 19.12, per 1000 atoms: 0.54 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: 13.93 Conformation dependent library (CDL) restraints added in 5.1 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: 2.19 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: 15.12 Time building geometry restraints manager: 14.84 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 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. 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: 3.020 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: 17.090 Check model and map are aligned: 0.550 Convert atoms to be neutral: 0.330 Process input model: 88.220 Find NCS groups from input model: 2.640 Set up NCS constraints: 0.270 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 114.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5280 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 : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer Outliers : 0.25 % 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 *********************** 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 : 4.311 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 outliers start: 9 outliers final: 2 residues processed: 1057 average time/residue: 0.5051 time to fit residues: 840.8502 Evaluate side-chains 555 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 553 time to evaluate : 3.891 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3078 time to fit residues: 6.7641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 117 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 183 optimal weight: 5.9990 chunk 355 optimal weight: 7.9990 chunk 137 optimal weight: 7.9990 chunk 215 optimal weight: 3.9990 chunk 264 optimal weight: 0.9990 chunk 411 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 ** A1107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1120 GLN A1138 ASN A1145 HIS A1206 GLN A1510 GLN A1543 GLN A1952 GLN A2177 GLN A2221 ASN A2244 GLN A2262 GLN A2285 GLN A2322 ASN C 798 GLN C1013 HIS C1138 ASN ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1503 GLN C1543 GLN C1668 GLN C1698 ASN ** C1789 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2391 GLN C2435 GLN E 798 GLN E 808 HIS E1013 HIS E1047 GLN 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: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5415 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.099 36588 Z= 0.301 Angle : 0.784 16.142 49746 Z= 0.395 Chirality : 0.046 0.271 5667 Planarity : 0.007 0.113 6246 Dihedral : 5.936 26.099 4941 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.87 % Favored : 92.11 % Rotamer Outliers : 4.06 % 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: -2.22 (0.12), residues: 4434 helix: -0.39 (0.09), residues: 2688 sheet: -2.99 (0.31), residues: 180 loop : -3.17 (0.14), residues: 1566 *********************** 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 779 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 633 time to evaluate : 3.924 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 outliers start: 146 outliers final: 81 residues processed: 740 average time/residue: 0.4499 time to fit residues: 547.0098 Evaluate side-chains 575 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 494 time to evaluate : 3.930 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 0 residues processed: 81 average time/residue: 0.3361 time to fit residues: 55.3816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 228 optimal weight: 30.0000 chunk 127 optimal weight: 0.4980 chunk 342 optimal weight: 10.0000 chunk 280 optimal weight: 3.9990 chunk 113 optimal weight: 0.6980 chunk 412 optimal weight: 5.9990 chunk 445 optimal weight: 0.7980 chunk 367 optimal weight: 1.9990 chunk 408 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 330 optimal weight: 20.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 A1200 GLN A1206 GLN A1225 ASN A1315 GLN A1510 GLN A2244 GLN C 927 HIS ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1668 GLN C2181 GLN ** C2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1543 GLN E2018 GLN E2221 ASN E2245 GLN ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5409 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 36588 Z= 0.209 Angle : 0.723 16.260 49746 Z= 0.356 Chirality : 0.043 0.232 5667 Planarity : 0.005 0.103 6246 Dihedral : 5.440 32.452 4941 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.83 % Favored : 93.14 % Rotamer Outliers : 2.92 % 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: -1.26 (0.12), residues: 4434 helix: 0.45 (0.10), residues: 2703 sheet: -2.59 (0.32), residues: 180 loop : -2.98 (0.15), residues: 1551 *********************** 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 694 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 589 time to evaluate : 4.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 105 outliers final: 30 residues processed: 665 average time/residue: 0.4440 time to fit residues: 490.2926 Evaluate side-chains 524 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 494 time to evaluate : 4.249 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.3759 time to fit residues: 27.0005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 407 optimal weight: 0.9990 chunk 309 optimal weight: 7.9990 chunk 213 optimal weight: 9.9990 chunk 45 optimal weight: 0.6980 chunk 196 optimal weight: 6.9990 chunk 276 optimal weight: 10.0000 chunk 413 optimal weight: 4.9990 chunk 437 optimal weight: 0.6980 chunk 216 optimal weight: 5.9990 chunk 391 optimal weight: 8.9990 chunk 118 optimal weight: 6.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1007 ASN ** A1047 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 GLN A1237 GLN A1324 ASN A1510 GLN A1952 GLN A2244 GLN A2285 GLN A2322 ASN C 808 HIS ** C 927 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1004 GLN ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1324 ASN C1356 GLN C1668 GLN ** C2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1668 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2027 GLN ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5472 moved from start: 0.4573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.139 36588 Z= 0.339 Angle : 0.809 18.104 49746 Z= 0.398 Chirality : 0.046 0.292 5667 Planarity : 0.006 0.098 6246 Dihedral : 5.472 24.555 4941 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.19 % Favored : 91.79 % Rotamer Outliers : 2.98 % 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: -1.12 (0.12), residues: 4434 helix: 0.59 (0.10), residues: 2697 sheet: -2.59 (0.32), residues: 180 loop : -2.98 (0.15), residues: 1557 *********************** 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 627 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 520 time to evaluate : 3.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 50 residues processed: 591 average time/residue: 0.4378 time to fit residues: 430.9575 Evaluate side-chains 523 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 473 time to evaluate : 3.916 Switching outliers to nearest non-outliers outliers start: 50 outliers final: 0 residues processed: 50 average time/residue: 0.3282 time to fit residues: 36.1150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 6 optimal weight: 7.9990 chunk 326 optimal weight: 0.0570 chunk 180 optimal weight: 8.9990 chunk 373 optimal weight: 1.9990 chunk 302 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 223 optimal weight: 0.0270 chunk 393 optimal weight: 0.8980 chunk 110 optimal weight: 0.3980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 A1344 GLN A1510 GLN A1527 HIS A1952 GLN A2177 GLN A2181 GLN A2285 GLN ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1304 HIS C1324 ASN C1493 HIS C1668 GLN ** C2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1004 GLN E1200 GLN E1668 GLN E2018 GLN ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5429 moved from start: 0.4783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.131 36588 Z= 0.205 Angle : 0.726 17.574 49746 Z= 0.356 Chirality : 0.043 0.267 5667 Planarity : 0.005 0.126 6246 Dihedral : 5.092 24.377 4941 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.65 % Favored : 93.32 % Rotamer Outliers : 1.95 % 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: -0.60 (0.13), residues: 4434 helix: 1.03 (0.10), residues: 2700 sheet: -2.18 (0.34), residues: 180 loop : -2.84 (0.15), residues: 1554 *********************** 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 618 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 548 time to evaluate : 4.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 31 residues processed: 589 average time/residue: 0.4293 time to fit residues: 427.4771 Evaluate side-chains 510 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 479 time to evaluate : 3.931 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.3470 time to fit residues: 25.4341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 147 optimal weight: 1.9990 chunk 394 optimal weight: 0.9980 chunk 86 optimal weight: 0.0470 chunk 257 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 438 optimal weight: 0.8980 chunk 363 optimal weight: 0.4980 chunk 202 optimal weight: 5.9990 chunk 36 optimal weight: 0.8980 chunk 144 optimal weight: 0.0870 chunk 230 optimal weight: 40.0000 overall best weight: 0.4856 ------------------------------------------------------------------------------- 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 A1225 ASN A1324 ASN ** A2285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1668 GLN ** C2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1206 GLN ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5422 moved from start: 0.4993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.195 36588 Z= 0.222 Angle : 0.733 20.968 49746 Z= 0.363 Chirality : 0.042 0.211 5667 Planarity : 0.005 0.105 6246 Dihedral : 4.886 24.723 4941 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.68 % Favored : 93.30 % Rotamer Outliers : 1.34 % 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: -0.37 (0.13), residues: 4434 helix: 1.20 (0.10), residues: 2715 sheet: -2.27 (0.33), residues: 198 loop : -2.73 (0.15), residues: 1521 *********************** 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 588 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 540 time to evaluate : 5.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 19 residues processed: 565 average time/residue: 0.4371 time to fit residues: 418.3668 Evaluate side-chains 499 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 480 time to evaluate : 4.320 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.3291 time to fit residues: 17.7757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 422 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 249 optimal weight: 0.9990 chunk 320 optimal weight: 20.0000 chunk 247 optimal weight: 3.9990 chunk 368 optimal weight: 5.9990 chunk 244 optimal weight: 0.9980 chunk 436 optimal weight: 0.7980 chunk 273 optimal weight: 8.9990 chunk 266 optimal weight: 0.7980 chunk 201 optimal weight: 6.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 829 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 GLN A1324 ASN A1952 GLN ** A2285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1007 ASN ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1668 GLN ** C2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1304 HIS ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2391 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5425 moved from start: 0.5078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.080 36588 Z= 0.742 Angle : 1.039 106.099 49746 Z= 0.466 Chirality : 0.044 0.431 5667 Planarity : 0.006 0.152 6246 Dihedral : 4.873 26.104 4941 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.92 % Favored : 93.03 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.07 % 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: -0.32 (0.13), residues: 4434 helix: 1.24 (0.10), residues: 2715 sheet: -2.20 (0.33), residues: 198 loop : -2.71 (0.15), residues: 1521 *********************** 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 519 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 493 time to evaluate : 3.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 14 residues processed: 505 average time/residue: 0.4410 time to fit residues: 378.9922 Evaluate side-chains 486 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 472 time to evaluate : 3.954 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.3632 time to fit residues: 14.7770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 270 optimal weight: 7.9990 chunk 174 optimal weight: 10.0000 chunk 260 optimal weight: 0.8980 chunk 131 optimal weight: 0.0770 chunk 85 optimal weight: 0.0020 chunk 84 optimal weight: 0.8980 chunk 277 optimal weight: 4.9990 chunk 297 optimal weight: 3.9990 chunk 215 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 343 optimal weight: 0.0470 overall best weight: 0.3844 ------------------------------------------------------------------------------- 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 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 GLN A1324 ASN ** A2285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1668 GLN ** C2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1304 HIS ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2391 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5425 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 1.066 36588 Z= 0.886 Angle : 1.190 106.099 49746 Z= 0.531 Chirality : 0.044 0.558 5667 Planarity : 0.005 0.115 6246 Dihedral : 4.896 32.899 4941 Min Nonbonded Distance : 1.639 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.92 % Favored : 93.01 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -0.32 (0.13), residues: 4434 helix: 1.24 (0.10), residues: 2715 sheet: -2.19 (0.33), residues: 198 loop : -2.73 (0.15), residues: 1521 *********************** 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 489 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 476 time to evaluate : 4.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 484 average time/residue: 0.4328 time to fit residues: 356.8795 Evaluate side-chains 478 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 471 time to evaluate : 3.906 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3108 time to fit residues: 9.8088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 397 optimal weight: 5.9990 chunk 418 optimal weight: 2.9990 chunk 381 optimal weight: 3.9990 chunk 406 optimal weight: 0.9990 chunk 244 optimal weight: 2.9990 chunk 177 optimal weight: 0.0040 chunk 319 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 367 optimal weight: 0.9980 chunk 384 optimal weight: 7.9990 chunk 405 optimal weight: 0.9990 overall best weight: 0.7796 ------------------------------------------------------------------------------- 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 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 GLN A1324 ASN A1952 GLN ** A2285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1668 GLN ** C2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1304 HIS E1336 GLN ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2391 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5425 moved from start: 0.5100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 1.056 36588 Z= 0.886 Angle : 1.252 98.080 49746 Z= 0.560 Chirality : 0.045 0.402 5667 Planarity : 0.005 0.109 6246 Dihedral : 4.907 31.829 4941 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.88 % Favored : 93.08 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -0.32 (0.13), residues: 4434 helix: 1.24 (0.10), residues: 2715 sheet: -2.18 (0.33), residues: 198 loop : -2.74 (0.15), residues: 1521 *********************** 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 489 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 476 time to evaluate : 4.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 7 residues processed: 482 average time/residue: 0.4460 time to fit residues: 365.1167 Evaluate side-chains 481 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 474 time to evaluate : 4.023 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3132 time to fit residues: 9.3998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 267 optimal weight: 0.8980 chunk 430 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 chunk 204 optimal weight: 9.9990 chunk 299 optimal weight: 0.8980 chunk 451 optimal weight: 1.9990 chunk 415 optimal weight: 4.9990 chunk 359 optimal weight: 0.0770 chunk 37 optimal weight: 1.9990 chunk 277 optimal weight: 2.9990 chunk 220 optimal weight: 1.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- 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 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 GLN A1324 ASN ** A2285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1668 GLN ** C2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1304 HIS E1336 GLN ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2391 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5425 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 1.056 36588 Z= 0.901 Angle : 1.263 98.080 49746 Z= 0.573 Chirality : 0.045 0.402 5667 Planarity : 0.006 0.131 6246 Dihedral : 4.907 31.829 4941 Min Nonbonded Distance : 1.532 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.88 % Favored : 93.08 % Rotamer Outliers : 0.03 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -0.32 (0.13), residues: 4434 helix: 1.24 (0.10), residues: 2715 sheet: -2.18 (0.33), residues: 198 loop : -2.74 (0.15), residues: 1521 ********************** 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 478 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 477 time to evaluate : 3.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 477 average time/residue: 0.4421 time to fit residues: 358.9863 Evaluate side-chains 471 residues out of total 4041 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 471 time to evaluate : 4.419 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 453 random chunks: chunk 285 optimal weight: 5.9990 chunk 382 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 331 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 359 optimal weight: 1.9990 chunk 150 optimal weight: 8.9990 chunk 369 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 897 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1206 GLN A1324 ASN A1952 GLN ** A2285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1668 GLN ** C2356 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C2364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1304 HIS E1336 GLN ** E2353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2391 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.225372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.221426 restraints weight = 62038.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.221062 restraints weight = 133310.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.220541 restraints weight = 133514.619| |-----------------------------------------------------------------------------| r_work (final): 0.4551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5470 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 1.056 36588 Z= 0.890 Angle : 1.286 98.080 49746 Z= 0.595 Chirality : 0.045 0.402 5667 Planarity : 0.006 0.246 6246 Dihedral : 4.907 31.829 4941 Min Nonbonded Distance : 1.532 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.88 % Favored : 93.08 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.00 % Twisted Proline : 0.49 % 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: -0.32 (0.13), residues: 4434 helix: 1.24 (0.10), residues: 2715 sheet: -2.18 (0.33), residues: 198 loop : -2.74 (0.15), residues: 1521 =============================================================================== Job complete usr+sys time: 7846.34 seconds wall clock time: 142 minutes 38.44 seconds (8558.44 seconds total)