Starting phenix.real_space_refine on Sat Mar 7 14:48:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s63_24848/03_2026/7s63_24848.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s63_24848/03_2026/7s63_24848.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7s63_24848/03_2026/7s63_24848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s63_24848/03_2026/7s63_24848.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7s63_24848/03_2026/7s63_24848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s63_24848/03_2026/7s63_24848.map" } resolution = 4.12 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 220 5.16 5 C 28704 2.51 5 N 7292 2.21 5 O 8992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 112 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 45208 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 11064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1420, 11064 Classifications: {'peptide': 1420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 62, 'TRANS': 1357} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 11064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1420, 11064 Classifications: {'peptide': 1420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 62, 'TRANS': 1357} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 11064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1420, 11064 Classifications: {'peptide': 1420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 62, 'TRANS': 1357} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 11064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1420, 11064 Classifications: {'peptide': 1420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 62, 'TRANS': 1357} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "B" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "C" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Chain: "D" Number of atoms: 238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 238 Unusual residues: {'NAG': 17} Classifications: {'undetermined': 17} Link IDs: {None: 16} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 17 Time building chain proxies: 9.84, per 1000 atoms: 0.22 Number of scatterers: 45208 At special positions: 0 Unit cell: (219.03, 230.79, 142.59, 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 220 16.00 O 8992 8.00 N 7292 7.00 C 28704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS A 42 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 205 " distance=2.03 Simple disulfide: pdb=" SG CYS A 262 " - pdb=" SG CYS A 283 " distance=2.04 Simple disulfide: pdb=" SG CYS A 467 " - pdb=" SG CYS A 559 " distance=2.03 Simple disulfide: pdb=" SG CYS A 591 " - pdb=" SG CYS A 758 " distance=2.03 Simple disulfide: pdb=" SG CYS A 640 " - pdb=" SG CYS A 688 " distance=2.03 Simple disulfide: pdb=" SG CYS A 809 " - pdb=" SG CYS A 836 " distance=2.03 Simple disulfide: pdb=" SG CYS A1327 " - pdb=" SG CYS A1441 " distance=2.03 Simple disulfide: pdb=" SG CYS B 42 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 205 " distance=2.03 Simple disulfide: pdb=" SG CYS B 262 " - pdb=" SG CYS B 283 " distance=2.04 Simple disulfide: pdb=" SG CYS B 467 " - pdb=" SG CYS B 559 " distance=2.03 Simple disulfide: pdb=" SG CYS B 591 " - pdb=" SG CYS B 758 " distance=2.03 Simple disulfide: pdb=" SG CYS B 640 " - pdb=" SG CYS B 688 " distance=2.03 Simple disulfide: pdb=" SG CYS B 809 " - pdb=" SG CYS B 836 " distance=2.03 Simple disulfide: pdb=" SG CYS B1327 " - pdb=" SG CYS B1441 " distance=2.03 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 80 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 205 " distance=2.03 Simple disulfide: pdb=" SG CYS C 262 " - pdb=" SG CYS C 283 " distance=2.04 Simple disulfide: pdb=" SG CYS C 467 " - pdb=" SG CYS C 559 " distance=2.03 Simple disulfide: pdb=" SG CYS C 591 " - pdb=" SG CYS C 758 " distance=2.03 Simple disulfide: pdb=" SG CYS C 640 " - pdb=" SG CYS C 688 " distance=2.03 Simple disulfide: pdb=" SG CYS C 809 " - pdb=" SG CYS C 836 " distance=2.03 Simple disulfide: pdb=" SG CYS C1327 " - pdb=" SG CYS C1441 " distance=2.03 Simple disulfide: pdb=" SG CYS D 42 " - pdb=" SG CYS D 80 " distance=2.03 Simple disulfide: pdb=" SG CYS D 122 " - pdb=" SG CYS D 205 " distance=2.03 Simple disulfide: pdb=" SG CYS D 262 " - pdb=" SG CYS D 283 " distance=2.04 Simple disulfide: pdb=" SG CYS D 467 " - pdb=" SG CYS D 559 " distance=2.03 Simple disulfide: pdb=" SG CYS D 591 " - pdb=" SG CYS D 758 " distance=2.03 Simple disulfide: pdb=" SG CYS D 640 " - pdb=" SG CYS D 688 " distance=2.03 Simple disulfide: pdb=" SG CYS D 809 " - pdb=" SG CYS D 836 " distance=2.03 Simple disulfide: pdb=" SG CYS D1327 " - pdb=" SG CYS D1441 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied NAG-ASN " NAG A2101 " - " ASN A 64 " " NAG A2102 " - " ASN A 81 " " NAG A2103 " - " ASN A 242 " " NAG A2104 " - " ASN A 285 " " NAG A2105 " - " ASN A 415 " " NAG A2106 " - " ASN A 472 " " NAG A2107 " - " ASN A 526 " " NAG A2108 " - " ASN A 578 " " NAG A2109 " - " ASN A 721 " " NAG A2110 " - " ASN A 773 " " NAG A2111 " - " ASN A 918 " " NAG A2112 " - " ASN A 977 " " NAG A2113 " - " ASN A1096 " " NAG A2114 " - " ASN A1266 " " NAG A2115 " - " ASN A1286 " " NAG A2116 " - " ASN A1292 " " NAG A2117 " - " ASN A1348 " " NAG B2101 " - " ASN B 64 " " NAG B2102 " - " ASN B 81 " " NAG B2103 " - " ASN B 242 " " NAG B2104 " - " ASN B 285 " " NAG B2105 " - " ASN B 415 " " NAG B2106 " - " ASN B 472 " " NAG B2107 " - " ASN B 526 " " NAG B2108 " - " ASN B 578 " " NAG B2109 " - " ASN B 721 " " NAG B2110 " - " ASN B 773 " " NAG B2111 " - " ASN B 918 " " NAG B2112 " - " ASN B 977 " " NAG B2113 " - " ASN B1096 " " NAG B2114 " - " ASN B1266 " " NAG B2115 " - " ASN B1286 " " NAG B2116 " - " ASN B1292 " " NAG B2117 " - " ASN B1348 " " NAG C2101 " - " ASN C 64 " " NAG C2102 " - " ASN C 81 " " NAG C2103 " - " ASN C 242 " " NAG C2104 " - " ASN C 285 " " NAG C2105 " - " ASN C 415 " " NAG C2106 " - " ASN C 472 " " NAG C2107 " - " ASN C 526 " " NAG C2108 " - " ASN C 578 " " NAG C2109 " - " ASN C 721 " " NAG C2110 " - " ASN C 773 " " NAG C2111 " - " ASN C 918 " " NAG C2112 " - " ASN C 977 " " NAG C2113 " - " ASN C1096 " " NAG C2114 " - " ASN C1266 " " NAG C2115 " - " ASN C1286 " " NAG C2116 " - " ASN C1292 " " NAG C2117 " - " ASN C1348 " " NAG D2101 " - " ASN D 64 " " NAG D2102 " - " ASN D 81 " " NAG D2103 " - " ASN D 242 " " NAG D2104 " - " ASN D 285 " " NAG D2105 " - " ASN D 415 " " NAG D2106 " - " ASN D 472 " " NAG D2107 " - " ASN D 526 " " NAG D2108 " - " ASN D 578 " " NAG D2109 " - " ASN D 721 " " NAG D2110 " - " ASN D 773 " " NAG D2111 " - " ASN D 918 " " NAG D2112 " - " ASN D 977 " " NAG D2113 " - " ASN D1096 " " NAG D2114 " - " ASN D1266 " " NAG D2115 " - " ASN D1286 " " NAG D2116 " - " ASN D1292 " " NAG D2117 " - " ASN D1348 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.85 Conformation dependent library (CDL) restraints added in 1.9 seconds 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10576 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 108 sheets defined 15.6% alpha, 29.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.21 Creating SS restraints... Processing helix chain 'A' and resid 597 through 601 removed outlier: 3.714A pdb=" N LEU A 600 " --> pdb=" O ASP A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 617 Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 942 through 946 removed outlier: 3.577A pdb=" N LEU A 945 " --> pdb=" O GLY A 942 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N SER A 946 " --> pdb=" O LEU A 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 942 through 946' Processing helix chain 'A' and resid 947 through 951 removed outlier: 4.008A pdb=" N LEU A 951 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 958 through 963 Processing helix chain 'A' and resid 967 through 979 removed outlier: 4.520A pdb=" N TYR A 971 " --> pdb=" O ALA A 967 " (cutoff:3.500A) Processing helix chain 'A' and resid 983 through 1002 Processing helix chain 'A' and resid 1003 through 1005 No H-bonds generated for 'chain 'A' and resid 1003 through 1005' Processing helix chain 'A' and resid 1022 through 1037 Processing helix chain 'A' and resid 1043 through 1057 removed outlier: 3.554A pdb=" N GLN A1047 " --> pdb=" O ASP A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1076 through 1078 No H-bonds generated for 'chain 'A' and resid 1076 through 1078' Processing helix chain 'A' and resid 1079 through 1095 Processing helix chain 'A' and resid 1101 through 1113 removed outlier: 3.546A pdb=" N ALA A1113 " --> pdb=" O GLY A1109 " (cutoff:3.500A) Processing helix chain 'A' and resid 1120 through 1134 Processing helix chain 'A' and resid 1138 through 1150 removed outlier: 3.600A pdb=" N SER A1149 " --> pdb=" O ASN A1145 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LYS A1150 " --> pdb=" O GLU A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1179 through 1195 removed outlier: 4.326A pdb=" N VAL A1183 " --> pdb=" O SER A1179 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU A1184 " --> pdb=" O PRO A1180 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE A1185 " --> pdb=" O ALA A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1217 removed outlier: 3.999A pdb=" N THR A1205 " --> pdb=" O HIS A1201 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N TYR A1206 " --> pdb=" O ASP A1202 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N TRP A1213 " --> pdb=" O GLN A1209 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A1214 " --> pdb=" O ILE A1210 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A1217 " --> pdb=" O TRP A1213 " (cutoff:3.500A) Processing helix chain 'A' and resid 1226 through 1243 removed outlier: 3.890A pdb=" N VAL A1232 " --> pdb=" O GLN A1228 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LEU A1243 " --> pdb=" O PHE A1239 " (cutoff:3.500A) Processing helix chain 'A' and resid 1366 through 1376 Processing helix chain 'B' and resid 597 through 601 removed outlier: 3.791A pdb=" N LEU B 600 " --> pdb=" O ASP B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 617 Processing helix chain 'B' and resid 664 through 669 Processing helix chain 'B' and resid 942 through 946 removed outlier: 3.615A pdb=" N LEU B 945 " --> pdb=" O GLY B 942 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N SER B 946 " --> pdb=" O LEU B 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 942 through 946' Processing helix chain 'B' and resid 958 through 963 Processing helix chain 'B' and resid 967 through 979 removed outlier: 4.415A pdb=" N TYR B 971 " --> pdb=" O ALA B 967 " (cutoff:3.500A) Processing helix chain 'B' and resid 983 through 1003 removed outlier: 3.853A pdb=" N ARG B1003 " --> pdb=" O TYR B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1022 through 1037 Processing helix chain 'B' and resid 1043 through 1057 removed outlier: 3.648A pdb=" N GLN B1047 " --> pdb=" O ASP B1043 " (cutoff:3.500A) Processing helix chain 'B' and resid 1076 through 1078 No H-bonds generated for 'chain 'B' and resid 1076 through 1078' Processing helix chain 'B' and resid 1079 through 1095 Processing helix chain 'B' and resid 1101 through 1113 removed outlier: 3.634A pdb=" N ALA B1113 " --> pdb=" O GLY B1109 " (cutoff:3.500A) Processing helix chain 'B' and resid 1120 through 1134 removed outlier: 3.779A pdb=" N TYR B1126 " --> pdb=" O TYR B1122 " (cutoff:3.500A) Processing helix chain 'B' and resid 1138 through 1150 removed outlier: 3.624A pdb=" N SER B1149 " --> pdb=" O ASN B1145 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS B1150 " --> pdb=" O GLU B1146 " (cutoff:3.500A) Processing helix chain 'B' and resid 1179 through 1195 removed outlier: 4.366A pdb=" N VAL B1183 " --> pdb=" O SER B1179 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU B1184 " --> pdb=" O PRO B1180 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE B1185 " --> pdb=" O ALA B1181 " (cutoff:3.500A) Processing helix chain 'B' and resid 1201 through 1217 removed outlier: 3.862A pdb=" N THR B1205 " --> pdb=" O HIS B1201 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR B1206 " --> pdb=" O ASP B1202 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP B1213 " --> pdb=" O GLN B1209 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B1214 " --> pdb=" O ILE B1210 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN B1217 " --> pdb=" O TRP B1213 " (cutoff:3.500A) Processing helix chain 'B' and resid 1226 through 1243 removed outlier: 3.915A pdb=" N VAL B1232 " --> pdb=" O GLN B1228 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LEU B1243 " --> pdb=" O PHE B1239 " (cutoff:3.500A) Processing helix chain 'B' and resid 1366 through 1376 Processing helix chain 'C' and resid 597 through 601 removed outlier: 3.779A pdb=" N LEU C 600 " --> pdb=" O ASP C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 612 through 617 Processing helix chain 'C' and resid 664 through 669 Processing helix chain 'C' and resid 939 through 946 removed outlier: 4.438A pdb=" N LEU C 943 " --> pdb=" O VAL C 940 " (cutoff:3.500A) Proline residue: C 944 - end of helix Processing helix chain 'C' and resid 947 through 951 removed outlier: 4.183A pdb=" N LEU C 951 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 958 through 963 Processing helix chain 'C' and resid 967 through 979 removed outlier: 4.542A pdb=" N TYR C 971 " --> pdb=" O ALA C 967 " (cutoff:3.500A) Processing helix chain 'C' and resid 983 through 1002 Processing helix chain 'C' and resid 1003 through 1005 No H-bonds generated for 'chain 'C' and resid 1003 through 1005' Processing helix chain 'C' and resid 1022 through 1037 Processing helix chain 'C' and resid 1043 through 1057 Processing helix chain 'C' and resid 1076 through 1078 No H-bonds generated for 'chain 'C' and resid 1076 through 1078' Processing helix chain 'C' and resid 1079 through 1095 Processing helix chain 'C' and resid 1101 through 1113 removed outlier: 3.748A pdb=" N ALA C1113 " --> pdb=" O GLY C1109 " (cutoff:3.500A) Processing helix chain 'C' and resid 1120 through 1134 removed outlier: 3.524A pdb=" N TYR C1126 " --> pdb=" O TYR C1122 " (cutoff:3.500A) Processing helix chain 'C' and resid 1138 through 1150 removed outlier: 3.559A pdb=" N SER C1149 " --> pdb=" O ASN C1145 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS C1150 " --> pdb=" O GLU C1146 " (cutoff:3.500A) Processing helix chain 'C' and resid 1179 through 1195 removed outlier: 4.360A pdb=" N VAL C1183 " --> pdb=" O SER C1179 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLU C1184 " --> pdb=" O PRO C1180 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE C1185 " --> pdb=" O ALA C1181 " (cutoff:3.500A) Processing helix chain 'C' and resid 1200 through 1217 removed outlier: 4.038A pdb=" N THR C1205 " --> pdb=" O HIS C1201 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N TYR C1206 " --> pdb=" O ASP C1202 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TRP C1213 " --> pdb=" O GLN C1209 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU C1214 " --> pdb=" O ILE C1210 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLN C1217 " --> pdb=" O TRP C1213 " (cutoff:3.500A) Processing helix chain 'C' and resid 1226 through 1243 removed outlier: 4.036A pdb=" N VAL C1232 " --> pdb=" O GLN C1228 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU C1243 " --> pdb=" O PHE C1239 " (cutoff:3.500A) Processing helix chain 'C' and resid 1366 through 1376 Processing helix chain 'D' and resid 597 through 601 removed outlier: 3.803A pdb=" N LEU D 600 " --> pdb=" O ASP D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 612 through 617 Processing helix chain 'D' and resid 664 through 669 Processing helix chain 'D' and resid 942 through 946 removed outlier: 3.613A pdb=" N LEU D 945 " --> pdb=" O GLY D 942 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER D 946 " --> pdb=" O LEU D 943 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 942 through 946' Processing helix chain 'D' and resid 958 through 963 Processing helix chain 'D' and resid 967 through 979 removed outlier: 4.457A pdb=" N TYR D 971 " --> pdb=" O ALA D 967 " (cutoff:3.500A) Processing helix chain 'D' and resid 983 through 1003 removed outlier: 3.870A pdb=" N ARG D1003 " --> pdb=" O TYR D 999 " (cutoff:3.500A) Processing helix chain 'D' and resid 1022 through 1037 Processing helix chain 'D' and resid 1043 through 1057 removed outlier: 3.656A pdb=" N GLN D1047 " --> pdb=" O ASP D1043 " (cutoff:3.500A) Processing helix chain 'D' and resid 1076 through 1078 No H-bonds generated for 'chain 'D' and resid 1076 through 1078' Processing helix chain 'D' and resid 1079 through 1095 Processing helix chain 'D' and resid 1101 through 1113 removed outlier: 3.605A pdb=" N ALA D1113 " --> pdb=" O GLY D1109 " (cutoff:3.500A) Processing helix chain 'D' and resid 1120 through 1134 removed outlier: 3.555A pdb=" N TYR D1126 " --> pdb=" O TYR D1122 " (cutoff:3.500A) Processing helix chain 'D' and resid 1138 through 1148 Processing helix chain 'D' and resid 1179 through 1195 removed outlier: 4.375A pdb=" N VAL D1183 " --> pdb=" O SER D1179 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N GLU D1184 " --> pdb=" O PRO D1180 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE D1185 " --> pdb=" O ALA D1181 " (cutoff:3.500A) Processing helix chain 'D' and resid 1200 through 1217 removed outlier: 3.886A pdb=" N THR D1205 " --> pdb=" O HIS D1201 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR D1206 " --> pdb=" O ASP D1202 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TRP D1213 " --> pdb=" O GLN D1209 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU D1214 " --> pdb=" O ILE D1210 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN D1217 " --> pdb=" O TRP D1213 " (cutoff:3.500A) Processing helix chain 'D' and resid 1226 through 1243 removed outlier: 3.887A pdb=" N VAL D1232 " --> pdb=" O GLN D1228 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N LEU D1243 " --> pdb=" O PHE D1239 " (cutoff:3.500A) Processing helix chain 'D' and resid 1366 through 1376 Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 84 removed outlier: 8.896A pdb=" N ARG A 40 " --> pdb=" O PRO A 30 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ILE A 29 " --> pdb=" O VAL A 675 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 34 removed outlier: 6.607A pdb=" N LEU A 33 " --> pdb=" O ALA A 116 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE A 95 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 52 through 53 Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 124 Processing sheet with id=AA5, first strand: chain 'A' and resid 136 through 138 Processing sheet with id=AA6, first strand: chain 'A' and resid 154 through 155 Processing sheet with id=AA7, first strand: chain 'A' and resid 170 through 171 removed outlier: 4.107A pdb=" N VAL A 158 " --> pdb=" O TRP A 171 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 223 through 225 Processing sheet with id=AA9, first strand: chain 'A' and resid 284 through 289 removed outlier: 3.579A pdb=" N THR A 284 " --> pdb=" O CYS A 261 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N CYS A 261 " --> pdb=" O THR A 284 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N SER A 256 " --> pdb=" O THR A 323 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 344 through 348 removed outlier: 3.586A pdb=" N ASN A 375 " --> pdb=" O ASP A 371 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 344 through 348 Processing sheet with id=AB3, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AB4, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AB5, first strand: chain 'A' and resid 454 through 458 Processing sheet with id=AB6, first strand: chain 'A' and resid 470 through 471 Processing sheet with id=AB7, first strand: chain 'A' and resid 503 through 512 removed outlier: 4.880A pdb=" N GLN A 505 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA A 497 " --> pdb=" O GLN A 505 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR A 492 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N ILE A 542 " --> pdb=" O THR A 492 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 567 through 568 Processing sheet with id=AB9, first strand: chain 'A' and resid 590 through 596 Processing sheet with id=AC1, first strand: chain 'A' and resid 647 through 648 Processing sheet with id=AC2, first strand: chain 'A' and resid 780 through 785 removed outlier: 3.745A pdb=" N SER A 785 " --> pdb=" O LYS A 799 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS A 799 " --> pdb=" O SER A 785 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN A 846 " --> pdb=" O ILE A 825 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 780 through 785 removed outlier: 3.745A pdb=" N SER A 785 " --> pdb=" O LYS A 799 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS A 799 " --> pdb=" O SER A 785 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY A 839 " --> pdb=" O ASN A 804 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 789 through 791 removed outlier: 6.358A pdb=" N LEU A 790 " --> pdb=" O GLN A 892 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'A' and resid 810 through 811 Processing sheet with id=AC6, first strand: chain 'A' and resid 896 through 909 removed outlier: 3.547A pdb=" N VAL A 908 " --> pdb=" O GLY A1295 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A1295 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY A1263 " --> pdb=" O LEU A1255 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'A' and resid 896 through 909 removed outlier: 3.547A pdb=" N VAL A 908 " --> pdb=" O GLY A1295 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A1295 " --> pdb=" O VAL A 908 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N LEU A1298 " --> pdb=" O VAL A 937 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL A 937 " --> pdb=" O LEU A1298 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'A' and resid 1152 through 1153 Processing sheet with id=AC9, first strand: chain 'A' and resid 1318 through 1324 removed outlier: 3.675A pdb=" N GLN A1364 " --> pdb=" O LEU A1408 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'A' and resid 1381 through 1385 removed outlier: 3.721A pdb=" N LYS A1381 " --> pdb=" O TYR A1392 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER A1420 " --> pdb=" O GLN A1358 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 77 through 84 removed outlier: 8.923A pdb=" N ARG B 40 " --> pdb=" O PRO B 30 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE B 29 " --> pdb=" O VAL B 675 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 32 through 34 removed outlier: 6.658A pdb=" N LEU B 33 " --> pdb=" O ALA B 116 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N PHE B 95 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 52 through 53 Processing sheet with id=AD5, first strand: chain 'B' and resid 121 through 124 Processing sheet with id=AD6, first strand: chain 'B' and resid 136 through 138 Processing sheet with id=AD7, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AD8, first strand: chain 'B' and resid 170 through 171 removed outlier: 3.976A pdb=" N VAL B 158 " --> pdb=" O TRP B 171 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 223 through 225 Processing sheet with id=AE1, first strand: chain 'B' and resid 284 through 290 removed outlier: 3.553A pdb=" N THR B 284 " --> pdb=" O CYS B 261 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N CYS B 261 " --> pdb=" O THR B 284 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 290 " --> pdb=" O GLY B 255 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY B 255 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B 256 " --> pdb=" O THR B 323 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 344 through 348 Processing sheet with id=AE3, first strand: chain 'B' and resid 344 through 348 Processing sheet with id=AE4, first strand: chain 'B' and resid 356 through 357 Processing sheet with id=AE5, first strand: chain 'B' and resid 394 through 395 Processing sheet with id=AE6, first strand: chain 'B' and resid 454 through 459 removed outlier: 4.456A pdb=" N SER B 474 " --> pdb=" O GLN B 459 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 470 through 471 Processing sheet with id=AE8, first strand: chain 'B' and resid 507 through 512 removed outlier: 6.877A pdb=" N THR B 492 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ILE B 542 " --> pdb=" O THR B 492 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 567 through 568 Processing sheet with id=AF1, first strand: chain 'B' and resid 572 through 573 removed outlier: 3.524A pdb=" N GLY B 573 " --> pdb=" O THR B 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'B' and resid 590 through 596 Processing sheet with id=AF3, first strand: chain 'B' and resid 780 through 785 removed outlier: 3.754A pdb=" N SER B 785 " --> pdb=" O LYS B 799 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS B 799 " --> pdb=" O SER B 785 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASN B 846 " --> pdb=" O ILE B 825 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'B' and resid 780 through 785 removed outlier: 3.754A pdb=" N SER B 785 " --> pdb=" O LYS B 799 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LYS B 799 " --> pdb=" O SER B 785 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'B' and resid 789 through 791 removed outlier: 6.294A pdb=" N LEU B 790 " --> pdb=" O GLN B 892 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'B' and resid 896 through 909 Processing sheet with id=AF7, first strand: chain 'B' and resid 896 through 909 removed outlier: 4.210A pdb=" N LEU B1298 " --> pdb=" O VAL B 937 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL B 937 " --> pdb=" O LEU B1298 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'B' and resid 1152 through 1153 Processing sheet with id=AF9, first strand: chain 'B' and resid 1318 through 1324 removed outlier: 3.911A pdb=" N GLN B1364 " --> pdb=" O LEU B1408 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'B' and resid 1381 through 1385 removed outlier: 3.650A pdb=" N LYS B1381 " --> pdb=" O TYR B1392 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N SER B1420 " --> pdb=" O GLN B1358 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 77 through 84 removed outlier: 8.950A pdb=" N ARG C 40 " --> pdb=" O PRO C 30 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ILE C 29 " --> pdb=" O VAL C 675 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.555A pdb=" N LEU C 33 " --> pdb=" O ALA C 116 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE C 95 " --> pdb=" O GLU C 59 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'C' and resid 52 through 53 Processing sheet with id=AG5, first strand: chain 'C' and resid 121 through 124 Processing sheet with id=AG6, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AG7, first strand: chain 'C' and resid 154 through 155 Processing sheet with id=AG8, first strand: chain 'C' and resid 170 through 171 removed outlier: 4.125A pdb=" N VAL C 158 " --> pdb=" O TRP C 171 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'C' and resid 223 through 225 Processing sheet with id=AH1, first strand: chain 'C' and resid 232 through 233 removed outlier: 3.782A pdb=" N SER C 256 " --> pdb=" O THR C 323 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N CYS C 261 " --> pdb=" O THR C 284 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR C 284 " --> pdb=" O CYS C 261 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'C' and resid 344 through 348 removed outlier: 3.580A pdb=" N ASN C 375 " --> pdb=" O ASP C 371 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'C' and resid 344 through 348 Processing sheet with id=AH4, first strand: chain 'C' and resid 356 through 357 Processing sheet with id=AH5, first strand: chain 'C' and resid 394 through 395 Processing sheet with id=AH6, first strand: chain 'C' and resid 454 through 459 removed outlier: 4.458A pdb=" N SER C 474 " --> pdb=" O GLN C 459 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'C' and resid 470 through 471 Processing sheet with id=AH8, first strand: chain 'C' and resid 503 through 512 removed outlier: 4.913A pdb=" N GLN C 505 " --> pdb=" O ALA C 497 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ALA C 497 " --> pdb=" O GLN C 505 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N THR C 492 " --> pdb=" O ILE C 542 " (cutoff:3.500A) removed outlier: 5.250A pdb=" N ILE C 542 " --> pdb=" O THR C 492 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'C' and resid 567 through 568 Processing sheet with id=AI1, first strand: chain 'C' and resid 590 through 596 Processing sheet with id=AI2, first strand: chain 'C' and resid 647 through 648 Processing sheet with id=AI3, first strand: chain 'C' and resid 780 through 785 removed outlier: 3.761A pdb=" N SER C 785 " --> pdb=" O LYS C 799 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS C 799 " --> pdb=" O SER C 785 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN C 846 " --> pdb=" O ILE C 825 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'C' and resid 780 through 785 removed outlier: 3.761A pdb=" N SER C 785 " --> pdb=" O LYS C 799 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS C 799 " --> pdb=" O SER C 785 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLY C 839 " --> pdb=" O ASN C 804 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'C' and resid 789 through 791 removed outlier: 6.337A pdb=" N LEU C 790 " --> pdb=" O GLN C 892 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR C 815 " --> pdb=" O SER C 860 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'C' and resid 896 through 909 removed outlier: 3.568A pdb=" N VAL C 908 " --> pdb=" O GLY C1295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C1295 " --> pdb=" O VAL C 908 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER C1257 " --> pdb=" O ASP C1261 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ASP C1261 " --> pdb=" O SER C1257 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'C' and resid 896 through 909 removed outlier: 3.568A pdb=" N VAL C 908 " --> pdb=" O GLY C1295 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C1295 " --> pdb=" O VAL C 908 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU C1298 " --> pdb=" O VAL C 937 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 937 " --> pdb=" O LEU C1298 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'C' and resid 1152 through 1153 Processing sheet with id=AI9, first strand: chain 'C' and resid 1318 through 1324 removed outlier: 3.906A pdb=" N GLN C1364 " --> pdb=" O LEU C1408 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'C' and resid 1381 through 1385 removed outlier: 3.797A pdb=" N LYS C1381 " --> pdb=" O TYR C1392 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER C1420 " --> pdb=" O GLN C1358 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'D' and resid 77 through 84 removed outlier: 8.817A pdb=" N ARG D 40 " --> pdb=" O PRO D 30 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE D 29 " --> pdb=" O VAL D 675 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'D' and resid 32 through 34 removed outlier: 6.670A pdb=" N LEU D 33 " --> pdb=" O ALA D 116 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE D 95 " --> pdb=" O GLU D 59 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'D' and resid 52 through 53 Processing sheet with id=AJ5, first strand: chain 'D' and resid 121 through 124 Processing sheet with id=AJ6, first strand: chain 'D' and resid 136 through 138 Processing sheet with id=AJ7, first strand: chain 'D' and resid 154 through 155 Processing sheet with id=AJ8, first strand: chain 'D' and resid 170 through 171 removed outlier: 4.109A pdb=" N VAL D 158 " --> pdb=" O TRP D 171 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'D' and resid 223 through 225 Processing sheet with id=AK1, first strand: chain 'D' and resid 284 through 290 removed outlier: 3.573A pdb=" N THR D 284 " --> pdb=" O CYS D 261 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N CYS D 261 " --> pdb=" O THR D 284 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU D 290 " --> pdb=" O GLY D 255 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N GLY D 255 " --> pdb=" O LEU D 290 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER D 256 " --> pdb=" O THR D 323 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'D' and resid 344 through 348 removed outlier: 3.530A pdb=" N ASN D 375 " --> pdb=" O ASP D 371 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'D' and resid 344 through 348 Processing sheet with id=AK4, first strand: chain 'D' and resid 356 through 357 Processing sheet with id=AK5, first strand: chain 'D' and resid 394 through 395 Processing sheet with id=AK6, first strand: chain 'D' and resid 454 through 459 removed outlier: 4.467A pdb=" N SER D 474 " --> pdb=" O GLN D 459 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'D' and resid 470 through 471 Processing sheet with id=AK8, first strand: chain 'D' and resid 507 through 512 removed outlier: 7.087A pdb=" N THR D 492 " --> pdb=" O ILE D 542 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ILE D 542 " --> pdb=" O THR D 492 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'D' and resid 567 through 568 Processing sheet with id=AL1, first strand: chain 'D' and resid 590 through 596 Processing sheet with id=AL2, first strand: chain 'D' and resid 780 through 785 removed outlier: 3.797A pdb=" N SER D 785 " --> pdb=" O LYS D 799 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS D 799 " --> pdb=" O SER D 785 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP D 845 " --> pdb=" O MET D 798 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ASN D 846 " --> pdb=" O ILE D 825 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'D' and resid 780 through 785 removed outlier: 3.797A pdb=" N SER D 785 " --> pdb=" O LYS D 799 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS D 799 " --> pdb=" O SER D 785 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY D 839 " --> pdb=" O ASN D 804 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'D' and resid 789 through 791 removed outlier: 6.307A pdb=" N LEU D 790 " --> pdb=" O GLN D 892 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'D' and resid 896 through 909 removed outlier: 3.507A pdb=" N GLY D1263 " --> pdb=" O LEU D1255 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'D' and resid 896 through 909 removed outlier: 4.157A pdb=" N LEU D1298 " --> pdb=" O VAL D 937 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL D 937 " --> pdb=" O LEU D1298 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'D' and resid 1152 through 1153 Processing sheet with id=AL8, first strand: chain 'D' and resid 1318 through 1324 removed outlier: 3.889A pdb=" N GLN D1364 " --> pdb=" O LEU D1408 " (cutoff:3.500A) Processing sheet with id=AL9, first strand: chain 'D' and resid 1381 through 1385 removed outlier: 3.668A pdb=" N LYS D1381 " --> pdb=" O TYR D1392 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N SER D1420 " --> pdb=" O GLN D1358 " (cutoff:3.500A) 1571 hydrogen bonds defined for protein. 4266 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: 13.99 Time building geometry restraints manager: 4.98 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: 14509 1.34 - 1.47: 11128 1.47 - 1.59: 20194 1.59 - 1.71: 1 1.71 - 1.83: 312 Bond restraints: 46144 Sorted by residual: bond pdb=" C1 NAG C2103 " pdb=" O5 NAG C2103 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C1 NAG B2103 " pdb=" O5 NAG B2103 " ideal model delta sigma weight residual 1.406 1.484 -0.078 2.00e-02 2.50e+03 1.52e+01 bond pdb=" C1 NAG D2103 " pdb=" O5 NAG D2103 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C1 NAG A2103 " pdb=" O5 NAG A2103 " ideal model delta sigma weight residual 1.406 1.483 -0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C1 NAG B2109 " pdb=" O5 NAG B2109 " ideal model delta sigma weight residual 1.406 1.482 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 46139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.93: 62613 4.93 - 9.86: 116 9.86 - 14.80: 3 14.80 - 19.73: 0 19.73 - 24.66: 4 Bond angle restraints: 62736 Sorted by residual: angle pdb=" CA PRO A 916 " pdb=" N PRO A 916 " pdb=" CD PRO A 916 " ideal model delta sigma weight residual 112.00 99.51 12.49 1.40e+00 5.10e-01 7.96e+01 angle pdb=" C GLN B 73 " pdb=" N PRO B 74 " pdb=" CD PRO B 74 " ideal model delta sigma weight residual 125.00 100.34 24.66 4.10e+00 5.95e-02 3.62e+01 angle pdb=" C GLN A 73 " pdb=" N PRO A 74 " pdb=" CD PRO A 74 " ideal model delta sigma weight residual 125.00 100.65 24.35 4.10e+00 5.95e-02 3.53e+01 angle pdb=" C GLN D 73 " pdb=" N PRO D 74 " pdb=" CD PRO D 74 " ideal model delta sigma weight residual 125.00 100.82 24.18 4.10e+00 5.95e-02 3.48e+01 angle pdb=" C ARG C 271 " pdb=" CA ARG C 271 " pdb=" CB ARG C 271 " ideal model delta sigma weight residual 116.54 109.87 6.67 1.15e+00 7.56e-01 3.37e+01 ... (remaining 62731 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.90: 26304 23.90 - 47.80: 1659 47.80 - 71.71: 339 71.71 - 95.61: 118 95.61 - 119.51: 124 Dihedral angle restraints: 28544 sinusoidal: 11992 harmonic: 16552 Sorted by residual: dihedral pdb=" CB CYS B 640 " pdb=" SG CYS B 640 " pdb=" SG CYS B 688 " pdb=" CB CYS B 688 " ideal model delta sinusoidal sigma weight residual -86.00 -174.82 88.82 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CB CYS A 640 " pdb=" SG CYS A 640 " pdb=" SG CYS A 688 " pdb=" CB CYS A 688 " ideal model delta sinusoidal sigma weight residual -86.00 -174.16 88.16 1 1.00e+01 1.00e-02 9.29e+01 dihedral pdb=" CB CYS D 640 " pdb=" SG CYS D 640 " pdb=" SG CYS D 688 " pdb=" CB CYS D 688 " ideal model delta sinusoidal sigma weight residual -86.00 -173.98 87.98 1 1.00e+01 1.00e-02 9.26e+01 ... (remaining 28541 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 7165 0.120 - 0.239: 164 0.239 - 0.359: 10 0.359 - 0.478: 0 0.478 - 0.598: 1 Chirality restraints: 7340 Sorted by residual: chirality pdb=" C1 NAG D2102 " pdb=" ND2 ASN D 81 " pdb=" C2 NAG D2102 " pdb=" O5 NAG D2102 " both_signs ideal model delta sigma weight residual False -2.40 -1.80 -0.60 2.00e-01 2.50e+01 8.93e+00 chirality pdb=" C1 NAG D2108 " pdb=" ND2 ASN D 578 " pdb=" C2 NAG D2108 " pdb=" O5 NAG D2108 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" C1 NAG B2108 " pdb=" ND2 ASN B 578 " pdb=" C2 NAG B2108 " pdb=" O5 NAG B2108 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 7337 not shown) Planarity restraints: 8072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 73 " -0.127 5.00e-02 4.00e+02 1.91e-01 5.84e+01 pdb=" N PRO B 74 " 0.330 5.00e-02 4.00e+02 pdb=" CA PRO B 74 " -0.117 5.00e-02 4.00e+02 pdb=" CD PRO B 74 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 73 " -0.126 5.00e-02 4.00e+02 1.90e-01 5.75e+01 pdb=" N PRO D 74 " 0.327 5.00e-02 4.00e+02 pdb=" CA PRO D 74 " -0.116 5.00e-02 4.00e+02 pdb=" CD PRO D 74 " -0.086 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A 73 " 0.125 5.00e-02 4.00e+02 1.89e-01 5.71e+01 pdb=" N PRO A 74 " -0.326 5.00e-02 4.00e+02 pdb=" CA PRO A 74 " 0.115 5.00e-02 4.00e+02 pdb=" CD PRO A 74 " 0.086 5.00e-02 4.00e+02 ... (remaining 8069 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 78 2.34 - 2.98: 22947 2.98 - 3.62: 65409 3.62 - 4.26: 94855 4.26 - 4.90: 158468 Nonbonded interactions: 341757 Sorted by model distance: nonbonded pdb=" SG CYS C 958 " pdb=" CD GLN C 961 " model vdw 1.697 3.630 nonbonded pdb=" SG CYS D 958 " pdb=" CD GLN D 961 " model vdw 1.697 3.630 nonbonded pdb=" SG CYS A 958 " pdb=" CD GLN A 961 " model vdw 1.698 3.630 nonbonded pdb=" SG CYS B 958 " pdb=" CD GLN B 961 " model vdw 1.698 3.630 nonbonded pdb=" SG CYS A 958 " pdb=" CG GLN A 961 " model vdw 1.919 3.800 ... (remaining 341752 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.560 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 44.240 Find NCS groups from input model: 0.910 Set up NCS constraints: 0.120 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6616 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 : 0.004 0.120 46248 Z= 0.201 Angle : 0.816 24.661 63004 Z= 0.425 Chirality : 0.050 0.598 7340 Planarity : 0.007 0.191 8004 Dihedral : 18.502 119.512 17872 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.77 % Favored : 90.02 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.11), residues: 5672 helix: 0.89 (0.18), residues: 804 sheet: -0.54 (0.12), residues: 1952 loop : -2.50 (0.11), residues: 2916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 447 TYR 0.035 0.002 TYR C 653 PHE 0.026 0.002 PHE A1030 TRP 0.026 0.001 TRP B1015 HIS 0.003 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00430 (46144) covalent geometry : angle 0.78940 (62736) SS BOND : bond 0.00277 ( 32) SS BOND : angle 1.89074 ( 64) hydrogen bonds : bond 0.12719 ( 1487) hydrogen bonds : angle 6.38671 ( 4266) Misc. bond : bond 0.00122 ( 4) link_NAG-ASN : bond 0.00672 ( 68) link_NAG-ASN : angle 3.62353 ( 204) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 468 time to evaluate : 1.453 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: A 131 TYR cc_start: 0.6334 (m-80) cc_final: 0.5086 (m-80) REVERT: A 446 MET cc_start: 0.8496 (mmm) cc_final: 0.8116 (mmm) REVERT: A 478 ILE cc_start: 0.8883 (tp) cc_final: 0.8644 (tt) REVERT: A 1337 ILE cc_start: 0.7541 (mt) cc_final: 0.7245 (mt) REVERT: B 430 TYR cc_start: 0.8144 (t80) cc_final: 0.7895 (t80) REVERT: B 446 MET cc_start: 0.8143 (mmm) cc_final: 0.7861 (mmm) REVERT: C 451 GLU cc_start: 0.7088 (pp20) cc_final: 0.6809 (pp20) REVERT: C 1337 ILE cc_start: 0.8102 (mt) cc_final: 0.7678 (mt) REVERT: D 277 LYS cc_start: 0.4640 (ptpp) cc_final: 0.3931 (ptpp) REVERT: D 430 TYR cc_start: 0.8006 (t80) cc_final: 0.7757 (t80) REVERT: D 446 MET cc_start: 0.8231 (mmm) cc_final: 0.7998 (mmm) REVERT: D 478 ILE cc_start: 0.8797 (tp) cc_final: 0.8458 (tt) REVERT: D 484 MET cc_start: 0.7556 (ppp) cc_final: 0.6839 (ppp) outliers start: 0 outliers final: 0 residues processed: 468 average time/residue: 0.2385 time to fit residues: 191.0929 Evaluate side-chains 364 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 364 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 0.9980 chunk 41 optimal weight: 0.0370 chunk 265 optimal weight: 30.0000 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 8.9990 chunk 310 optimal weight: 3.9990 chunk 488 optimal weight: 0.6980 chunk 366 optimal weight: 30.0000 chunk 223 optimal weight: 8.9990 overall best weight: 2.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A 274 ASN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 GLN A1415 ASN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN C1047 GLN C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1047 GLN D1235 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.176758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.160629 restraints weight = 100600.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.157271 restraints weight = 138710.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.155699 restraints weight = 140402.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.154570 restraints weight = 140025.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.153324 restraints weight = 148009.960| |-----------------------------------------------------------------------------| r_work (final): 0.4178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.1013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 46248 Z= 0.189 Angle : 0.742 12.325 63004 Z= 0.360 Chirality : 0.050 0.382 7340 Planarity : 0.006 0.138 8004 Dihedral : 13.370 106.138 7592 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.84 % Favored : 89.95 % Rotamer: Outliers : 0.12 % Allowed : 6.97 % Favored : 92.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.11), residues: 5672 helix: 1.07 (0.18), residues: 808 sheet: -0.36 (0.12), residues: 1860 loop : -2.51 (0.11), residues: 3004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 447 TYR 0.026 0.002 TYR C 540 PHE 0.019 0.002 PHE C 83 TRP 0.028 0.001 TRP B 433 HIS 0.005 0.001 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00445 (46144) covalent geometry : angle 0.71106 (62736) SS BOND : bond 0.00528 ( 32) SS BOND : angle 1.42522 ( 64) hydrogen bonds : bond 0.03688 ( 1487) hydrogen bonds : angle 5.68146 ( 4266) Misc. bond : bond 0.00092 ( 4) link_NAG-ASN : bond 0.00716 ( 68) link_NAG-ASN : angle 3.70470 ( 204) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 455 time to evaluate : 1.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6797 (m-80) cc_final: 0.5401 (m-80) REVERT: A 430 TYR cc_start: 0.8123 (t80) cc_final: 0.7916 (t80) REVERT: A 457 ASP cc_start: 0.8448 (t0) cc_final: 0.7960 (t0) REVERT: A 750 THR cc_start: 0.6368 (p) cc_final: 0.6155 (p) REVERT: A 1337 ILE cc_start: 0.7655 (mt) cc_final: 0.7384 (mt) REVERT: B 126 MET cc_start: 0.8543 (tpp) cc_final: 0.8212 (tpp) REVERT: B 235 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7303 (pp) REVERT: B 446 MET cc_start: 0.8007 (mmm) cc_final: 0.7741 (mmm) REVERT: C 74 PRO cc_start: 0.6737 (OUTLIER) cc_final: 0.6508 (Cg_endo) REVERT: C 430 TYR cc_start: 0.8334 (t80) cc_final: 0.8083 (t80) REVERT: C 451 GLU cc_start: 0.7185 (pp20) cc_final: 0.6827 (pp20) REVERT: C 1001 GLN cc_start: 0.7342 (pt0) cc_final: 0.7011 (tm-30) REVERT: C 1337 ILE cc_start: 0.8146 (mt) cc_final: 0.7759 (mt) REVERT: D 126 MET cc_start: 0.8531 (tpp) cc_final: 0.8214 (tpp) REVERT: D 277 LYS cc_start: 0.4726 (ptpp) cc_final: 0.3720 (ptpp) REVERT: D 430 TYR cc_start: 0.8371 (t80) cc_final: 0.8008 (t80) REVERT: D 457 ASP cc_start: 0.8362 (t0) cc_final: 0.7970 (t0) REVERT: D 478 ILE cc_start: 0.8857 (tp) cc_final: 0.8582 (tt) REVERT: D 484 MET cc_start: 0.7013 (ppp) cc_final: 0.6546 (ppp) REVERT: D 778 LEU cc_start: 0.7919 (tt) cc_final: 0.7706 (tt) REVERT: D 983 THR cc_start: 0.6303 (m) cc_final: 0.6070 (m) REVERT: D 1001 GLN cc_start: 0.5681 (tm-30) cc_final: 0.5436 (tm-30) outliers start: 6 outliers final: 1 residues processed: 461 average time/residue: 0.2386 time to fit residues: 187.6206 Evaluate side-chains 351 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 348 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 263 optimal weight: 9.9990 chunk 308 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 540 optimal weight: 0.9990 chunk 309 optimal weight: 0.9990 chunk 96 optimal weight: 10.0000 chunk 271 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.175431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.157032 restraints weight = 99682.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.153785 restraints weight = 155183.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.152342 restraints weight = 148559.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.151767 restraints weight = 141578.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.151131 restraints weight = 119880.448| |-----------------------------------------------------------------------------| r_work (final): 0.4132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 46248 Z= 0.178 Angle : 0.739 14.830 63004 Z= 0.355 Chirality : 0.050 0.526 7340 Planarity : 0.006 0.153 8004 Dihedral : 10.440 103.853 7592 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.82 % Favored : 89.97 % Rotamer: Outliers : 0.04 % Allowed : 4.86 % Favored : 95.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.11), residues: 5672 helix: 1.08 (0.18), residues: 808 sheet: -0.28 (0.13), residues: 1824 loop : -2.55 (0.10), residues: 3040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1162 TYR 0.048 0.002 TYR A 268 PHE 0.016 0.002 PHE A 448 TRP 0.030 0.001 TRP B 433 HIS 0.005 0.001 HIS B 506 Details of bonding type rmsd covalent geometry : bond 0.00420 (46144) covalent geometry : angle 0.70745 (62736) SS BOND : bond 0.00482 ( 32) SS BOND : angle 1.52446 ( 64) hydrogen bonds : bond 0.03602 ( 1487) hydrogen bonds : angle 5.56393 ( 4266) Misc. bond : bond 0.00103 ( 4) link_NAG-ASN : bond 0.00863 ( 68) link_NAG-ASN : angle 3.72437 ( 204) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 467 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6687 (m-80) cc_final: 0.5409 (m-80) REVERT: A 430 TYR cc_start: 0.8093 (t80) cc_final: 0.7782 (t80) REVERT: A 457 ASP cc_start: 0.8380 (t0) cc_final: 0.7923 (t0) REVERT: A 750 THR cc_start: 0.6797 (p) cc_final: 0.6535 (p) REVERT: A 1337 ILE cc_start: 0.7739 (mt) cc_final: 0.7441 (mt) REVERT: B 282 ILE cc_start: 0.8047 (tt) cc_final: 0.7826 (tt) REVERT: B 430 TYR cc_start: 0.8226 (t80) cc_final: 0.7978 (t80) REVERT: B 446 MET cc_start: 0.8108 (mmm) cc_final: 0.7850 (mmm) REVERT: B 1115 MET cc_start: 0.0893 (mmp) cc_final: 0.0686 (mmp) REVERT: B 1375 ASN cc_start: 0.7228 (p0) cc_final: 0.6977 (p0) REVERT: C 74 PRO cc_start: 0.6761 (OUTLIER) cc_final: 0.6553 (Cg_endo) REVERT: C 430 TYR cc_start: 0.8298 (t80) cc_final: 0.8047 (t80) REVERT: C 446 MET cc_start: 0.8240 (mmm) cc_final: 0.8028 (mmm) REVERT: C 457 ASP cc_start: 0.8351 (t0) cc_final: 0.8068 (t0) REVERT: C 1337 ILE cc_start: 0.7783 (mt) cc_final: 0.7348 (mt) REVERT: D 430 TYR cc_start: 0.8396 (t80) cc_final: 0.8037 (t80) REVERT: D 457 ASP cc_start: 0.8274 (t0) cc_final: 0.7804 (t0) REVERT: D 478 ILE cc_start: 0.8868 (tp) cc_final: 0.8630 (tt) REVERT: D 623 LEU cc_start: 0.7344 (mp) cc_final: 0.7022 (mt) REVERT: D 778 LEU cc_start: 0.8026 (tt) cc_final: 0.7762 (tt) REVERT: D 1175 TYR cc_start: 0.6237 (t80) cc_final: 0.5952 (t80) outliers start: 2 outliers final: 0 residues processed: 469 average time/residue: 0.2377 time to fit residues: 189.3122 Evaluate side-chains 351 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 350 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 353 optimal weight: 9.9990 chunk 240 optimal weight: 0.7980 chunk 467 optimal weight: 0.7980 chunk 143 optimal weight: 3.9990 chunk 559 optimal weight: 10.0000 chunk 134 optimal weight: 20.0000 chunk 65 optimal weight: 0.9980 chunk 393 optimal weight: 50.0000 chunk 440 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 417 optimal weight: 20.0000 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1235 GLN A1387 ASN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 833 GLN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 833 GLN ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.176389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.160006 restraints weight = 100201.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.157058 restraints weight = 124864.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.155391 restraints weight = 102186.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.153726 restraints weight = 125365.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.152554 restraints weight = 119972.481| |-----------------------------------------------------------------------------| r_work (final): 0.4148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 46248 Z= 0.148 Angle : 0.699 13.042 63004 Z= 0.337 Chirality : 0.048 0.386 7340 Planarity : 0.006 0.144 8004 Dihedral : 9.243 102.759 7592 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.71 % Favored : 90.11 % Rotamer: Outliers : 0.06 % Allowed : 4.12 % Favored : 95.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.11), residues: 5672 helix: 1.00 (0.18), residues: 808 sheet: -0.26 (0.13), residues: 1832 loop : -2.54 (0.10), residues: 3032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D1074 TYR 0.032 0.001 TYR A 268 PHE 0.019 0.002 PHE C 83 TRP 0.021 0.001 TRP B 433 HIS 0.003 0.001 HIS D 506 Details of bonding type rmsd covalent geometry : bond 0.00346 (46144) covalent geometry : angle 0.66417 (62736) SS BOND : bond 0.00376 ( 32) SS BOND : angle 1.38146 ( 64) hydrogen bonds : bond 0.03350 ( 1487) hydrogen bonds : angle 5.46049 ( 4266) Misc. bond : bond 0.00344 ( 4) link_NAG-ASN : bond 0.00769 ( 68) link_NAG-ASN : angle 3.81177 ( 204) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 469 time to evaluate : 1.156 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: A 131 TYR cc_start: 0.6591 (m-80) cc_final: 0.5207 (m-80) REVERT: A 430 TYR cc_start: 0.8121 (t80) cc_final: 0.7825 (t80) REVERT: A 457 ASP cc_start: 0.8284 (t0) cc_final: 0.7807 (t0) REVERT: A 750 THR cc_start: 0.6456 (p) cc_final: 0.6186 (p) REVERT: A 1337 ILE cc_start: 0.7711 (mt) cc_final: 0.7057 (mt) REVERT: B 282 ILE cc_start: 0.8010 (tt) cc_final: 0.7779 (tt) REVERT: B 430 TYR cc_start: 0.8245 (t80) cc_final: 0.7963 (t80) REVERT: B 446 MET cc_start: 0.8102 (mmm) cc_final: 0.7818 (mmm) REVERT: B 822 PHE cc_start: 0.4568 (p90) cc_final: 0.4218 (p90) REVERT: B 1375 ASN cc_start: 0.7344 (p0) cc_final: 0.7044 (p0) REVERT: C 430 TYR cc_start: 0.8258 (t80) cc_final: 0.8048 (t80) REVERT: C 446 MET cc_start: 0.8207 (mmm) cc_final: 0.7929 (mmm) REVERT: C 1337 ILE cc_start: 0.7931 (mt) cc_final: 0.7635 (mt) REVERT: D 430 TYR cc_start: 0.8401 (t80) cc_final: 0.8064 (t80) REVERT: D 457 ASP cc_start: 0.8259 (t0) cc_final: 0.7703 (t0) REVERT: D 478 ILE cc_start: 0.8887 (tp) cc_final: 0.8678 (tt) REVERT: D 484 MET cc_start: 0.7170 (ppp) cc_final: 0.6306 (ppp) REVERT: D 1001 GLN cc_start: 0.6176 (tm-30) cc_final: 0.5780 (tm-30) REVERT: D 1175 TYR cc_start: 0.6290 (t80) cc_final: 0.6002 (t80) outliers start: 3 outliers final: 0 residues processed: 472 average time/residue: 0.2400 time to fit residues: 193.7213 Evaluate side-chains 353 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 353 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 421 optimal weight: 6.9990 chunk 279 optimal weight: 7.9990 chunk 545 optimal weight: 0.8980 chunk 449 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 124 optimal weight: 40.0000 chunk 558 optimal weight: 0.0870 chunk 519 optimal weight: 20.0000 chunk 18 optimal weight: 8.9990 chunk 518 optimal weight: 8.9990 chunk 416 optimal weight: 8.9990 overall best weight: 2.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1049 GLN A1235 GLN A1264 GLN A1387 ASN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1168 GLN B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1168 GLN C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN D1378 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.173846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.154115 restraints weight = 99668.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.152160 restraints weight = 164734.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.150802 restraints weight = 154622.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.150192 restraints weight = 149592.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.148957 restraints weight = 154849.407| |-----------------------------------------------------------------------------| r_work (final): 0.4105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 46248 Z= 0.205 Angle : 0.740 14.062 63004 Z= 0.362 Chirality : 0.050 0.639 7340 Planarity : 0.006 0.149 8004 Dihedral : 8.900 100.422 7592 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.93 % Favored : 88.88 % Rotamer: Outliers : 0.02 % Allowed : 3.88 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.11), residues: 5672 helix: 0.98 (0.18), residues: 804 sheet: -0.32 (0.13), residues: 1832 loop : -2.60 (0.10), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D1140 TYR 0.041 0.002 TYR A 268 PHE 0.031 0.002 PHE D 448 TRP 0.024 0.001 TRP B 433 HIS 0.005 0.001 HIS A 443 Details of bonding type rmsd covalent geometry : bond 0.00491 (46144) covalent geometry : angle 0.70917 (62736) SS BOND : bond 0.00298 ( 32) SS BOND : angle 1.59654 ( 64) hydrogen bonds : bond 0.03588 ( 1487) hydrogen bonds : angle 5.56554 ( 4266) Misc. bond : bond 0.00205 ( 4) link_NAG-ASN : bond 0.00704 ( 68) link_NAG-ASN : angle 3.67218 ( 204) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 457 time to evaluate : 1.449 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 131 TYR cc_start: 0.6781 (m-80) cc_final: 0.6572 (m-80) REVERT: A 430 TYR cc_start: 0.8167 (t80) cc_final: 0.7790 (t80) REVERT: A 1245 PHE cc_start: 0.6806 (t80) cc_final: 0.6596 (t80) REVERT: A 1337 ILE cc_start: 0.7946 (mt) cc_final: 0.7643 (mt) REVERT: B 126 MET cc_start: 0.8717 (tpp) cc_final: 0.8473 (tpp) REVERT: B 430 TYR cc_start: 0.8307 (t80) cc_final: 0.7996 (t80) REVERT: B 446 MET cc_start: 0.8310 (mmm) cc_final: 0.7990 (mmm) REVERT: B 822 PHE cc_start: 0.4570 (p90) cc_final: 0.4287 (p90) REVERT: B 1175 TYR cc_start: 0.6519 (t80) cc_final: 0.6150 (t80) REVERT: C 377 MET cc_start: 0.9031 (mmm) cc_final: 0.8152 (mpp) REVERT: C 430 TYR cc_start: 0.8313 (t80) cc_final: 0.7973 (t80) REVERT: C 446 MET cc_start: 0.8265 (mmm) cc_final: 0.8021 (mmm) REVERT: C 1337 ILE cc_start: 0.8145 (mt) cc_final: 0.7861 (mt) REVERT: D 126 MET cc_start: 0.8650 (tpp) cc_final: 0.8425 (tpp) REVERT: D 430 TYR cc_start: 0.8494 (t80) cc_final: 0.8093 (t80) REVERT: D 457 ASP cc_start: 0.8253 (t0) cc_final: 0.7767 (t0) REVERT: D 478 ILE cc_start: 0.8970 (tp) cc_final: 0.8766 (tt) REVERT: D 778 LEU cc_start: 0.7954 (tt) cc_final: 0.7739 (tt) REVERT: D 1001 GLN cc_start: 0.6150 (tm-30) cc_final: 0.5809 (tm-30) REVERT: D 1175 TYR cc_start: 0.6374 (t80) cc_final: 0.6104 (t80) outliers start: 1 outliers final: 0 residues processed: 457 average time/residue: 0.2293 time to fit residues: 180.0394 Evaluate side-chains 339 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 339 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 473 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 431 optimal weight: 0.4980 chunk 509 optimal weight: 30.0000 chunk 198 optimal weight: 9.9990 chunk 201 optimal weight: 0.8980 chunk 546 optimal weight: 20.0000 chunk 137 optimal weight: 20.0000 chunk 283 optimal weight: 20.0000 chunk 406 optimal weight: 7.9990 chunk 374 optimal weight: 0.0000 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 HIS A 833 GLN A1049 GLN A1058 GLN A1235 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 512 HIS ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1136 ASN B1235 GLN B1264 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 HIS C 817 GLN ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 512 HIS ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.177542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.158084 restraints weight = 100301.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.155095 restraints weight = 154072.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.153105 restraints weight = 146713.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.152786 restraints weight = 137855.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.151593 restraints weight = 123143.058| |-----------------------------------------------------------------------------| r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6789 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 46248 Z= 0.123 Angle : 0.681 15.796 63004 Z= 0.331 Chirality : 0.048 0.398 7340 Planarity : 0.005 0.155 8004 Dihedral : 8.410 100.484 7592 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.19 % Favored : 90.66 % Rotamer: Outliers : 0.06 % Allowed : 2.57 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.11), residues: 5672 helix: 1.02 (0.18), residues: 796 sheet: -0.23 (0.13), residues: 1852 loop : -2.49 (0.10), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1000 TYR 0.029 0.001 TYR A 268 PHE 0.016 0.001 PHE C1434 TRP 0.029 0.001 TRP B 433 HIS 0.003 0.001 HIS B 506 Details of bonding type rmsd covalent geometry : bond 0.00280 (46144) covalent geometry : angle 0.64989 (62736) SS BOND : bond 0.00280 ( 32) SS BOND : angle 1.47690 ( 64) hydrogen bonds : bond 0.03132 ( 1487) hydrogen bonds : angle 5.35109 ( 4266) Misc. bond : bond 0.00262 ( 4) link_NAG-ASN : bond 0.00730 ( 68) link_NAG-ASN : angle 3.58168 ( 204) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 477 time to evaluate : 1.674 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6559 (m-80) cc_final: 0.4981 (m-80) REVERT: A 430 TYR cc_start: 0.8134 (t80) cc_final: 0.7804 (t80) REVERT: A 457 ASP cc_start: 0.8325 (t0) cc_final: 0.7767 (t0) REVERT: A 798 MET cc_start: 0.4673 (ppp) cc_final: 0.4441 (ppp) REVERT: A 1245 PHE cc_start: 0.6820 (t80) cc_final: 0.6589 (t80) REVERT: A 1337 ILE cc_start: 0.7798 (mt) cc_final: 0.7302 (mt) REVERT: B 430 TYR cc_start: 0.8250 (t80) cc_final: 0.8034 (t80) REVERT: B 446 MET cc_start: 0.8228 (mmm) cc_final: 0.7791 (mmm) REVERT: B 822 PHE cc_start: 0.5156 (p90) cc_final: 0.4805 (p90) REVERT: C 430 TYR cc_start: 0.8194 (t80) cc_final: 0.7894 (t80) REVERT: C 798 MET cc_start: 0.4662 (ppp) cc_final: 0.4425 (ppp) REVERT: C 991 VAL cc_start: 0.9062 (t) cc_final: 0.8722 (p) REVERT: C 1071 LEU cc_start: 0.6148 (mp) cc_final: 0.5876 (tt) REVERT: C 1337 ILE cc_start: 0.7947 (mt) cc_final: 0.7740 (mt) REVERT: D 307 MET cc_start: 0.6347 (mmp) cc_final: 0.6046 (mmp) REVERT: D 315 SER cc_start: 0.8683 (t) cc_final: 0.8162 (m) REVERT: D 430 TYR cc_start: 0.8480 (t80) cc_final: 0.8056 (t80) REVERT: D 457 ASP cc_start: 0.8392 (t0) cc_final: 0.7799 (t0) REVERT: D 1175 TYR cc_start: 0.6420 (t80) cc_final: 0.6127 (t80) outliers start: 3 outliers final: 0 residues processed: 480 average time/residue: 0.2313 time to fit residues: 192.3791 Evaluate side-chains 342 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 512 optimal weight: 8.9990 chunk 125 optimal weight: 20.0000 chunk 225 optimal weight: 20.0000 chunk 380 optimal weight: 9.9990 chunk 500 optimal weight: 5.9990 chunk 253 optimal weight: 20.0000 chunk 279 optimal weight: 5.9990 chunk 256 optimal weight: 20.0000 chunk 344 optimal weight: 6.9990 chunk 214 optimal weight: 8.9990 chunk 166 optimal weight: 0.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN A 833 GLN A1047 GLN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 GLN B 24 GLN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 GLN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1136 ASN C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 210 GLN D 427 GLN ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.169384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.151154 restraints weight = 99729.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.148586 restraints weight = 175030.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.146999 restraints weight = 164281.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.145851 restraints weight = 170009.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.145183 restraints weight = 144287.370| |-----------------------------------------------------------------------------| r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.137 46248 Z= 0.378 Angle : 0.933 22.420 63004 Z= 0.459 Chirality : 0.054 0.394 7340 Planarity : 0.007 0.183 8004 Dihedral : 8.896 95.515 7592 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 15.56 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.20 % Favored : 87.57 % Rotamer: Outliers : 0.02 % Allowed : 3.46 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.13 (0.11), residues: 5672 helix: 0.78 (0.18), residues: 804 sheet: -0.54 (0.12), residues: 1844 loop : -2.72 (0.10), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1000 TYR 0.042 0.003 TYR A 268 PHE 0.050 0.003 PHE C 411 TRP 0.023 0.002 TRP B 433 HIS 0.006 0.001 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00908 (46144) covalent geometry : angle 0.90703 (62736) SS BOND : bond 0.00501 ( 32) SS BOND : angle 1.74025 ( 64) hydrogen bonds : bond 0.04530 ( 1487) hydrogen bonds : angle 5.90640 ( 4266) Misc. bond : bond 0.00358 ( 4) link_NAG-ASN : bond 0.00672 ( 68) link_NAG-ASN : angle 3.82893 ( 204) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 431 time to evaluate : 1.564 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 74 PRO cc_start: 0.6932 (OUTLIER) cc_final: 0.6731 (Cg_endo) REVERT: A 84 MET cc_start: 0.8281 (tmm) cc_final: 0.7862 (tmm) REVERT: A 377 MET cc_start: 0.9055 (mmm) cc_final: 0.7913 (mpp) REVERT: A 430 TYR cc_start: 0.8345 (t80) cc_final: 0.7919 (t80) REVERT: A 550 ASP cc_start: 0.8386 (t0) cc_final: 0.8147 (t0) REVERT: A 798 MET cc_start: 0.4787 (ppp) cc_final: 0.4545 (ppp) REVERT: A 1072 PHE cc_start: 0.2621 (p90) cc_final: 0.2398 (p90) REVERT: A 1245 PHE cc_start: 0.6761 (t80) cc_final: 0.6526 (t80) REVERT: A 1337 ILE cc_start: 0.8179 (mt) cc_final: 0.7792 (mt) REVERT: A 1359 MET cc_start: 0.6972 (mmm) cc_final: 0.6728 (mmm) REVERT: B 377 MET cc_start: 0.9156 (mmm) cc_final: 0.8083 (mpp) REVERT: B 822 PHE cc_start: 0.5268 (p90) cc_final: 0.5059 (p90) REVERT: B 1175 TYR cc_start: 0.6584 (t80) cc_final: 0.6252 (t80) REVERT: C 377 MET cc_start: 0.9092 (mmm) cc_final: 0.7865 (mpp) REVERT: D 377 MET cc_start: 0.9131 (mmm) cc_final: 0.7881 (mpp) REVERT: D 778 LEU cc_start: 0.8144 (tt) cc_final: 0.7924 (mm) REVERT: D 915 MET cc_start: 0.3008 (ppp) cc_final: 0.2667 (ppp) REVERT: D 1001 GLN cc_start: 0.6238 (tm-30) cc_final: 0.5824 (tm-30) REVERT: D 1175 TYR cc_start: 0.6380 (t80) cc_final: 0.6145 (t80) outliers start: 1 outliers final: 0 residues processed: 432 average time/residue: 0.2322 time to fit residues: 172.6735 Evaluate side-chains 321 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 50 optimal weight: 0.5980 chunk 337 optimal weight: 1.9990 chunk 309 optimal weight: 2.9990 chunk 286 optimal weight: 0.8980 chunk 26 optimal weight: 8.9990 chunk 284 optimal weight: 0.6980 chunk 518 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 288 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 GLN B 210 GLN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1049 GLN B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1235 GLN C1329 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.174700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.156460 restraints weight = 99954.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.153606 restraints weight = 151800.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.151637 restraints weight = 146172.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.150926 restraints weight = 150128.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.149506 restraints weight = 141170.202| |-----------------------------------------------------------------------------| r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 46248 Z= 0.146 Angle : 0.745 20.042 63004 Z= 0.359 Chirality : 0.050 0.428 7340 Planarity : 0.006 0.172 8004 Dihedral : 8.393 97.036 7592 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.89 % Favored : 89.90 % Rotamer: Outliers : 0.02 % Allowed : 1.35 % Favored : 98.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.11), residues: 5672 helix: 0.82 (0.18), residues: 812 sheet: -0.42 (0.12), residues: 1848 loop : -2.60 (0.10), residues: 3012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D1000 TYR 0.029 0.001 TYR D 430 PHE 0.018 0.002 PHE B 83 TRP 0.033 0.001 TRP A 433 HIS 0.005 0.001 HIS B 506 Details of bonding type rmsd covalent geometry : bond 0.00342 (46144) covalent geometry : angle 0.71413 (62736) SS BOND : bond 0.00275 ( 32) SS BOND : angle 1.73046 ( 64) hydrogen bonds : bond 0.03322 ( 1487) hydrogen bonds : angle 5.58582 ( 4266) Misc. bond : bond 0.00231 ( 4) link_NAG-ASN : bond 0.00693 ( 68) link_NAG-ASN : angle 3.71702 ( 204) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 452 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8294 (tmm) cc_final: 0.7873 (tmm) REVERT: A 430 TYR cc_start: 0.8241 (t80) cc_final: 0.7674 (t80) REVERT: A 457 ASP cc_start: 0.8331 (t0) cc_final: 0.7784 (t0) REVERT: A 550 ASP cc_start: 0.8250 (t0) cc_final: 0.8024 (t0) REVERT: A 1031 LYS cc_start: 0.7395 (mmtt) cc_final: 0.7095 (mmtt) REVERT: A 1245 PHE cc_start: 0.6728 (t80) cc_final: 0.6490 (t80) REVERT: A 1337 ILE cc_start: 0.8151 (mt) cc_final: 0.7856 (mt) REVERT: B 377 MET cc_start: 0.8901 (mmm) cc_final: 0.8157 (mpp) REVERT: B 430 TYR cc_start: 0.8299 (t80) cc_final: 0.8069 (t80) REVERT: B 446 MET cc_start: 0.8458 (mmm) cc_final: 0.8185 (mmm) REVERT: B 1031 LYS cc_start: 0.7638 (mttm) cc_final: 0.7353 (mmtt) REVERT: B 1207 MET cc_start: 0.5129 (mmt) cc_final: 0.4587 (mmt) REVERT: D 307 MET cc_start: 0.6640 (mmp) cc_final: 0.6351 (mmp) REVERT: D 377 MET cc_start: 0.8934 (mmm) cc_final: 0.8285 (mpp) REVERT: D 457 ASP cc_start: 0.8267 (t0) cc_final: 0.7735 (t0) REVERT: D 550 ASP cc_start: 0.8189 (t0) cc_final: 0.7929 (t0) REVERT: D 915 MET cc_start: 0.2931 (ppp) cc_final: 0.2630 (ppp) REVERT: D 1115 MET cc_start: 0.1082 (mmp) cc_final: 0.0585 (mmm) REVERT: D 1175 TYR cc_start: 0.6475 (t80) cc_final: 0.6224 (t80) outliers start: 1 outliers final: 0 residues processed: 453 average time/residue: 0.2292 time to fit residues: 179.3779 Evaluate side-chains 321 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 321 time to evaluate : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 49 optimal weight: 0.9980 chunk 430 optimal weight: 0.9990 chunk 499 optimal weight: 0.9980 chunk 287 optimal weight: 9.9990 chunk 523 optimal weight: 9.9990 chunk 534 optimal weight: 0.6980 chunk 148 optimal weight: 1.9990 chunk 129 optimal weight: 0.5980 chunk 451 optimal weight: 10.0000 chunk 452 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1047 GLN B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 274 ASN ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.176131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.158362 restraints weight = 99826.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.155296 restraints weight = 144427.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.153530 restraints weight = 143866.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.153162 restraints weight = 145209.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.152137 restraints weight = 134348.802| |-----------------------------------------------------------------------------| r_work (final): 0.4145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6773 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 46248 Z= 0.130 Angle : 0.714 17.221 63004 Z= 0.346 Chirality : 0.049 0.358 7340 Planarity : 0.006 0.160 8004 Dihedral : 8.160 97.936 7592 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.00 % Favored : 89.81 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.11), residues: 5672 helix: 0.79 (0.18), residues: 816 sheet: -0.30 (0.12), residues: 1852 loop : -2.52 (0.10), residues: 3004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1000 TYR 0.024 0.001 TYR D 430 PHE 0.017 0.002 PHE D 276 TRP 0.037 0.001 TRP C 433 HIS 0.004 0.001 HIS B 506 Details of bonding type rmsd covalent geometry : bond 0.00303 (46144) covalent geometry : angle 0.68400 (62736) SS BOND : bond 0.00296 ( 32) SS BOND : angle 1.78660 ( 64) hydrogen bonds : bond 0.03137 ( 1487) hydrogen bonds : angle 5.41335 ( 4266) Misc. bond : bond 0.00206 ( 4) link_NAG-ASN : bond 0.00674 ( 68) link_NAG-ASN : angle 3.57568 ( 204) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.534 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 84 MET cc_start: 0.8338 (tmm) cc_final: 0.7933 (tmm) REVERT: A 430 TYR cc_start: 0.8100 (t80) cc_final: 0.7769 (t80) REVERT: A 457 ASP cc_start: 0.8242 (t0) cc_final: 0.7694 (t0) REVERT: A 550 ASP cc_start: 0.8408 (t0) cc_final: 0.8189 (t0) REVERT: A 948 LEU cc_start: 0.7848 (tt) cc_final: 0.7328 (tt) REVERT: A 954 MET cc_start: 0.4782 (tmm) cc_final: 0.4501 (tmm) REVERT: A 1245 PHE cc_start: 0.6737 (t80) cc_final: 0.6502 (t80) REVERT: B 377 MET cc_start: 0.8595 (mmm) cc_final: 0.7749 (mpp) REVERT: B 430 TYR cc_start: 0.8255 (t80) cc_final: 0.7946 (t80) REVERT: B 446 MET cc_start: 0.8530 (mmm) cc_final: 0.8196 (mmm) REVERT: C 84 MET cc_start: 0.8236 (tmm) cc_final: 0.7780 (tmm) REVERT: C 430 TYR cc_start: 0.8306 (t80) cc_final: 0.8080 (t80) REVERT: C 991 VAL cc_start: 0.8987 (t) cc_final: 0.8665 (p) REVERT: C 1073 MET cc_start: 0.5686 (mmm) cc_final: 0.5369 (mtt) REVERT: D 277 LYS cc_start: 0.5615 (mtmt) cc_final: 0.5387 (mtmt) REVERT: D 377 MET cc_start: 0.8923 (mmm) cc_final: 0.8156 (mpp) REVERT: D 430 TYR cc_start: 0.8509 (t80) cc_final: 0.8298 (t80) REVERT: D 457 ASP cc_start: 0.8265 (t0) cc_final: 0.7703 (t0) REVERT: D 550 ASP cc_start: 0.8135 (t0) cc_final: 0.7919 (t0) REVERT: D 623 LEU cc_start: 0.7727 (mp) cc_final: 0.7322 (mt) REVERT: D 1001 GLN cc_start: 0.6276 (tm-30) cc_final: 0.6033 (tm-30) REVERT: D 1115 MET cc_start: 0.0688 (mmp) cc_final: 0.0132 (mmm) REVERT: D 1175 TYR cc_start: 0.6389 (t80) cc_final: 0.6126 (t80) outliers start: 0 outliers final: 0 residues processed: 456 average time/residue: 0.2233 time to fit residues: 176.1978 Evaluate side-chains 329 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 329 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 549 optimal weight: 20.0000 chunk 62 optimal weight: 0.0470 chunk 141 optimal weight: 0.0050 chunk 4 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 88 optimal weight: 9.9990 chunk 482 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 245 optimal weight: 9.9990 chunk 48 optimal weight: 4.9990 overall best weight: 0.9496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN A 962 ASN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 978 ASN B1235 GLN B1242 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN D1378 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.175909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.156398 restraints weight = 100466.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.153512 restraints weight = 146405.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.151822 restraints weight = 141429.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.151296 restraints weight = 139262.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.150462 restraints weight = 127842.072| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.2730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 46248 Z= 0.132 Angle : 0.708 16.017 63004 Z= 0.343 Chirality : 0.048 0.334 7340 Planarity : 0.006 0.156 8004 Dihedral : 8.026 96.933 7592 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.33 % Favored : 90.48 % Rotamer: Outliers : 0.02 % Allowed : 0.40 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.11), residues: 5672 helix: 0.80 (0.18), residues: 816 sheet: -0.22 (0.13), residues: 1812 loop : -2.45 (0.10), residues: 3044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1000 TYR 0.036 0.001 TYR C 268 PHE 0.021 0.002 PHE B1072 TRP 0.045 0.001 TRP A 433 HIS 0.004 0.001 HIS B 506 Details of bonding type rmsd covalent geometry : bond 0.00307 (46144) covalent geometry : angle 0.67793 (62736) SS BOND : bond 0.00331 ( 32) SS BOND : angle 1.79393 ( 64) hydrogen bonds : bond 0.03074 ( 1487) hydrogen bonds : angle 5.29651 ( 4266) Misc. bond : bond 0.00195 ( 4) link_NAG-ASN : bond 0.00672 ( 68) link_NAG-ASN : angle 3.50273 ( 204) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11344 Ramachandran restraints generated. 5672 Oldfield, 0 Emsley, 5672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 453 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 452 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8318 (tmm) cc_final: 0.7918 (tmm) REVERT: A 430 TYR cc_start: 0.8191 (t80) cc_final: 0.7763 (t80) REVERT: A 457 ASP cc_start: 0.8218 (t0) cc_final: 0.7697 (t0) REVERT: A 1207 MET cc_start: 0.4859 (mmt) cc_final: 0.4401 (mmt) REVERT: A 1245 PHE cc_start: 0.6739 (t80) cc_final: 0.6471 (t80) REVERT: B 84 MET cc_start: 0.8218 (tmm) cc_final: 0.7660 (tmm) REVERT: B 430 TYR cc_start: 0.8294 (t80) cc_final: 0.7994 (t80) REVERT: B 446 MET cc_start: 0.8189 (mmm) cc_final: 0.7781 (mmm) REVERT: C 84 MET cc_start: 0.8040 (tmm) cc_final: 0.7577 (tmm) REVERT: C 131 TYR cc_start: 0.7517 (m-10) cc_final: 0.6897 (m-10) REVERT: C 430 TYR cc_start: 0.8278 (t80) cc_final: 0.8066 (t80) REVERT: C 991 VAL cc_start: 0.8948 (t) cc_final: 0.8615 (p) REVERT: D 377 MET cc_start: 0.8692 (mmm) cc_final: 0.7894 (mpp) REVERT: D 430 TYR cc_start: 0.8578 (t80) cc_final: 0.8271 (t80) REVERT: D 451 GLU cc_start: 0.6726 (pm20) cc_final: 0.6508 (pm20) REVERT: D 457 ASP cc_start: 0.8204 (t0) cc_final: 0.7662 (t0) REVERT: D 623 LEU cc_start: 0.7738 (mp) cc_final: 0.7351 (mt) REVERT: D 1001 GLN cc_start: 0.6338 (tm-30) cc_final: 0.6093 (tm-30) REVERT: D 1115 MET cc_start: 0.0362 (mmp) cc_final: 0.0155 (mmm) REVERT: D 1175 TYR cc_start: 0.6352 (t80) cc_final: 0.6104 (t80) REVERT: D 1375 ASN cc_start: 0.7312 (p0) cc_final: 0.6910 (p0) outliers start: 1 outliers final: 1 residues processed: 453 average time/residue: 0.2231 time to fit residues: 174.7018 Evaluate side-chains 341 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 340 time to evaluate : 1.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 568 random chunks: chunk 299 optimal weight: 0.9980 chunk 73 optimal weight: 2.9990 chunk 366 optimal weight: 40.0000 chunk 81 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 152 optimal weight: 0.7980 chunk 519 optimal weight: 30.0000 chunk 291 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 84 optimal weight: 40.0000 chunk 436 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN A1235 GLN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1001 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 GLN C 833 GLN C1001 GLN C1235 GLN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN D1378 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.175258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.157439 restraints weight = 100415.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.154452 restraints weight = 149800.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.152995 restraints weight = 142888.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.151883 restraints weight = 133087.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.150680 restraints weight = 141906.805| |-----------------------------------------------------------------------------| r_work (final): 0.4126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.2809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 46248 Z= 0.157 Angle : 0.717 15.322 63004 Z= 0.349 Chirality : 0.049 0.335 7340 Planarity : 0.006 0.153 8004 Dihedral : 8.010 95.359 7592 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.33 % Favored : 89.47 % Rotamer: Outliers : 0.02 % Allowed : 0.66 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.61 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.11), residues: 5672 helix: 0.83 (0.18), residues: 812 sheet: -0.25 (0.12), residues: 1852 loop : -2.44 (0.11), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A1000 TYR 0.021 0.001 TYR D 430 PHE 0.020 0.002 PHE C 780 TRP 0.049 0.001 TRP A 433 HIS 0.003 0.001 HIS B 443 Details of bonding type rmsd covalent geometry : bond 0.00374 (46144) covalent geometry : angle 0.68759 (62736) SS BOND : bond 0.00350 ( 32) SS BOND : angle 1.84175 ( 64) hydrogen bonds : bond 0.03189 ( 1487) hydrogen bonds : angle 5.32860 ( 4266) Misc. bond : bond 0.00191 ( 4) link_NAG-ASN : bond 0.00660 ( 68) link_NAG-ASN : angle 3.49768 ( 204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5854.37 seconds wall clock time: 103 minutes 34.19 seconds (6214.19 seconds total)