Starting phenix.real_space_refine on Tue Jul 7 06:34:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7s63_24848/07_2026/7s63_24848.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s63_24848/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7s63_24848/07_2026/7s63_24848.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s63_24848/07_2026/7s63_24848.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7s63_24848/07_2026/7s63_24848.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7s63_24848/07_2026/7s63_24848.cif" model { file = "/net/cci-nas-00/data/ceres_data/7s63_24848/07_2026/7s63_24848.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s63_24848/07_2026/7s63_24848.cif" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/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 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 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 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 chiralities: 17 Time building chain proxies: 9.46, per 1000 atoms: 0.21 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: 4.11 Conformation dependent library (CDL) restraints added in 2.1 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: 2.37 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: 14.14 Time building geometry restraints manager: 5.32 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 - 17.81: 24344 17.81 - 35.63: 2221 35.63 - 53.44: 387 53.44 - 71.25: 104 71.25 - 89.06: 60 Dihedral angle restraints: 27116 sinusoidal: 10564 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 27113 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: 0.03 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: 1.410 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: 0.060 Extract box with map and model: 0.510 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 44.620 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.110 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 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 : 14.550 89.063 16444 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/Z covalent geometry : bond 0.00430 / 0.20 (46144) covalent geometry : angle 0.78940 / 0.42 (62736) SS BOND : bond 0.00277 / 0.18 ( 32) SS BOND : angle 1.89074 / 1.21 ( 64) hydrogen bonds : bond 0.12719 / 8.25 ( 1487) hydrogen bonds : angle 6.38671 / 4.39 ( 4266) Misc. bond : bond 0.00122 / 0.06 ( 4) link_NAG-ASN : bond 0.00672 / 0.42 ( 68) link_NAG-ASN : angle 3.62353 / 2.37 ( 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 : 1.576 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: 0.2271 time to fit residues: 180.1072 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 : 1.721 ------------------------------------------------------------------------------- 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... ** 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 = 0.176786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.160149 restraints weight = 100561.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.157234 restraints weight = 145141.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.156017 restraints weight = 141126.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.154918 restraints weight = 142670.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.154269 restraints weight = 143405.706| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 46248 Z= 0.186 Angle : 0.706 12.318 63004 Z= 0.351 Chirality : 0.050 0.372 7340 Planarity : 0.006 0.140 8004 Dihedral : 5.443 50.926 6164 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.21 % Allowed : 9.89 % Favored : 89.90 % Rotamer: Outliers : 0.14 % Allowed : 7.01 % Favored : 92.85 % 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 0.018 0.001 ARG A 447 TYR 0.026 0.002 TYR C 540 PHE 0.019 0.002 PHE C 83 TRP 0.027 0.001 TRP B 433 HIS 0.005 0.001 HIS D 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.19 (46144) covalent geometry : angle 0.67511 / 0.34 (62736) SS BOND : bond 0.00980 / 0.45 ( 32) SS BOND : angle 1.51351 / 0.96 ( 64) hydrogen bonds : bond 0.03713 / 2.46 ( 1487) hydrogen bonds : angle 5.68229 / 3.92 ( 4266) Misc. bond : bond 0.00092 / 0.05 ( 4) link_NAG-ASN : bond 0.00693 / 0.42 ( 68) link_NAG-ASN : angle 3.59198 / 2.34 ( 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 462 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 455 time to evaluate : 1.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6806 (m-80) cc_final: 0.5419 (m-80) REVERT: A 457 ASP cc_start: 0.8230 (t0) cc_final: 0.7812 (t0) REVERT: A 750 THR cc_start: 0.6353 (p) cc_final: 0.6141 (p) REVERT: A 1337 ILE cc_start: 0.7620 (mt) cc_final: 0.7344 (mt) REVERT: B 126 MET cc_start: 0.8537 (tpp) cc_final: 0.8199 (tpp) REVERT: B 235 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7276 (pp) REVERT: B 446 MET cc_start: 0.8000 (mmm) cc_final: 0.7741 (mmm) REVERT: C 74 PRO cc_start: 0.6721 (OUTLIER) cc_final: 0.6497 (Cg_endo) REVERT: C 430 TYR cc_start: 0.8315 (t80) cc_final: 0.8087 (t80) REVERT: C 446 MET cc_start: 0.8367 (mmm) cc_final: 0.8049 (mmm) REVERT: C 451 GLU cc_start: 0.7079 (pp20) cc_final: 0.6754 (pp20) REVERT: C 1001 GLN cc_start: 0.7246 (pt0) cc_final: 0.6946 (tm-30) REVERT: C 1337 ILE cc_start: 0.8126 (mt) cc_final: 0.7735 (mt) REVERT: D 126 MET cc_start: 0.8517 (tpp) cc_final: 0.8196 (tpp) REVERT: D 277 LYS cc_start: 0.4683 (ptpp) cc_final: 0.3672 (ptpp) REVERT: D 430 TYR cc_start: 0.8345 (t80) cc_final: 0.8047 (t80) REVERT: D 457 ASP cc_start: 0.8183 (t0) cc_final: 0.7809 (t0) REVERT: D 478 ILE cc_start: 0.8848 (tp) cc_final: 0.8581 (tt) REVERT: D 484 MET cc_start: 0.7029 (ppp) cc_final: 0.6569 (ppp) REVERT: D 983 THR cc_start: 0.6236 (m) cc_final: 0.6010 (m) REVERT: D 1001 GLN cc_start: 0.5584 (tm-30) cc_final: 0.5370 (tm-30) outliers start: 7 outliers final: 2 residues processed: 462 average time/residue: 0.2396 time to fit residues: 188.3630 Evaluate side-chains 353 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 349 time to evaluate : 2.277 ------------------------------------------------------------------------------- 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: 10.0000 chunk 308 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 134 optimal weight: 10.0000 chunk 61 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 182 optimal weight: 3.9990 chunk 540 optimal weight: 2.9990 chunk 309 optimal weight: 0.6980 chunk 96 optimal weight: 10.0000 chunk 271 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.174750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.157268 restraints weight = 99458.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.153973 restraints weight = 136767.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.152542 restraints weight = 126074.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.151570 restraints weight = 129435.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.150169 restraints weight = 138810.123| |-----------------------------------------------------------------------------| r_work (final): 0.4122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.1340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 46248 Z= 0.202 Angle : 0.725 15.056 63004 Z= 0.358 Chirality : 0.051 0.521 7340 Planarity : 0.006 0.155 8004 Dihedral : 5.496 48.130 6164 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.21 % Allowed : 10.19 % Favored : 89.60 % Rotamer: Outliers : 0.02 % Allowed : 5.00 % Favored : 94.98 % 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: -1.84 (0.11), residues: 5672 helix: 1.06 (0.18), residues: 808 sheet: -0.32 (0.13), residues: 1828 loop : -2.56 (0.10), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 652 TYR 0.052 0.002 TYR A 268 PHE 0.018 0.002 PHE A 448 TRP 0.029 0.001 TRP B 433 HIS 0.006 0.001 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (46144) covalent geometry : angle 0.69662 / 0.35 (62736) SS BOND : bond 0.00399 / 0.29 ( 32) SS BOND : angle 1.41013 / 0.89 ( 64) hydrogen bonds : bond 0.03741 / 2.47 ( 1487) hydrogen bonds : angle 5.62448 / 3.87 ( 4266) Misc. bond : bond 0.00109 / 0.05 ( 4) link_NAG-ASN : bond 0.00766 / 0.51 ( 68) link_NAG-ASN : angle 3.55367 / 2.30 ( 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 461 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 460 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 131 TYR cc_start: 0.6718 (m-80) cc_final: 0.5420 (m-80) REVERT: A 457 ASP cc_start: 0.8447 (t0) cc_final: 0.7981 (t0) REVERT: A 750 THR cc_start: 0.6882 (p) cc_final: 0.6621 (p) REVERT: A 1207 MET cc_start: 0.5714 (mmt) cc_final: 0.5292 (mmt) REVERT: A 1337 ILE cc_start: 0.7734 (mt) cc_final: 0.7411 (mt) REVERT: B 126 MET cc_start: 0.8714 (tpp) cc_final: 0.8499 (tpp) REVERT: B 282 ILE cc_start: 0.8096 (tt) cc_final: 0.7882 (tt) REVERT: B 430 TYR cc_start: 0.8274 (t80) cc_final: 0.8047 (t80) REVERT: B 446 MET cc_start: 0.8123 (mmm) cc_final: 0.7858 (mmm) REVERT: B 1115 MET cc_start: 0.1186 (mmp) cc_final: 0.0942 (mmp) REVERT: B 1375 ASN cc_start: 0.7296 (p0) cc_final: 0.7046 (p0) REVERT: C 430 TYR cc_start: 0.8361 (t80) cc_final: 0.8079 (t80) REVERT: C 446 MET cc_start: 0.8284 (mmm) cc_final: 0.8079 (mmm) REVERT: C 457 ASP cc_start: 0.8396 (t0) cc_final: 0.8103 (t0) REVERT: C 550 ASP cc_start: 0.8355 (t70) cc_final: 0.8116 (t0) REVERT: C 1337 ILE cc_start: 0.7826 (mt) cc_final: 0.7514 (mt) REVERT: D 430 TYR cc_start: 0.8450 (t80) cc_final: 0.8086 (t80) REVERT: D 457 ASP cc_start: 0.8308 (t0) cc_final: 0.7818 (t0) REVERT: D 478 ILE cc_start: 0.8804 (tp) cc_final: 0.8562 (tt) REVERT: D 770 TYR cc_start: 0.6989 (m-80) cc_final: 0.6783 (m-80) REVERT: D 778 LEU cc_start: 0.8090 (tt) cc_final: 0.7829 (tt) REVERT: D 1001 GLN cc_start: 0.5958 (tm-30) cc_final: 0.5680 (tm-30) REVERT: D 1175 TYR cc_start: 0.6251 (t80) cc_final: 0.5976 (t80) outliers start: 1 outliers final: 0 residues processed: 461 average time/residue: 0.2300 time to fit residues: 178.3825 Evaluate side-chains 350 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 1.429 ------------------------------------------------------------------------------- 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: 9.9990 chunk 467 optimal weight: 0.0470 chunk 143 optimal weight: 3.9990 chunk 559 optimal weight: 7.9990 chunk 134 optimal weight: 20.0000 chunk 65 optimal weight: 0.0000 chunk 393 optimal weight: 2.9990 chunk 440 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 417 optimal weight: 20.0000 overall best weight: 1.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.176112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.157736 restraints weight = 100012.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.154441 restraints weight = 155280.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.153372 restraints weight = 147341.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.152560 restraints weight = 146857.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.151899 restraints weight = 122338.223| |-----------------------------------------------------------------------------| r_work (final): 0.4142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 46248 Z= 0.151 Angle : 0.685 12.951 63004 Z= 0.336 Chirality : 0.049 0.373 7340 Planarity : 0.006 0.142 8004 Dihedral : 5.316 47.620 6164 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.57 % Favored : 90.23 % Rotamer: Outliers : 0.06 % Allowed : 4.30 % Favored : 95.64 % 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: -1.83 (0.11), residues: 5672 helix: 0.98 (0.18), residues: 808 sheet: -0.30 (0.13), residues: 1836 loop : -2.55 (0.10), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1074 TYR 0.030 0.001 TYR A1122 PHE 0.020 0.002 PHE C 83 TRP 0.014 0.001 TRP A 433 HIS 0.003 0.001 HIS D 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.15 (46144) covalent geometry : angle 0.65560 / 0.33 (62736) SS BOND : bond 0.00247 / 0.15 ( 32) SS BOND : angle 1.30389 / 0.83 ( 64) hydrogen bonds : bond 0.03384 / 2.23 ( 1487) hydrogen bonds : angle 5.49453 / 3.79 ( 4266) Misc. bond : bond 0.00345 / 0.18 ( 4) link_NAG-ASN : bond 0.00681 / 0.42 ( 68) link_NAG-ASN : angle 3.52329 / 2.26 ( 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 : 1.444 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 457 ASP cc_start: 0.8322 (t0) cc_final: 0.7882 (t0) REVERT: A 750 THR cc_start: 0.6443 (p) cc_final: 0.6176 (p) REVERT: A 1337 ILE cc_start: 0.7703 (mt) cc_final: 0.7062 (mt) REVERT: B 282 ILE cc_start: 0.8019 (tt) cc_final: 0.7794 (tt) REVERT: B 446 MET cc_start: 0.8022 (mmm) cc_final: 0.7751 (mmm) REVERT: B 457 ASP cc_start: 0.8366 (t0) cc_final: 0.8127 (t0) REVERT: B 822 PHE cc_start: 0.4587 (p90) cc_final: 0.4198 (p90) REVERT: B 1073 MET cc_start: 0.5460 (mtt) cc_final: 0.5255 (mtt) REVERT: C 430 TYR cc_start: 0.8216 (t80) cc_final: 0.8015 (t80) REVERT: C 446 MET cc_start: 0.8218 (mmm) cc_final: 0.7982 (mmm) REVERT: C 457 ASP cc_start: 0.8098 (t0) cc_final: 0.7754 (t0) REVERT: C 1337 ILE cc_start: 0.7930 (mt) cc_final: 0.7613 (mt) REVERT: D 430 TYR cc_start: 0.8415 (t80) cc_final: 0.8018 (t80) REVERT: D 457 ASP cc_start: 0.8323 (t0) cc_final: 0.7832 (t0) REVERT: D 484 MET cc_start: 0.7236 (ppp) cc_final: 0.6332 (ppp) REVERT: D 778 LEU cc_start: 0.7891 (tt) cc_final: 0.7676 (tt) REVERT: D 1001 GLN cc_start: 0.5903 (tm-30) cc_final: 0.5689 (tm-30) REVERT: D 1175 TYR cc_start: 0.6276 (t80) cc_final: 0.5994 (t80) outliers start: 3 outliers final: 0 residues processed: 472 average time/residue: 0.2255 time to fit residues: 182.2518 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 : 1.301 ------------------------------------------------------------------------------- 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: 1.9990 chunk 279 optimal weight: 4.9990 chunk 545 optimal weight: 3.9990 chunk 449 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 124 optimal weight: 30.0000 chunk 558 optimal weight: 2.9990 chunk 519 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 518 optimal weight: 8.9990 chunk 416 optimal weight: 6.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 512 HIS A1235 GLN A1264 GLN A1387 ASN ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1049 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** D1141 ASN D1235 GLN D1378 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.173667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.156375 restraints weight = 99399.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.152799 restraints weight = 137365.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.151584 restraints weight = 137105.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.150433 restraints weight = 135594.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.149041 restraints weight = 142475.109| |-----------------------------------------------------------------------------| r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 46248 Z= 0.214 Angle : 0.740 13.068 63004 Z= 0.363 Chirality : 0.051 0.356 7340 Planarity : 0.006 0.145 8004 Dihedral : 5.590 49.527 6164 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.93 % Favored : 88.88 % Rotamer: Outliers : 0.06 % Allowed : 3.92 % Favored : 96.02 % 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: -1.90 (0.11), residues: 5672 helix: 0.97 (0.18), residues: 804 sheet: -0.34 (0.12), residues: 1832 loop : -2.61 (0.10), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1140 TYR 0.020 0.002 TYR C 48 PHE 0.031 0.002 PHE D 448 TRP 0.013 0.001 TRP C 433 HIS 0.005 0.001 HIS A 443 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.21 (46144) covalent geometry : angle 0.71162 / 0.36 (62736) SS BOND : bond 0.00315 / 0.19 ( 32) SS BOND : angle 1.61678 / 1.05 ( 64) hydrogen bonds : bond 0.03657 / 2.42 ( 1487) hydrogen bonds : angle 5.61073 / 3.87 ( 4266) Misc. bond : bond 0.00360 / 0.18 ( 4) link_NAG-ASN : bond 0.00662 / 0.41 ( 68) link_NAG-ASN : angle 3.52467 / 2.26 ( 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: 3 poor density : 455 time to evaluate : 1.493 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 430 TYR cc_start: 0.8294 (t80) cc_final: 0.8088 (t80) REVERT: A 1207 MET cc_start: 0.5540 (mmt) cc_final: 0.5230 (mmt) REVERT: A 1337 ILE cc_start: 0.7848 (mt) cc_final: 0.7551 (mt) REVERT: B 430 TYR cc_start: 0.8358 (t80) cc_final: 0.8044 (t80) REVERT: B 446 MET cc_start: 0.8172 (mmm) cc_final: 0.7861 (mmm) REVERT: B 822 PHE cc_start: 0.4578 (p90) cc_final: 0.4271 (p90) REVERT: B 1175 TYR cc_start: 0.6491 (t80) cc_final: 0.6119 (t80) REVERT: C 377 MET cc_start: 0.9032 (mmm) cc_final: 0.8188 (mpp) REVERT: C 430 TYR cc_start: 0.8333 (t80) cc_final: 0.7968 (t80) REVERT: C 446 MET cc_start: 0.8362 (mmm) cc_final: 0.8027 (mmm) REVERT: C 1337 ILE cc_start: 0.8162 (mt) cc_final: 0.7876 (mt) REVERT: D 430 TYR cc_start: 0.8510 (t80) cc_final: 0.8102 (t80) REVERT: D 457 ASP cc_start: 0.8302 (t0) cc_final: 0.7826 (t0) REVERT: D 550 ASP cc_start: 0.8240 (t0) cc_final: 0.8011 (t0) REVERT: D 778 LEU cc_start: 0.7922 (tt) cc_final: 0.7698 (tt) REVERT: D 1175 TYR cc_start: 0.6373 (t80) cc_final: 0.6100 (t80) outliers start: 3 outliers final: 0 residues processed: 457 average time/residue: 0.2287 time to fit residues: 179.4012 Evaluate side-chains 331 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 331 time to evaluate : 1.427 ------------------------------------------------------------------------------- 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: 0.9990 chunk 431 optimal weight: 0.7980 chunk 509 optimal weight: 20.0000 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: 0.0030 chunk 406 optimal weight: 10.0000 chunk 374 optimal weight: 30.0000 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 833 GLN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 ** 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.177097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.159348 restraints weight = 100156.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.156882 restraints weight = 154299.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.155314 restraints weight = 120351.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.153969 restraints weight = 128033.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.152739 restraints weight = 138681.177| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.1987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 46248 Z= 0.125 Angle : 0.683 14.996 63004 Z= 0.332 Chirality : 0.050 0.547 7340 Planarity : 0.006 0.152 8004 Dihedral : 5.193 47.306 6164 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.06 % Favored : 90.76 % Rotamer: Outliers : 0.02 % Allowed : 2.51 % Favored : 97.47 % 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: -1.78 (0.11), residues: 5672 helix: 0.97 (0.18), residues: 808 sheet: -0.24 (0.13), residues: 1836 loop : -2.52 (0.10), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A1000 TYR 0.027 0.001 TYR B1422 PHE 0.018 0.001 PHE B 444 TRP 0.016 0.001 TRP A 433 HIS 0.004 0.001 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (46144) covalent geometry : angle 0.65391 / 0.33 (62736) SS BOND : bond 0.00253 / 0.16 ( 32) SS BOND : angle 1.51364 / 0.97 ( 64) hydrogen bonds : bond 0.03151 / 2.08 ( 1487) hydrogen bonds : angle 5.40441 / 3.72 ( 4266) Misc. bond : bond 0.00259 / 0.13 ( 4) link_NAG-ASN : bond 0.00694 / 0.43 ( 68) link_NAG-ASN : angle 3.45935 / 2.23 ( 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: 1 poor density : 479 time to evaluate : 1.734 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: 0.7273 (m-80) cc_final: 0.5249 (m-80) REVERT: A 457 ASP cc_start: 0.8339 (t0) cc_final: 0.7816 (t0) REVERT: A 1245 PHE cc_start: 0.6837 (t80) cc_final: 0.6592 (t80) REVERT: A 1337 ILE cc_start: 0.7838 (mt) cc_final: 0.7327 (mt) REVERT: B 430 TYR cc_start: 0.8288 (t80) cc_final: 0.8040 (t80) REVERT: B 446 MET cc_start: 0.8190 (mmm) cc_final: 0.7786 (mmm) REVERT: B 457 ASP cc_start: 0.7945 (t0) cc_final: 0.7665 (t0) REVERT: B 822 PHE cc_start: 0.5196 (p90) cc_final: 0.4792 (p90) REVERT: B 1031 LYS cc_start: 0.6810 (tttt) cc_final: 0.6511 (tttt) REVERT: B 1175 TYR cc_start: 0.6509 (t80) cc_final: 0.6159 (t80) REVERT: C 377 MET cc_start: 0.8930 (mmm) cc_final: 0.7976 (mpp) REVERT: C 430 TYR cc_start: 0.8204 (t80) cc_final: 0.7886 (t80) REVERT: C 457 ASP cc_start: 0.8261 (t0) cc_final: 0.7719 (t0) REVERT: C 798 MET cc_start: 0.4614 (ppp) cc_final: 0.4295 (ppp) REVERT: C 822 PHE cc_start: 0.5448 (p90) cc_final: 0.4559 (p90) REVERT: C 991 VAL cc_start: 0.9060 (t) cc_final: 0.8724 (p) REVERT: D 307 MET cc_start: 0.6279 (mmp) cc_final: 0.5986 (mmp) REVERT: D 315 SER cc_start: 0.8643 (t) cc_final: 0.8160 (m) REVERT: D 430 TYR cc_start: 0.8501 (t80) cc_final: 0.8083 (t80) REVERT: D 457 ASP cc_start: 0.8238 (t0) cc_final: 0.7700 (t0) REVERT: D 1001 GLN cc_start: 0.6218 (tm-30) cc_final: 0.5871 (tm-30) REVERT: D 1175 TYR cc_start: 0.6394 (t80) cc_final: 0.6105 (t80) outliers start: 1 outliers final: 0 residues processed: 480 average time/residue: 0.2254 time to fit residues: 185.9495 Evaluate side-chains 341 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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: 30.0000 chunk 125 optimal weight: 30.0000 chunk 225 optimal weight: 1.9990 chunk 380 optimal weight: 10.0000 chunk 500 optimal weight: 5.9990 chunk 253 optimal weight: 20.0000 chunk 279 optimal weight: 0.9980 chunk 256 optimal weight: 20.0000 chunk 344 optimal weight: 0.0770 chunk 214 optimal weight: 8.9990 chunk 166 optimal weight: 0.6980 overall best weight: 1.9542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 B1264 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 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.174441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.155108 restraints weight = 99728.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.152976 restraints weight = 163517.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.151407 restraints weight = 160715.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.150279 restraints weight = 152173.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.148858 restraints weight = 154046.074| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 46248 Z= 0.165 Angle : 0.709 22.215 63004 Z= 0.345 Chirality : 0.050 0.419 7340 Planarity : 0.006 0.179 8004 Dihedral : 5.274 46.975 6164 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.21 % Favored : 89.60 % Rotamer: Outliers : 0.08 % Allowed : 2.47 % Favored : 97.45 % 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: -1.78 (0.11), residues: 5672 helix: 1.00 (0.18), residues: 808 sheet: -0.28 (0.13), residues: 1840 loop : -2.50 (0.10), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 683 TYR 0.025 0.001 TYR A 268 PHE 0.022 0.002 PHE C 83 TRP 0.015 0.001 TRP A 433 HIS 0.004 0.001 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (46144) covalent geometry : angle 0.68097 / 0.34 (62736) SS BOND : bond 0.00264 / 0.17 ( 32) SS BOND : angle 1.67452 / 1.04 ( 64) hydrogen bonds : bond 0.03310 / 2.18 ( 1487) hydrogen bonds : angle 5.41028 / 3.72 ( 4266) Misc. bond : bond 0.00238 / 0.12 ( 4) link_NAG-ASN : bond 0.00666 / 0.41 ( 68) link_NAG-ASN : angle 3.40400 / 2.20 ( 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 457 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 453 time to evaluate : 1.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 PRO cc_start: 0.6709 (OUTLIER) cc_final: 0.6445 (Cg_endo) REVERT: A 457 ASP cc_start: 0.8522 (t0) cc_final: 0.8060 (t0) REVERT: A 1245 PHE cc_start: 0.6824 (t80) cc_final: 0.6574 (t80) REVERT: A 1337 ILE cc_start: 0.7902 (mt) cc_final: 0.7597 (mt) REVERT: A 1359 MET cc_start: 0.6965 (mmm) cc_final: 0.6687 (mmm) REVERT: B 430 TYR cc_start: 0.8368 (t80) cc_final: 0.8082 (t80) REVERT: B 822 PHE cc_start: 0.5188 (p90) cc_final: 0.4860 (p90) REVERT: C 430 TYR cc_start: 0.8203 (t80) cc_final: 0.7849 (t80) REVERT: C 457 ASP cc_start: 0.8346 (t0) cc_final: 0.7870 (t0) REVERT: D 430 TYR cc_start: 0.8512 (t80) cc_final: 0.8130 (t80) REVERT: D 457 ASP cc_start: 0.8325 (t0) cc_final: 0.7756 (t0) REVERT: D 1001 GLN cc_start: 0.6234 (tm-30) cc_final: 0.5972 (tm-30) REVERT: D 1175 TYR cc_start: 0.6359 (t80) cc_final: 0.6061 (t80) outliers start: 4 outliers final: 0 residues processed: 457 average time/residue: 0.2246 time to fit residues: 176.6451 Evaluate side-chains 336 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 335 time to evaluate : 1.328 ------------------------------------------------------------------------------- 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: 4.9990 chunk 337 optimal weight: 1.9990 chunk 309 optimal weight: 5.9990 chunk 286 optimal weight: 0.9980 chunk 26 optimal weight: 9.9990 chunk 284 optimal weight: 0.7980 chunk 518 optimal weight: 0.0970 chunk 55 optimal weight: 20.0000 chunk 49 optimal weight: 2.9990 chunk 288 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.3782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 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** ** 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.176315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.158550 restraints weight = 100309.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.155543 restraints weight = 150660.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.153839 restraints weight = 138614.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.153130 restraints weight = 139287.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.151845 restraints weight = 134894.591| |-----------------------------------------------------------------------------| r_work (final): 0.4143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.2280 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= 0.142 Angle : 0.709 24.701 63004 Z= 0.341 Chirality : 0.049 0.374 7340 Planarity : 0.006 0.188 8004 Dihedral : 5.212 46.365 6164 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.68 % Favored : 90.14 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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: -1.72 (0.11), residues: 5672 helix: 1.00 (0.18), residues: 800 sheet: -0.24 (0.12), residues: 1856 loop : -2.45 (0.10), residues: 3016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A1000 TYR 0.038 0.001 TYR A 268 PHE 0.021 0.002 PHE C 83 TRP 0.018 0.001 TRP A 433 HIS 0.004 0.001 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (46144) covalent geometry : angle 0.68199 / 0.33 (62736) SS BOND : bond 0.00260 / 0.17 ( 32) SS BOND : angle 1.72882 / 1.12 ( 64) hydrogen bonds : bond 0.03180 / 2.09 ( 1487) hydrogen bonds : angle 5.34092 / 3.69 ( 4266) Misc. bond : bond 0.00197 / 0.10 ( 4) link_NAG-ASN : bond 0.00671 / 0.42 ( 68) link_NAG-ASN : angle 3.36023 / 2.16 ( 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 448 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 448 time to evaluate : 1.620 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: 0.8197 (tmm) cc_final: 0.7671 (tmm) REVERT: A 457 ASP cc_start: 0.8441 (t0) cc_final: 0.7933 (t0) REVERT: A 798 MET cc_start: 0.4574 (ppp) cc_final: 0.4299 (ppp) REVERT: A 1031 LYS cc_start: 0.7286 (mmtt) cc_final: 0.7025 (mmtt) REVERT: A 1337 ILE cc_start: 0.7871 (mt) cc_final: 0.7604 (mt) REVERT: B 430 TYR cc_start: 0.8369 (t80) cc_final: 0.8051 (t80) REVERT: B 822 PHE cc_start: 0.5194 (p90) cc_final: 0.4869 (p90) REVERT: C 131 TYR cc_start: 0.6773 (m-80) cc_final: 0.5081 (m-80) REVERT: C 430 TYR cc_start: 0.8226 (t80) cc_final: 0.7812 (t80) REVERT: C 457 ASP cc_start: 0.8207 (t0) cc_final: 0.7706 (t0) REVERT: C 991 VAL cc_start: 0.8967 (t) cc_final: 0.8663 (p) REVERT: D 430 TYR cc_start: 0.8477 (t80) cc_final: 0.8092 (t80) REVERT: D 457 ASP cc_start: 0.8392 (t0) cc_final: 0.7794 (t0) REVERT: D 1031 LYS cc_start: 0.7458 (mttm) cc_final: 0.7006 (mmtt) REVERT: D 1175 TYR cc_start: 0.6291 (t80) cc_final: 0.6006 (t80) outliers start: 0 outliers final: 0 residues processed: 448 average time/residue: 0.2220 time to fit residues: 172.4151 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 : 1.700 ------------------------------------------------------------------------------- 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: 5.9990 chunk 430 optimal weight: 0.0970 chunk 499 optimal weight: 0.8980 chunk 287 optimal weight: 0.9990 chunk 523 optimal weight: 5.9990 chunk 534 optimal weight: 8.9990 chunk 148 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 451 optimal weight: 3.9990 chunk 452 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 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 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1235 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.176758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.158755 restraints weight = 99925.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.156387 restraints weight = 153160.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.154937 restraints weight = 122565.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.154035 restraints weight = 125004.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.152821 restraints weight = 126362.101| |-----------------------------------------------------------------------------| r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 46248 Z= 0.128 Angle : 0.694 20.461 63004 Z= 0.333 Chirality : 0.049 0.354 7340 Planarity : 0.006 0.172 8004 Dihedral : 5.098 44.736 6164 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.38 % Favored : 90.46 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % 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: -1.67 (0.11), residues: 5672 helix: 1.04 (0.18), residues: 804 sheet: -0.22 (0.13), residues: 1856 loop : -2.41 (0.11), residues: 3012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG B1256 TYR 0.034 0.001 TYR A 268 PHE 0.020 0.001 PHE C 83 TRP 0.020 0.001 TRP A 433 HIS 0.004 0.001 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (46144) covalent geometry : angle 0.66764 / 0.33 (62736) SS BOND : bond 0.00286 / 0.19 ( 32) SS BOND : angle 1.71037 / 1.11 ( 64) hydrogen bonds : bond 0.03050 / 2.01 ( 1487) hydrogen bonds : angle 5.25100 / 3.62 ( 4266) Misc. bond : bond 0.00144 / 0.07 ( 4) link_NAG-ASN : bond 0.00674 / 0.42 ( 68) link_NAG-ASN : angle 3.28874 / 2.12 ( 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 461 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 461 time to evaluate : 1.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 84 MET cc_start: 0.8217 (tmm) cc_final: 0.7685 (tmm) REVERT: A 237 ASP cc_start: 0.5929 (p0) cc_final: 0.5692 (p0) REVERT: A 457 ASP cc_start: 0.8348 (t0) cc_final: 0.7860 (t0) REVERT: A 798 MET cc_start: 0.4861 (ppp) cc_final: 0.4641 (ppp) REVERT: A 1337 ILE cc_start: 0.7904 (mt) cc_final: 0.7437 (mt) REVERT: B 430 TYR cc_start: 0.8392 (t80) cc_final: 0.7939 (t80) REVERT: B 822 PHE cc_start: 0.5172 (p90) cc_final: 0.4936 (p90) REVERT: C 131 TYR cc_start: 0.6691 (m-80) cc_final: 0.5268 (m-80) REVERT: C 430 TYR cc_start: 0.8225 (t80) cc_final: 0.7789 (t80) REVERT: D 430 TYR cc_start: 0.8490 (t80) cc_final: 0.8101 (t80) REVERT: D 457 ASP cc_start: 0.8289 (t0) cc_final: 0.7762 (t0) REVERT: D 1031 LYS cc_start: 0.7638 (mttm) cc_final: 0.7416 (mmtt) REVERT: D 1033 PHE cc_start: 0.6517 (m-10) cc_final: 0.6224 (m-10) REVERT: D 1175 TYR cc_start: 0.6292 (t80) cc_final: 0.6001 (t80) outliers start: 0 outliers final: 0 residues processed: 461 average time/residue: 0.2194 time to fit residues: 175.8405 Evaluate side-chains 341 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 1.212 ------------------------------------------------------------------------------- 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: 0.0170 chunk 141 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 192 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 482 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 179 optimal weight: 4.9990 chunk 245 optimal weight: 20.0000 chunk 48 optimal weight: 0.6980 overall best weight: 2.5424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 50 GLN A1047 GLN ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1058 GLN A1235 GLN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1047 GLN B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 962 ASN C1001 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.174232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.155416 restraints weight = 100149.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.153213 restraints weight = 161515.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.151645 restraints weight = 137725.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.150939 restraints weight = 140053.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.149576 restraints weight = 138862.913| |-----------------------------------------------------------------------------| r_work (final): 0.4115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6943 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 46248 Z= 0.194 Angle : 0.747 18.186 63004 Z= 0.364 Chirality : 0.051 0.529 7340 Planarity : 0.006 0.164 8004 Dihedral : 5.422 47.626 6164 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.54 % Favored : 89.30 % Rotamer: Outliers : 0.02 % Allowed : 0.60 % Favored : 99.38 % 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: 0.92 (0.18), residues: 808 sheet: -0.26 (0.12), residues: 1848 loop : -2.45 (0.11), residues: 3016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1256 TYR 0.031 0.002 TYR A 268 PHE 0.027 0.002 PHE D 448 TRP 0.019 0.001 TRP A 433 HIS 0.005 0.001 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 (46144) covalent geometry : angle 0.72054 / 0.36 (62736) SS BOND : bond 0.00334 / 0.20 ( 32) SS BOND : angle 1.74361 / 1.11 ( 64) hydrogen bonds : bond 0.03433 / 2.25 ( 1487) hydrogen bonds : angle 5.42389 / 3.74 ( 4266) Misc. bond : bond 0.00205 / 0.10 ( 4) link_NAG-ASN : bond 0.00644 / 0.40 ( 68) link_NAG-ASN : angle 3.40022 / 2.22 ( 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 440 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 439 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.7069 (pp30) REVERT: A 84 MET cc_start: 0.8209 (tmm) cc_final: 0.7731 (tmm) REVERT: A 433 TRP cc_start: 0.7606 (p-90) cc_final: 0.7392 (p-90) REVERT: A 798 MET cc_start: 0.4619 (ppp) cc_final: 0.4399 (ppp) REVERT: A 1101 MET cc_start: 0.4399 (ptt) cc_final: 0.4173 (ptt) REVERT: A 1337 ILE cc_start: 0.8065 (mt) cc_final: 0.7816 (mt) REVERT: B 314 MET cc_start: 0.4990 (mmp) cc_final: 0.4752 (mmp) REVERT: B 430 TYR cc_start: 0.8433 (t80) cc_final: 0.7992 (t80) REVERT: B 822 PHE cc_start: 0.5060 (p90) cc_final: 0.4762 (p90) REVERT: B 954 MET cc_start: 0.4640 (tmm) cc_final: 0.4418 (tmm) REVERT: B 1031 LYS cc_start: 0.7297 (mttm) cc_final: 0.6890 (mmtt) REVERT: C 430 TYR cc_start: 0.8240 (t80) cc_final: 0.7847 (t80) REVERT: D 377 MET cc_start: 0.9043 (mmm) cc_final: 0.8253 (mpp) REVERT: D 430 TYR cc_start: 0.8490 (t80) cc_final: 0.8046 (t80) REVERT: D 457 ASP cc_start: 0.8352 (t0) cc_final: 0.7813 (t0) REVERT: D 1001 GLN cc_start: 0.7528 (pt0) cc_final: 0.6981 (tm-30) REVERT: D 1175 TYR cc_start: 0.6290 (t80) cc_final: 0.6009 (t80) outliers start: 1 outliers final: 0 residues processed: 440 average time/residue: 0.2252 time to fit residues: 171.4499 Evaluate side-chains 331 residues out of total 4976 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 330 time to evaluate : 1.503 ------------------------------------------------------------------------------- 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: 7.9990 chunk 73 optimal weight: 0.9980 chunk 366 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 152 optimal weight: 0.9980 chunk 519 optimal weight: 10.0000 chunk 291 optimal weight: 5.9990 chunk 187 optimal weight: 0.8980 chunk 84 optimal weight: 30.0000 chunk 436 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1049 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1235 GLN ** B 878 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1235 GLN ** C 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 ASN C 962 ASN ** 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** D1001 GLN D1235 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.176964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.161089 restraints weight = 100687.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.157764 restraints weight = 137636.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.156945 restraints weight = 139812.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.155439 restraints weight = 135750.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.154016 restraints weight = 147740.294| |-----------------------------------------------------------------------------| r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 46248 Z= 0.157 Angle : 0.716 16.783 63004 Z= 0.348 Chirality : 0.050 0.364 7340 Planarity : 0.006 0.159 8004 Dihedral : 5.334 48.636 6164 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 9.68 % Favored : 90.16 % Rotamer: Outliers : 0.02 % Allowed : 0.44 % Favored : 99.54 % 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: -1.70 (0.11), residues: 5672 helix: 1.02 (0.18), residues: 804 sheet: -0.23 (0.13), residues: 1852 loop : -2.44 (0.11), residues: 3016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1000 TYR 0.029 0.001 TYR A 247 PHE 0.030 0.002 PHE D 780 TRP 0.021 0.001 TRP A 433 HIS 0.004 0.001 HIS B 506 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (46144) covalent geometry : angle 0.69011 / 0.34 (62736) SS BOND : bond 0.00294 / 0.18 ( 32) SS BOND : angle 1.72303 / 1.11 ( 64) hydrogen bonds : bond 0.03217 / 2.12 ( 1487) hydrogen bonds : angle 5.35916 / 3.70 ( 4266) Misc. bond : bond 0.00186 / 0.09 ( 4) link_NAG-ASN : bond 0.00647 / 0.40 ( 68) link_NAG-ASN : angle 3.33881 / 2.17 ( 204) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5818.52 seconds wall clock time: 102 minutes 23.23 seconds (6143.23 seconds total)