Starting phenix.real_space_refine on Tue Jun 17 04:23:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dk1_27480/06_2025/8dk1_27480.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dk1_27480/06_2025/8dk1_27480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dk1_27480/06_2025/8dk1_27480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dk1_27480/06_2025/8dk1_27480.map" model { file = "/net/cci-nas-00/data/ceres_data/8dk1_27480/06_2025/8dk1_27480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dk1_27480/06_2025/8dk1_27480.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 44 5.16 5 C 12210 2.51 5 N 3622 2.21 5 O 3624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 19500 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2796 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 336} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 2796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 349, 2796 Classifications: {'peptide': 349} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 12, 'TRANS': 336} Chain breaks: 3 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 4035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4035 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 14, 'TRANS': 494} Chain breaks: 5 Chain: "D" Number of atoms: 4035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4035 Classifications: {'peptide': 509} Link IDs: {'PTRANS': 14, 'TRANS': 494} Chain breaks: 5 Chain: "E" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1413 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain breaks: 2 Chain: "F" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1506 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Chain: "G" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1413 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain breaks: 2 Chain: "H" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1506 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Time building chain proxies: 11.88, per 1000 atoms: 0.61 Number of scatterers: 19500 At special positions: 0 Unit cell: (183.96, 101.64, 138.6, 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 44 16.00 O 3624 8.00 N 3622 7.00 C 12210 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.58 Conformation dependent library (CDL) restraints added in 2.4 seconds 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4632 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 16 sheets defined 65.2% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.93 Creating SS restraints... Processing helix chain 'A' and resid 5 through 19 removed outlier: 3.852A pdb=" N SER A 9 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU A 10 " --> pdb=" O GLN A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 26 Processing helix chain 'A' and resid 29 through 41 Processing helix chain 'A' and resid 52 through 63 removed outlier: 3.847A pdb=" N ALA A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 104 through 116 removed outlier: 3.718A pdb=" N GLU A 108 " --> pdb=" O THR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 143 Processing helix chain 'A' and resid 148 through 170 removed outlier: 3.555A pdb=" N ALA A 170 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 193 Processing helix chain 'A' and resid 194 through 197 removed outlier: 3.533A pdb=" N ALA A 197 " --> pdb=" O SER A 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 194 through 197' Processing helix chain 'A' and resid 198 through 220 removed outlier: 3.665A pdb=" N VAL A 202 " --> pdb=" O ASP A 198 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU A 203 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 234 removed outlier: 3.793A pdb=" N VAL A 228 " --> pdb=" O ARG A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.501A pdb=" N VAL A 246 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG A 255 " --> pdb=" O GLN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 272 removed outlier: 3.508A pdb=" N LEU A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 272 " --> pdb=" O ARG A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 290 through 320 removed outlier: 3.908A pdb=" N VAL A 302 " --> pdb=" O GLU A 298 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN A 304 " --> pdb=" O GLN A 300 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 305 " --> pdb=" O ALA A 301 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 320 " --> pdb=" O PHE A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 339 Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 346 through 351 Processing helix chain 'B' and resid 6 through 19 removed outlier: 3.509A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 26 Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 52 through 63 removed outlier: 3.973A pdb=" N ALA B 63 " --> pdb=" O GLU B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 91 Processing helix chain 'B' and resid 104 through 116 removed outlier: 3.680A pdb=" N GLU B 108 " --> pdb=" O THR B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 143 Processing helix chain 'B' and resid 146 through 170 removed outlier: 3.559A pdb=" N ARG B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 170 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 193 Processing helix chain 'B' and resid 194 through 197 removed outlier: 3.531A pdb=" N ALA B 197 " --> pdb=" O SER B 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 194 through 197' Processing helix chain 'B' and resid 198 through 220 removed outlier: 3.678A pdb=" N VAL B 202 " --> pdb=" O ASP B 198 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N GLU B 203 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 234 removed outlier: 3.789A pdb=" N VAL B 228 " --> pdb=" O ARG B 224 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 removed outlier: 3.501A pdb=" N VAL B 246 " --> pdb=" O PRO B 242 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 255 " --> pdb=" O GLN B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 272 removed outlier: 3.507A pdb=" N LEU B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL B 262 " --> pdb=" O ALA B 258 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 272 " --> pdb=" O ARG B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 290 through 320 removed outlier: 3.908A pdb=" N VAL B 302 " --> pdb=" O GLU B 298 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLN B 304 " --> pdb=" O GLN B 300 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ALA B 305 " --> pdb=" O ALA B 301 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLY B 320 " --> pdb=" O PHE B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 339 Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 346 through 351 Processing helix chain 'C' and resid 48 through 59 removed outlier: 3.759A pdb=" N VAL C 53 " --> pdb=" O LYS C 49 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N LEU C 59 " --> pdb=" O ALA C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 86 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 152 through 164 Processing helix chain 'C' and resid 165 through 171 removed outlier: 3.798A pdb=" N MET C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 195 Processing helix chain 'C' and resid 200 through 208 Processing helix chain 'C' and resid 216 through 224 Processing helix chain 'C' and resid 231 through 274 removed outlier: 3.581A pdb=" N ALA C 235 " --> pdb=" O ALA C 231 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA C 236 " --> pdb=" O PHE C 232 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU C 237 " --> pdb=" O GLU C 233 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP C 247 " --> pdb=" O ASP C 243 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ILE C 248 " --> pdb=" O ASP C 244 " (cutoff:3.500A) Proline residue: C 264 - end of helix Processing helix chain 'C' and resid 793 through 808 removed outlier: 3.510A pdb=" N ALA C 807 " --> pdb=" O ASP C 803 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 835 Processing helix chain 'C' and resid 835 through 855 removed outlier: 3.589A pdb=" N GLU C 839 " --> pdb=" O GLU C 835 " (cutoff:3.500A) Processing helix chain 'C' and resid 855 through 882 removed outlier: 3.662A pdb=" N LEU C 859 " --> pdb=" O GLY C 855 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU C 860 " --> pdb=" O VAL C 856 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER C 861 " --> pdb=" O THR C 857 " (cutoff:3.500A) Processing helix chain 'C' and resid 901 through 917 Processing helix chain 'C' and resid 918 through 920 No H-bonds generated for 'chain 'C' and resid 918 through 920' Processing helix chain 'C' and resid 924 through 944 removed outlier: 3.685A pdb=" N ALA C 933 " --> pdb=" O LYS C 929 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU C 934 " --> pdb=" O ALA C 930 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N HIS C 944 " --> pdb=" O ASP C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 955 removed outlier: 3.638A pdb=" N LEU C 953 " --> pdb=" O GLY C 949 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU C 954 " --> pdb=" O ALA C 950 " (cutoff:3.500A) Processing helix chain 'C' and resid 956 through 958 No H-bonds generated for 'chain 'C' and resid 956 through 958' Processing helix chain 'C' and resid 989 through 1005 Processing helix chain 'C' and resid 1028 through 1043 removed outlier: 3.914A pdb=" N ARG C1034 " --> pdb=" O ALA C1030 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE C1035 " --> pdb=" O VAL C1031 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE C1036 " --> pdb=" O ALA C1032 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA C1037 " --> pdb=" O GLY C1033 " (cutoff:3.500A) Processing helix chain 'C' and resid 1057 through 1062 Processing helix chain 'D' and resid 48 through 59 removed outlier: 3.759A pdb=" N VAL D 53 " --> pdb=" O LYS D 49 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU D 59 " --> pdb=" O ALA D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 86 removed outlier: 3.520A pdb=" N TYR D 83 " --> pdb=" O ASP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 152 through 164 Processing helix chain 'D' and resid 165 through 170 Processing helix chain 'D' and resid 171 through 174 Processing helix chain 'D' and resid 183 through 195 Processing helix chain 'D' and resid 200 through 208 Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 231 through 274 removed outlier: 3.599A pdb=" N ALA D 235 " --> pdb=" O ALA D 231 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA D 236 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU D 237 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASP D 247 " --> pdb=" O ASP D 243 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE D 248 " --> pdb=" O ASP D 244 " (cutoff:3.500A) Proline residue: D 264 - end of helix Processing helix chain 'D' and resid 793 through 808 Processing helix chain 'D' and resid 818 through 820 No H-bonds generated for 'chain 'D' and resid 818 through 820' Processing helix chain 'D' and resid 821 through 835 Processing helix chain 'D' and resid 835 through 855 removed outlier: 3.611A pdb=" N GLU D 839 " --> pdb=" O GLU D 835 " (cutoff:3.500A) Processing helix chain 'D' and resid 855 through 881 removed outlier: 3.652A pdb=" N LEU D 859 " --> pdb=" O GLY D 855 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU D 860 " --> pdb=" O VAL D 856 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER D 861 " --> pdb=" O THR D 857 " (cutoff:3.500A) Processing helix chain 'D' and resid 901 through 917 Processing helix chain 'D' and resid 918 through 920 No H-bonds generated for 'chain 'D' and resid 918 through 920' Processing helix chain 'D' and resid 924 through 944 removed outlier: 3.682A pdb=" N ALA D 933 " --> pdb=" O LYS D 929 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 934 " --> pdb=" O ALA D 930 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS D 944 " --> pdb=" O ASP D 940 " (cutoff:3.500A) Processing helix chain 'D' and resid 947 through 955 removed outlier: 3.637A pdb=" N LEU D 953 " --> pdb=" O GLY D 949 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU D 954 " --> pdb=" O ALA D 950 " (cutoff:3.500A) Processing helix chain 'D' and resid 956 through 958 No H-bonds generated for 'chain 'D' and resid 956 through 958' Processing helix chain 'D' and resid 989 through 1005 Processing helix chain 'D' and resid 1028 through 1043 removed outlier: 3.902A pdb=" N ARG D1034 " --> pdb=" O ALA D1030 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE D1035 " --> pdb=" O VAL D1031 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALA D1037 " --> pdb=" O GLY D1033 " (cutoff:3.500A) Processing helix chain 'D' and resid 1057 through 1062 Processing helix chain 'E' and resid 49 through 63 Processing helix chain 'E' and resid 70 through 79 Processing helix chain 'E' and resid 80 through 89 Processing helix chain 'E' and resid 130 through 150 removed outlier: 4.075A pdb=" N LEU E 136 " --> pdb=" O GLU E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.791A pdb=" N ILE E 166 " --> pdb=" O VAL E 162 " (cutoff:3.500A) Proline residue: E 167 - end of helix removed outlier: 4.119A pdb=" N TYR E 172 " --> pdb=" O GLN E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 178 through 196 removed outlier: 3.571A pdb=" N HIS E 196 " --> pdb=" O GLN E 192 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 217 Processing helix chain 'E' and resid 219 through 236 Processing helix chain 'F' and resid 49 through 63 Processing helix chain 'F' and resid 70 through 79 Processing helix chain 'F' and resid 80 through 89 Processing helix chain 'F' and resid 130 through 150 removed outlier: 3.689A pdb=" N GLU F 150 " --> pdb=" O ALA F 146 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 Proline residue: F 167 - end of helix removed outlier: 4.001A pdb=" N TYR F 172 " --> pdb=" O GLN F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 195 removed outlier: 3.899A pdb=" N GLU F 182 " --> pdb=" O SER F 178 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY F 195 " --> pdb=" O ASP F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 217 Processing helix chain 'F' and resid 219 through 235 Processing helix chain 'G' and resid 49 through 63 Processing helix chain 'G' and resid 70 through 79 Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 130 through 150 removed outlier: 4.119A pdb=" N LEU G 136 " --> pdb=" O GLU G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 174 removed outlier: 3.769A pdb=" N ILE G 166 " --> pdb=" O VAL G 162 " (cutoff:3.500A) Proline residue: G 167 - end of helix removed outlier: 4.019A pdb=" N TYR G 172 " --> pdb=" O GLN G 168 " (cutoff:3.500A) Processing helix chain 'G' and resid 178 through 196 removed outlier: 3.528A pdb=" N HIS G 196 " --> pdb=" O GLN G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 217 Processing helix chain 'G' and resid 219 through 236 Processing helix chain 'H' and resid 49 through 63 Processing helix chain 'H' and resid 70 through 79 Processing helix chain 'H' and resid 80 through 89 Processing helix chain 'H' and resid 130 through 150 removed outlier: 3.689A pdb=" N GLU H 150 " --> pdb=" O ALA H 146 " (cutoff:3.500A) Processing helix chain 'H' and resid 162 through 174 Proline residue: H 167 - end of helix removed outlier: 4.000A pdb=" N TYR H 172 " --> pdb=" O GLN H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 178 through 195 removed outlier: 3.983A pdb=" N GLU H 182 " --> pdb=" O SER H 178 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY H 195 " --> pdb=" O ASP H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 217 Processing helix chain 'H' and resid 219 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 94 through 96 Processing sheet with id=AA2, first strand: chain 'B' and resid 94 through 96 Processing sheet with id=AA3, first strand: chain 'C' and resid 29 through 33 removed outlier: 6.934A pdb=" N THR C 113 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ILE C 18 " --> pdb=" O ALA C 111 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA C 111 " --> pdb=" O ILE C 18 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LEU C 20 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ALA C 109 " --> pdb=" O LEU C 20 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ALA C 119 " --> pdb=" O ARG C 116 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 1017 through 1021 removed outlier: 3.980A pdb=" N THR C 39 " --> pdb=" O ALA C1046 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR C1050 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N VAL C1066 " --> pdb=" O GLY C 38 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ALA C 40 " --> pdb=" O VAL C1066 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL C1068 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE C 42 " --> pdb=" O VAL C1068 " (cutoff:3.500A) removed outlier: 9.013A pdb=" N ARG C1070 " --> pdb=" O ILE C 42 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 893 through 898 Processing sheet with id=AA6, first strand: chain 'D' and resid 29 through 33 removed outlier: 6.925A pdb=" N THR D 113 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N ILE D 18 " --> pdb=" O ALA D 111 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA D 111 " --> pdb=" O ILE D 18 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LEU D 20 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N ALA D 109 " --> pdb=" O LEU D 20 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA D 119 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 1017 through 1021 removed outlier: 3.977A pdb=" N THR D 39 " --> pdb=" O ALA D1046 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N THR D1050 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N VAL D1066 " --> pdb=" O GLY D 38 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA D 40 " --> pdb=" O VAL D1066 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N VAL D1068 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N ILE D 42 " --> pdb=" O VAL D1068 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N ARG D1070 " --> pdb=" O ILE D 42 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU D1074 " --> pdb=" O ARG D1071 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 893 through 898 Processing sheet with id=AA9, first strand: chain 'E' and resid 64 through 66 Processing sheet with id=AB1, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.291A pdb=" N ALA E 158 " --> pdb=" O ILE E 210 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 64 through 66 Processing sheet with id=AB3, first strand: chain 'F' and resid 158 through 161 removed outlier: 4.733A pdb=" N ALA F 158 " --> pdb=" O ILE F 210 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 64 through 66 Processing sheet with id=AB5, first strand: chain 'G' and resid 158 through 161 removed outlier: 4.290A pdb=" N ALA G 158 " --> pdb=" O ILE G 210 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 64 through 66 Processing sheet with id=AB7, first strand: chain 'H' and resid 158 through 161 removed outlier: 4.730A pdb=" N ALA H 158 " --> pdb=" O ILE H 210 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3435 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: 5.99 Time building geometry restraints manager: 5.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 6808 1.34 - 1.46: 2728 1.46 - 1.57: 10178 1.57 - 1.69: 0 1.69 - 1.81: 78 Bond restraints: 19792 Sorted by residual: bond pdb=" CA ILE H 166 " pdb=" CB ILE H 166 " ideal model delta sigma weight residual 1.539 1.532 0.007 5.40e-03 3.43e+04 1.63e+00 bond pdb=" CA ILE F 166 " pdb=" CB ILE F 166 " ideal model delta sigma weight residual 1.539 1.533 0.006 5.40e-03 3.43e+04 1.17e+00 bond pdb=" CA VAL D 822 " pdb=" CB VAL D 822 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 9.74e-01 bond pdb=" CA VAL C 822 " pdb=" CB VAL C 822 " ideal model delta sigma weight residual 1.539 1.534 0.005 5.40e-03 3.43e+04 7.46e-01 bond pdb=" CA GLN D 263 " pdb=" C GLN D 263 " ideal model delta sigma weight residual 1.522 1.532 -0.011 1.26e-02 6.30e+03 7.18e-01 ... (remaining 19787 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 26217 1.16 - 2.33: 415 2.33 - 3.49: 76 3.49 - 4.66: 20 4.66 - 5.82: 12 Bond angle restraints: 26740 Sorted by residual: angle pdb=" C GLN F 116 " pdb=" N ASP F 117 " pdb=" CA ASP F 117 " ideal model delta sigma weight residual 121.54 126.94 -5.40 1.91e+00 2.74e-01 7.99e+00 angle pdb=" N VAL C 225 " pdb=" CA VAL C 225 " pdb=" C VAL C 225 " ideal model delta sigma weight residual 111.62 109.47 2.15 7.90e-01 1.60e+00 7.42e+00 angle pdb=" C GLN H 116 " pdb=" N ASP H 117 " pdb=" CA ASP H 117 " ideal model delta sigma weight residual 121.54 126.11 -4.57 1.91e+00 2.74e-01 5.71e+00 angle pdb=" C VAL A 114 " pdb=" N ASP A 115 " pdb=" CA ASP A 115 " ideal model delta sigma weight residual 122.38 118.39 3.99 1.81e+00 3.05e-01 4.86e+00 angle pdb=" C LEU C 224 " pdb=" N VAL C 225 " pdb=" CA VAL C 225 " ideal model delta sigma weight residual 123.16 120.87 2.29 1.06e+00 8.90e-01 4.66e+00 ... (remaining 26735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 11516 16.31 - 32.61: 501 32.61 - 48.92: 112 48.92 - 65.22: 15 65.22 - 81.53: 6 Dihedral angle restraints: 12150 sinusoidal: 5048 harmonic: 7102 Sorted by residual: dihedral pdb=" N LEU B 54 " pdb=" CA LEU B 54 " pdb=" CB LEU B 54 " pdb=" CG LEU B 54 " ideal model delta sinusoidal sigma weight residual -60.00 -118.75 58.75 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" N LEU A 85 " pdb=" CA LEU A 85 " pdb=" CB LEU A 85 " pdb=" CG LEU A 85 " ideal model delta sinusoidal sigma weight residual -60.00 -118.28 58.28 3 1.50e+01 4.44e-03 9.46e+00 dihedral pdb=" N ARG F 183 " pdb=" CA ARG F 183 " pdb=" CB ARG F 183 " pdb=" CG ARG F 183 " ideal model delta sinusoidal sigma weight residual -60.00 -117.68 57.68 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 12147 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1864 0.026 - 0.051: 696 0.051 - 0.077: 312 0.077 - 0.103: 116 0.103 - 0.129: 68 Chirality restraints: 3056 Sorted by residual: chirality pdb=" CA PRO H 220 " pdb=" N PRO H 220 " pdb=" C PRO H 220 " pdb=" CB PRO H 220 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA PRO F 220 " pdb=" N PRO F 220 " pdb=" C PRO F 220 " pdb=" CB PRO F 220 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.12 2.00e-01 2.50e+01 3.90e-01 chirality pdb=" CA VAL B 94 " pdb=" N VAL B 94 " pdb=" C VAL B 94 " pdb=" CB VAL B 94 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 3053 not shown) Planarity restraints: 3488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 366 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO A 367 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 367 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 367 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 357 " 0.022 5.00e-02 4.00e+02 3.40e-02 1.85e+00 pdb=" N PRO B 358 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 358 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 358 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP C 179 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO C 180 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 180 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 180 " -0.018 5.00e-02 4.00e+02 ... (remaining 3485 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 4963 2.82 - 3.34: 17809 3.34 - 3.86: 29525 3.86 - 4.38: 32661 4.38 - 4.90: 59821 Nonbonded interactions: 144779 Sorted by model distance: nonbonded pdb=" O LEU B 93 " pdb=" OG1 THR B 104 " model vdw 2.294 3.040 nonbonded pdb=" O LEU A 93 " pdb=" OG1 THR A 104 " model vdw 2.296 3.040 nonbonded pdb=" OE2 GLU D 147 " pdb=" OH TYR D 194 " model vdw 2.298 3.040 nonbonded pdb=" OE2 GLU C 147 " pdb=" OH TYR C 194 " model vdw 2.304 3.040 nonbonded pdb=" OG SER C 133 " pdb=" OD2 ASP C 138 " model vdw 2.309 3.040 ... (remaining 144774 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 48 through 110 or resid 120 through 151 or resid 156 throu \ gh 236)) selection = chain 'G' selection = (chain 'H' and (resid 48 through 110 or resid 120 through 151 or resid 156 throu \ gh 236)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.950 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: 0.020 Extract box with map and model: 0.820 Check model and map are aligned: 0.140 Set scattering table: 0.170 Process input model: 43.190 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:12.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 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 : 0.002 0.036 19792 Z= 0.110 Angle : 0.421 5.822 26740 Z= 0.227 Chirality : 0.038 0.129 3056 Planarity : 0.004 0.042 3488 Dihedral : 9.972 81.528 7518 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.44 % Allowed : 3.55 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.18), residues: 2390 helix: 2.68 (0.14), residues: 1428 sheet: 0.30 (0.34), residues: 250 loop : -0.93 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 128 HIS 0.002 0.001 HIS B 19 PHE 0.010 0.001 PHE A 250 TYR 0.010 0.001 TYR C 825 ARG 0.002 0.000 ARG B 286 Details of bonding type rmsd hydrogen bonds : bond 0.13017 ( 1176) hydrogen bonds : angle 4.81129 ( 3435) covalent geometry : bond 0.00238 (19792) covalent geometry : angle 0.42079 (26740) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 2.234 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: C 869 MET cc_start: 0.9033 (mmm) cc_final: 0.8819 (mmp) REVERT: D 171 MET cc_start: 0.9049 (mtm) cc_final: 0.8843 (mtp) REVERT: D 818 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8686 (mp0) REVERT: D 869 MET cc_start: 0.9021 (mmm) cc_final: 0.8804 (mmp) REVERT: E 147 TYR cc_start: 0.7115 (t80) cc_final: 0.6874 (t80) REVERT: F 92 ASP cc_start: 0.9118 (m-30) cc_final: 0.8805 (m-30) REVERT: F 178 SER cc_start: 0.8509 (t) cc_final: 0.8291 (p) REVERT: F 206 ASP cc_start: 0.8797 (t0) cc_final: 0.8556 (t0) REVERT: G 147 TYR cc_start: 0.7230 (t80) cc_final: 0.6972 (t80) REVERT: H 92 ASP cc_start: 0.9097 (m-30) cc_final: 0.8776 (m-30) REVERT: H 178 SER cc_start: 0.8560 (t) cc_final: 0.8357 (p) REVERT: H 206 ASP cc_start: 0.8791 (t0) cc_final: 0.8552 (t0) outliers start: 30 outliers final: 7 residues processed: 225 average time/residue: 1.7174 time to fit residues: 424.8032 Evaluate side-chains 105 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 98 time to evaluate : 2.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 916 SER Chi-restraints excluded: chain D residue 916 SER Chi-restraints excluded: chain E residue 168 GLN Chi-restraints excluded: chain F residue 117 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 5.9990 chunk 180 optimal weight: 20.0000 chunk 100 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 186 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 6.9990 chunk 138 optimal weight: 0.9990 chunk 216 optimal weight: 10.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 19 HIS A 80 GLN B 6 GLN B 19 HIS B 80 GLN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 858 GLN ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 858 GLN D 887 GLN E 57 GLN E 110 GLN E 127 GLN E 130 ASN E 170 GLN F 57 GLN F 110 GLN F 116 GLN F 127 GLN F 142 GLN F 149 GLN F 157 GLN F 168 GLN F 205 HIS G 57 GLN G 110 GLN G 127 GLN G 130 ASN H 57 GLN H 110 GLN H 116 GLN H 127 GLN H 142 GLN H 149 GLN H 157 GLN H 168 GLN H 205 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.088031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.057987 restraints weight = 52552.337| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.35 r_work: 0.2822 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 19792 Z= 0.201 Angle : 0.537 8.320 26740 Z= 0.277 Chirality : 0.041 0.153 3056 Planarity : 0.005 0.063 3488 Dihedral : 3.994 72.660 2731 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.87 % Allowed : 8.50 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.18), residues: 2390 helix: 2.77 (0.14), residues: 1440 sheet: 0.25 (0.34), residues: 250 loop : -1.08 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 119 HIS 0.004 0.001 HIS G 69 PHE 0.009 0.001 PHE C 187 TYR 0.019 0.001 TYR G 74 ARG 0.007 0.001 ARG E 75 Details of bonding type rmsd hydrogen bonds : bond 0.05270 ( 1176) hydrogen bonds : angle 4.10826 ( 3435) covalent geometry : bond 0.00484 (19792) covalent geometry : angle 0.53655 (26740) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 100 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 MET cc_start: 0.7263 (OUTLIER) cc_final: 0.7053 (mtp) REVERT: B 101 ILE cc_start: 0.7604 (OUTLIER) cc_final: 0.7156 (pp) REVERT: C 842 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9191 (ttpm) REVERT: C 869 MET cc_start: 0.9104 (mmm) cc_final: 0.8897 (mmp) REVERT: D 797 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7806 (tt) REVERT: D 827 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8196 (tm-30) REVERT: D 842 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9195 (ttpm) REVERT: D 869 MET cc_start: 0.9067 (mmm) cc_final: 0.8853 (mmp) REVERT: D 922 ASP cc_start: 0.8223 (m-30) cc_final: 0.8009 (m-30) REVERT: D 1053 LYS cc_start: 0.8301 (mptt) cc_final: 0.8081 (pmtt) REVERT: F 92 ASP cc_start: 0.9189 (m-30) cc_final: 0.8980 (m-30) REVERT: F 206 ASP cc_start: 0.8728 (t0) cc_final: 0.8381 (t0) REVERT: H 206 ASP cc_start: 0.8738 (t0) cc_final: 0.8395 (t0) outliers start: 39 outliers final: 10 residues processed: 129 average time/residue: 1.3164 time to fit residues: 193.2580 Evaluate side-chains 104 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 842 LYS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 842 LYS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 184 optimal weight: 6.9990 chunk 200 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 220 optimal weight: 3.9990 chunk 151 optimal weight: 0.0980 chunk 63 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 149 GLN F 80 ASN G 69 HIS H 80 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.090475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.060916 restraints weight = 52157.988| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.32 r_work: 0.2923 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 19792 Z= 0.105 Angle : 0.453 8.222 26740 Z= 0.232 Chirality : 0.038 0.146 3056 Planarity : 0.004 0.040 3488 Dihedral : 3.436 43.296 2720 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.39 % Allowed : 8.65 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.29 (0.18), residues: 2390 helix: 2.91 (0.14), residues: 1446 sheet: 0.24 (0.34), residues: 250 loop : -1.15 (0.22), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 128 HIS 0.003 0.000 HIS G 69 PHE 0.005 0.001 PHE D 195 TYR 0.022 0.001 TYR E 74 ARG 0.004 0.000 ARG H 51 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 1176) hydrogen bonds : angle 3.74874 ( 3435) covalent geometry : bond 0.00236 (19792) covalent geometry : angle 0.45300 (26740) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 102 time to evaluate : 2.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.7002 (ttt) REVERT: B 101 ILE cc_start: 0.7716 (OUTLIER) cc_final: 0.7423 (pp) REVERT: C 869 MET cc_start: 0.9101 (mmm) cc_final: 0.8876 (mmp) REVERT: D 869 MET cc_start: 0.9069 (mmm) cc_final: 0.8843 (mmp) REVERT: F 92 ASP cc_start: 0.9168 (m-30) cc_final: 0.8948 (m-30) REVERT: F 206 ASP cc_start: 0.8646 (t0) cc_final: 0.8281 (t0) REVERT: H 206 ASP cc_start: 0.8658 (t0) cc_final: 0.8303 (t0) outliers start: 29 outliers final: 10 residues processed: 126 average time/residue: 1.3152 time to fit residues: 188.9827 Evaluate side-chains 105 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain E residue 98 ASP Chi-restraints excluded: chain G residue 98 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 205 optimal weight: 9.9990 chunk 178 optimal weight: 2.9990 chunk 154 optimal weight: 5.9990 chunk 56 optimal weight: 0.2980 chunk 132 optimal weight: 0.6980 chunk 33 optimal weight: 9.9990 chunk 44 optimal weight: 5.9990 chunk 213 optimal weight: 8.9990 chunk 75 optimal weight: 0.1980 chunk 107 optimal weight: 1.9990 chunk 237 optimal weight: 0.4980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.093020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.063571 restraints weight = 52782.353| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.34 r_work: 0.2929 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19792 Z= 0.094 Angle : 0.449 8.805 26740 Z= 0.227 Chirality : 0.037 0.146 3056 Planarity : 0.003 0.040 3488 Dihedral : 3.311 40.207 2720 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.44 % Allowed : 9.32 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.18), residues: 2390 helix: 3.00 (0.14), residues: 1450 sheet: 0.36 (0.35), residues: 234 loop : -1.07 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 128 HIS 0.002 0.000 HIS G 69 PHE 0.023 0.001 PHE D 886 TYR 0.011 0.001 TYR E 74 ARG 0.005 0.000 ARG E 231 Details of bonding type rmsd hydrogen bonds : bond 0.03518 ( 1176) hydrogen bonds : angle 3.61912 ( 3435) covalent geometry : bond 0.00205 (19792) covalent geometry : angle 0.44915 (26740) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 96 time to evaluate : 2.202 Fit side-chains revert: symmetry clash REVERT: B 101 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7444 (pp) REVERT: C 869 MET cc_start: 0.9092 (mmm) cc_final: 0.8849 (mmp) REVERT: D 1080 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8940 (mm) REVERT: F 92 ASP cc_start: 0.9167 (m-30) cc_final: 0.8932 (m-30) REVERT: F 206 ASP cc_start: 0.8600 (t0) cc_final: 0.8243 (t0) REVERT: H 206 ASP cc_start: 0.8610 (t0) cc_final: 0.8259 (t0) outliers start: 30 outliers final: 15 residues processed: 119 average time/residue: 1.3023 time to fit residues: 177.8918 Evaluate side-chains 107 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 90 time to evaluate : 2.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 54 LEU Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 797 LEU Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 131 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 59 optimal weight: 5.9990 chunk 176 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 173 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 186 optimal weight: 6.9990 chunk 75 optimal weight: 0.9990 chunk 132 optimal weight: 0.9990 chunk 42 optimal weight: 5.9990 chunk 218 optimal weight: 9.9990 chunk 208 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.089995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.059279 restraints weight = 53188.373| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.47 r_work: 0.2848 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8866 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 19792 Z= 0.230 Angle : 0.543 8.541 26740 Z= 0.276 Chirality : 0.041 0.154 3056 Planarity : 0.004 0.038 3488 Dihedral : 3.601 43.827 2720 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.59 % Allowed : 9.89 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.24 (0.18), residues: 2390 helix: 2.83 (0.14), residues: 1450 sheet: 0.41 (0.35), residues: 236 loop : -1.15 (0.22), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 119 HIS 0.003 0.001 HIS D 249 PHE 0.018 0.001 PHE D 886 TYR 0.008 0.001 TYR D 928 ARG 0.011 0.000 ARG G 125 Details of bonding type rmsd hydrogen bonds : bond 0.05319 ( 1176) hydrogen bonds : angle 3.91095 ( 3435) covalent geometry : bond 0.00560 (19792) covalent geometry : angle 0.54255 (26740) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 2.536 Fit side-chains revert: symmetry clash REVERT: B 101 ILE cc_start: 0.7702 (OUTLIER) cc_final: 0.7324 (pp) REVERT: C 797 LEU cc_start: 0.7966 (OUTLIER) cc_final: 0.7645 (tt) REVERT: C 842 LYS cc_start: 0.9451 (OUTLIER) cc_final: 0.9239 (ttpm) REVERT: C 869 MET cc_start: 0.9138 (mmm) cc_final: 0.8936 (mmp) REVERT: C 1080 LEU cc_start: 0.9175 (mp) cc_final: 0.8959 (mm) REVERT: D 842 LYS cc_start: 0.9454 (OUTLIER) cc_final: 0.9241 (ttpm) REVERT: D 1080 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8970 (mm) REVERT: F 206 ASP cc_start: 0.8729 (t0) cc_final: 0.8321 (t0) REVERT: H 206 ASP cc_start: 0.8757 (t0) cc_final: 0.8318 (t0) outliers start: 33 outliers final: 14 residues processed: 112 average time/residue: 1.1704 time to fit residues: 151.5439 Evaluate side-chains 103 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 84 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 797 LEU Chi-restraints excluded: chain C residue 842 LYS Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 842 LYS Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 162 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 182 optimal weight: 10.0000 chunk 158 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 135 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 0.1980 chunk 163 optimal weight: 7.9990 chunk 173 optimal weight: 9.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN D 213 GLN D 215 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.092309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.061881 restraints weight = 52772.668| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 3.51 r_work: 0.2904 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19792 Z= 0.094 Angle : 0.454 9.122 26740 Z= 0.228 Chirality : 0.037 0.147 3056 Planarity : 0.003 0.034 3488 Dihedral : 3.392 42.072 2720 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.14 % Favored : 96.82 % Rotamer: Outliers : 1.39 % Allowed : 10.37 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.39 (0.18), residues: 2390 helix: 2.98 (0.14), residues: 1450 sheet: 0.45 (0.36), residues: 230 loop : -1.14 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 128 HIS 0.002 0.000 HIS E 143 PHE 0.019 0.001 PHE D 886 TYR 0.014 0.001 TYR G 147 ARG 0.005 0.000 ARG G 125 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 1176) hydrogen bonds : angle 3.59116 ( 3435) covalent geometry : bond 0.00209 (19792) covalent geometry : angle 0.45389 (26740) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 95 time to evaluate : 2.370 Fit side-chains revert: symmetry clash REVERT: B 101 ILE cc_start: 0.7809 (OUTLIER) cc_final: 0.7550 (pp) REVERT: C 801 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7727 (mpp) REVERT: C 869 MET cc_start: 0.9078 (mmm) cc_final: 0.8845 (mmp) REVERT: C 1080 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8925 (mm) REVERT: D 1080 LEU cc_start: 0.9140 (mp) cc_final: 0.8939 (mm) REVERT: F 92 ASP cc_start: 0.9189 (m-30) cc_final: 0.8918 (m-30) REVERT: F 206 ASP cc_start: 0.8720 (t0) cc_final: 0.8263 (t0) REVERT: H 206 ASP cc_start: 0.8779 (t0) cc_final: 0.8328 (t0) outliers start: 29 outliers final: 12 residues processed: 121 average time/residue: 1.2918 time to fit residues: 178.4829 Evaluate side-chains 102 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 2.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 916 SER Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 162 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 139 optimal weight: 0.8980 chunk 141 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 145 optimal weight: 4.9990 chunk 201 optimal weight: 0.8980 chunk 236 optimal weight: 0.5980 chunk 225 optimal weight: 2.9990 chunk 36 optimal weight: 0.0000 chunk 211 optimal weight: 10.0000 chunk 63 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN ** D 215 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.091178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.061721 restraints weight = 52346.503| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 3.21 r_work: 0.2945 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 19792 Z= 0.092 Angle : 0.459 9.224 26740 Z= 0.230 Chirality : 0.037 0.173 3056 Planarity : 0.003 0.035 3488 Dihedral : 3.270 38.007 2720 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 1.15 % Allowed : 11.34 % Favored : 87.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.50 (0.18), residues: 2390 helix: 3.07 (0.14), residues: 1450 sheet: 0.48 (0.36), residues: 234 loop : -1.10 (0.22), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 128 HIS 0.002 0.000 HIS G 143 PHE 0.018 0.001 PHE D 886 TYR 0.035 0.001 TYR E 147 ARG 0.005 0.000 ARG F 51 Details of bonding type rmsd hydrogen bonds : bond 0.03238 ( 1176) hydrogen bonds : angle 3.49975 ( 3435) covalent geometry : bond 0.00204 (19792) covalent geometry : angle 0.45891 (26740) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 2.231 Fit side-chains revert: symmetry clash REVERT: B 101 ILE cc_start: 0.7850 (OUTLIER) cc_final: 0.7597 (pp) REVERT: C 801 MET cc_start: 0.7981 (OUTLIER) cc_final: 0.7636 (mpp) REVERT: C 869 MET cc_start: 0.9102 (mmm) cc_final: 0.8856 (mmp) REVERT: D 801 MET cc_start: 0.7976 (OUTLIER) cc_final: 0.7676 (mpp) REVERT: F 206 ASP cc_start: 0.8648 (t0) cc_final: 0.8245 (t0) outliers start: 24 outliers final: 11 residues processed: 109 average time/residue: 1.2917 time to fit residues: 161.3005 Evaluate side-chains 98 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 2.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 801 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 162 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 23 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 5.9990 chunk 143 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 223 optimal weight: 0.9980 chunk 190 optimal weight: 0.9990 chunk 216 optimal weight: 10.0000 chunk 66 optimal weight: 0.2980 chunk 174 optimal weight: 0.1980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 216 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.092665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.062351 restraints weight = 52621.234| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 3.40 r_work: 0.2935 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 19792 Z= 0.091 Angle : 0.464 9.617 26740 Z= 0.230 Chirality : 0.037 0.216 3056 Planarity : 0.003 0.034 3488 Dihedral : 3.113 14.928 2718 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.47 % Favored : 96.49 % Rotamer: Outliers : 1.20 % Allowed : 11.14 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.53 (0.18), residues: 2390 helix: 3.09 (0.14), residues: 1448 sheet: 0.54 (0.36), residues: 234 loop : -1.09 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 128 HIS 0.002 0.000 HIS G 196 PHE 0.017 0.001 PHE D 886 TYR 0.010 0.001 TYR G 74 ARG 0.003 0.000 ARG F 51 Details of bonding type rmsd hydrogen bonds : bond 0.03075 ( 1176) hydrogen bonds : angle 3.47236 ( 3435) covalent geometry : bond 0.00205 (19792) covalent geometry : angle 0.46446 (26740) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 85 time to evaluate : 2.197 Fit side-chains revert: symmetry clash REVERT: A 28 ARG cc_start: 0.6986 (ttt180) cc_final: 0.6480 (ttp-170) REVERT: B 60 MET cc_start: 0.7682 (OUTLIER) cc_final: 0.7405 (tpp) REVERT: B 101 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7721 (pp) REVERT: B 159 GLN cc_start: 0.9374 (tt0) cc_final: 0.8842 (tm-30) REVERT: C 801 MET cc_start: 0.8009 (OUTLIER) cc_final: 0.7673 (mpp) REVERT: C 869 MET cc_start: 0.9090 (mmm) cc_final: 0.8844 (mmp) REVERT: D 801 MET cc_start: 0.7929 (OUTLIER) cc_final: 0.7673 (mpp) REVERT: G 59 MET cc_start: 0.9501 (ttm) cc_final: 0.9294 (ttm) outliers start: 25 outliers final: 14 residues processed: 105 average time/residue: 1.1686 time to fit residues: 141.7455 Evaluate side-chains 98 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 2.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 916 SER Chi-restraints excluded: chain C residue 1080 LEU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 801 MET Chi-restraints excluded: chain D residue 1080 LEU Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 162 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 205 optimal weight: 8.9990 chunk 148 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 98 optimal weight: 0.7980 chunk 123 optimal weight: 5.9990 chunk 155 optimal weight: 0.0970 chunk 135 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 211 optimal weight: 6.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.092130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.061555 restraints weight = 52622.042| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.51 r_work: 0.2921 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 19792 Z= 0.101 Angle : 0.473 10.472 26740 Z= 0.233 Chirality : 0.037 0.232 3056 Planarity : 0.003 0.035 3488 Dihedral : 3.112 14.715 2718 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.35 % Favored : 96.61 % Rotamer: Outliers : 1.01 % Allowed : 11.19 % Favored : 87.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.18), residues: 2390 helix: 3.13 (0.14), residues: 1448 sheet: 0.55 (0.36), residues: 234 loop : -1.09 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 128 HIS 0.002 0.000 HIS B 19 PHE 0.016 0.001 PHE D 886 TYR 0.010 0.001 TYR G 74 ARG 0.003 0.000 ARG F 51 Details of bonding type rmsd hydrogen bonds : bond 0.03312 ( 1176) hydrogen bonds : angle 3.47755 ( 3435) covalent geometry : bond 0.00237 (19792) covalent geometry : angle 0.47259 (26740) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 2.280 Fit side-chains revert: symmetry clash REVERT: B 101 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7693 (pp) REVERT: B 159 GLN cc_start: 0.9364 (tt0) cc_final: 0.8826 (tm-30) REVERT: C 801 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7655 (mpp) REVERT: C 869 MET cc_start: 0.9073 (mmm) cc_final: 0.8821 (mmp) REVERT: D 801 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7706 (mpp) outliers start: 21 outliers final: 13 residues processed: 102 average time/residue: 1.2377 time to fit residues: 145.7791 Evaluate side-chains 95 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 2.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 916 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 801 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 6 optimal weight: 2.9990 chunk 208 optimal weight: 6.9990 chunk 182 optimal weight: 0.7980 chunk 212 optimal weight: 30.0000 chunk 187 optimal weight: 1.9990 chunk 233 optimal weight: 0.0670 chunk 191 optimal weight: 8.9990 chunk 119 optimal weight: 0.1980 chunk 154 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.091892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.061234 restraints weight = 52515.920| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 3.55 r_work: 0.2927 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 19792 Z= 0.103 Angle : 0.482 12.273 26740 Z= 0.237 Chirality : 0.038 0.191 3056 Planarity : 0.003 0.034 3488 Dihedral : 3.114 14.813 2718 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.39 % Favored : 96.57 % Rotamer: Outliers : 0.96 % Allowed : 11.29 % Favored : 87.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.18), residues: 2390 helix: 3.11 (0.14), residues: 1448 sheet: 0.55 (0.36), residues: 234 loop : -1.08 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 128 HIS 0.002 0.000 HIS C1061 PHE 0.016 0.001 PHE D 886 TYR 0.009 0.001 TYR G 74 ARG 0.003 0.000 ARG F 51 Details of bonding type rmsd hydrogen bonds : bond 0.03310 ( 1176) hydrogen bonds : angle 3.48000 ( 3435) covalent geometry : bond 0.00244 (19792) covalent geometry : angle 0.48215 (26740) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4780 Ramachandran restraints generated. 2390 Oldfield, 0 Emsley, 2390 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 2.439 Fit side-chains revert: symmetry clash REVERT: B 60 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7333 (tpp) REVERT: B 101 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7694 (pp) REVERT: B 159 GLN cc_start: 0.9377 (tt0) cc_final: 0.8838 (tm-30) REVERT: C 801 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7663 (mpp) REVERT: C 869 MET cc_start: 0.9082 (mmm) cc_final: 0.8833 (mmp) REVERT: C 922 ASP cc_start: 0.8156 (t0) cc_final: 0.7840 (t0) REVERT: D 801 MET cc_start: 0.7934 (OUTLIER) cc_final: 0.7694 (mpp) outliers start: 20 outliers final: 13 residues processed: 98 average time/residue: 1.2572 time to fit residues: 141.6697 Evaluate side-chains 94 residues out of total 2088 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 2.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain B residue 60 MET Chi-restraints excluded: chain B residue 101 ILE Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain C residue 127 LEU Chi-restraints excluded: chain C residue 801 MET Chi-restraints excluded: chain C residue 884 VAL Chi-restraints excluded: chain C residue 916 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 801 MET Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 162 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 162 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 0.0870 chunk 135 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 216 optimal weight: 0.1980 chunk 112 optimal weight: 0.0670 chunk 99 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.091012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.060913 restraints weight = 52773.941| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 3.48 r_work: 0.2904 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 19792 Z= 0.086 Angle : 0.471 12.851 26740 Z= 0.230 Chirality : 0.037 0.223 3056 Planarity : 0.003 0.036 3488 Dihedral : 3.038 14.884 2718 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.22 % Favored : 96.74 % Rotamer: Outliers : 0.77 % Allowed : 11.53 % Favored : 87.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.61 (0.18), residues: 2390 helix: 3.15 (0.14), residues: 1448 sheet: 0.59 (0.36), residues: 234 loop : -1.05 (0.22), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 128 HIS 0.001 0.000 HIS B 19 PHE 0.017 0.001 PHE D 886 TYR 0.007 0.001 TYR G 74 ARG 0.003 0.000 ARG H 51 Details of bonding type rmsd hydrogen bonds : bond 0.02718 ( 1176) hydrogen bonds : angle 3.39752 ( 3435) covalent geometry : bond 0.00193 (19792) covalent geometry : angle 0.47123 (26740) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11833.96 seconds wall clock time: 202 minutes 8.79 seconds (12128.79 seconds total)