Starting phenix.real_space_refine on Mon Dec 11 23:19:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk1_27480/12_2023/8dk1_27480.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk1_27480/12_2023/8dk1_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk1_27480/12_2023/8dk1_27480.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk1_27480/12_2023/8dk1_27480.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk1_27480/12_2023/8dk1_27480.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dk1_27480/12_2023/8dk1_27480.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 10.14, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.04 Conformation dependent library (CDL) restraints added in 3.6 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: 1.97 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: 5.97 Time building geometry restraints manager: 7.60 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: 99.74 - 106.59: 453 106.59 - 113.45: 11046 113.45 - 120.30: 7127 120.30 - 127.15: 7907 127.15 - 134.01: 207 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 2.440 nonbonded pdb=" O LEU A 93 " pdb=" OG1 THR A 104 " model vdw 2.296 2.440 nonbonded pdb=" OE2 GLU D 147 " pdb=" OH TYR D 194 " model vdw 2.298 2.440 nonbonded pdb=" OE2 GLU C 147 " pdb=" OH TYR C 194 " model vdw 2.304 2.440 nonbonded pdb=" OG SER C 133 " pdb=" OD2 ASP C 138 " model vdw 2.309 2.440 ... (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 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: 3.430 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: 0.010 Extract box with map and model: 12.500 Check model and map are aligned: 0.280 Set scattering table: 0.190 Process input model: 49.650 Find NCS groups from input model: 1.000 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.840 ------------------------------------------------------------------------------- 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= 0.157 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 *********************** 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 fitting. rotamer outliers: 30 poor density : 199 time to evaluate : 2.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 7 residues processed: 225 average time/residue: 1.7079 time to fit residues: 423.1256 Evaluate side-chains 99 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 92 time to evaluate : 2.324 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 3.1104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 0.2980 chunk 180 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 121 optimal weight: 9.9990 chunk 96 optimal weight: 0.6980 chunk 186 optimal weight: 6.9990 chunk 72 optimal weight: 3.9990 chunk 113 optimal weight: 5.9990 chunk 138 optimal weight: 0.7980 chunk 216 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 858 GLN D 858 GLN D 887 GLN E 110 GLN E 127 GLN E 130 ASN ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 233 GLN F 57 GLN F 80 ASN 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 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 GLN G 127 GLN G 130 ASN ** G 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 233 GLN H 57 GLN H 80 ASN 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: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 19792 Z= 0.162 Angle : 0.473 8.254 26740 Z= 0.242 Chirality : 0.038 0.155 3056 Planarity : 0.004 0.072 3488 Dihedral : 3.282 15.806 2718 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.92 % Allowed : 8.93 % Favored : 89.15 % 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: 2.33 (0.18), residues: 2390 helix: 2.90 (0.14), residues: 1448 sheet: 0.34 (0.34), residues: 250 loop : -1.06 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 128 HIS 0.004 0.001 HIS G 69 PHE 0.007 0.001 PHE A 247 TYR 0.016 0.001 TYR G 74 ARG 0.007 0.000 ARG E 75 *********************** 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 fitting. rotamer outliers: 40 poor density : 99 time to evaluate : 2.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 13 residues processed: 126 average time/residue: 1.3755 time to fit residues: 197.0618 Evaluate side-chains 94 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 81 time to evaluate : 2.488 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 12 residues processed: 1 average time/residue: 0.1695 time to fit residues: 3.3102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 chunk 179 optimal weight: 10.0000 chunk 147 optimal weight: 4.9990 chunk 59 optimal weight: 0.0770 chunk 216 optimal weight: 10.0000 chunk 233 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 214 optimal weight: 30.0000 chunk 73 optimal weight: 5.9990 chunk 173 optimal weight: 0.9990 overall best weight: 3.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 HIS ** G 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 19792 Z= 0.375 Angle : 0.538 8.061 26740 Z= 0.275 Chirality : 0.041 0.151 3056 Planarity : 0.004 0.039 3488 Dihedral : 3.471 16.171 2718 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.40 % Allowed : 8.74 % Favored : 88.86 % 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: 2.17 (0.18), residues: 2390 helix: 2.79 (0.14), residues: 1448 sheet: 0.24 (0.34), residues: 250 loop : -1.18 (0.22), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 119 HIS 0.003 0.001 HIS C1061 PHE 0.011 0.001 PHE B 250 TYR 0.014 0.001 TYR E 74 ARG 0.004 0.000 ARG E 125 *********************** 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 138 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 88 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 25 residues processed: 129 average time/residue: 1.2790 time to fit residues: 188.9771 Evaluate side-chains 107 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 82 time to evaluate : 2.252 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 20 residues processed: 5 average time/residue: 0.4081 time to fit residues: 5.9664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 213 optimal weight: 0.9990 chunk 162 optimal weight: 0.0870 chunk 112 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 217 optimal weight: 0.0980 chunk 230 optimal weight: 5.9990 chunk 113 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 196 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1773 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= 0.129 Angle : 0.447 9.056 26740 Z= 0.226 Chirality : 0.037 0.138 3056 Planarity : 0.003 0.038 3488 Dihedral : 3.274 15.750 2718 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.40 % Allowed : 9.32 % Favored : 88.28 % 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: 1452 sheet: 0.38 (0.35), residues: 230 loop : -1.07 (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 F 205 PHE 0.006 0.001 PHE C 221 TYR 0.016 0.001 TYR G 147 ARG 0.003 0.000 ARG E 125 *********************** 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 145 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 95 time to evaluate : 2.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 30 residues processed: 134 average time/residue: 1.2377 time to fit residues: 190.9276 Evaluate side-chains 113 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 83 time to evaluate : 2.194 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 26 residues processed: 4 average time/residue: 0.2579 time to fit residues: 4.6543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 0.0670 chunk 130 optimal weight: 8.9990 chunk 3 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 196 optimal weight: 0.9990 chunk 159 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 206 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 170 GLN ** G 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 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 : 0.005 0.043 19792 Z= 0.307 Angle : 0.507 8.625 26740 Z= 0.257 Chirality : 0.040 0.159 3056 Planarity : 0.004 0.040 3488 Dihedral : 3.376 14.977 2718 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.11 % Allowed : 10.04 % Favored : 87.85 % 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: 2.35 (0.18), residues: 2390 helix: 2.94 (0.14), residues: 1450 sheet: 0.40 (0.36), residues: 230 loop : -1.11 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 119 HIS 0.003 0.001 HIS C1061 PHE 0.022 0.001 PHE D 886 TYR 0.022 0.001 TYR G 147 ARG 0.004 0.000 ARG E 125 *********************** 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 130 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 86 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 32 residues processed: 123 average time/residue: 1.1061 time to fit residues: 158.7004 Evaluate side-chains 112 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 80 time to evaluate : 2.112 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 28 residues processed: 4 average time/residue: 0.4149 time to fit residues: 5.1414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 0.9990 chunk 207 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 chunk 230 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 120 optimal weight: 6.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 GLN E 149 GLN G 57 GLN ** G 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1882 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= 0.165 Angle : 0.456 8.950 26740 Z= 0.229 Chirality : 0.038 0.151 3056 Planarity : 0.003 0.036 3488 Dihedral : 3.283 15.302 2718 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.11 % Allowed : 10.47 % Favored : 87.42 % 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: 2.46 (0.18), residues: 2390 helix: 3.04 (0.14), residues: 1452 sheet: 0.40 (0.36), residues: 230 loop : -1.10 (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 C1045 PHE 0.021 0.001 PHE D 886 TYR 0.030 0.001 TYR G 74 ARG 0.004 0.000 ARG E 125 *********************** 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 133 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 89 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 30 residues processed: 128 average time/residue: 1.1665 time to fit residues: 173.2849 Evaluate side-chains 112 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 82 time to evaluate : 2.220 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 27 residues processed: 3 average time/residue: 0.5930 time to fit residues: 5.2837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 2.9990 chunk 25 optimal weight: 0.0060 chunk 131 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 193 optimal weight: 3.9990 chunk 128 optimal weight: 6.9990 chunk 229 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 139 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 HIS G 57 GLN ** G 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 19792 Z= 0.208 Angle : 0.476 9.858 26740 Z= 0.238 Chirality : 0.038 0.174 3056 Planarity : 0.004 0.036 3488 Dihedral : 3.281 15.058 2718 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.02 % Allowed : 10.61 % Favored : 87.37 % 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: 2.41 (0.18), residues: 2390 helix: 3.03 (0.14), residues: 1452 sheet: 0.31 (0.34), residues: 240 loop : -1.18 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 128 HIS 0.002 0.001 HIS D1061 PHE 0.020 0.001 PHE D 886 TYR 0.023 0.001 TYR G 74 ARG 0.003 0.000 ARG E 125 *********************** 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 127 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 85 time to evaluate : 2.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 33 residues processed: 123 average time/residue: 1.3146 time to fit residues: 185.1742 Evaluate side-chains 115 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 82 time to evaluate : 2.292 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 30 residues processed: 3 average time/residue: 0.9109 time to fit residues: 6.2527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 chunk 137 optimal weight: 0.0040 chunk 69 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 156 optimal weight: 2.9990 chunk 113 optimal weight: 0.5980 chunk 21 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 GLN G 57 GLN ** G 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.2072 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= 0.134 Angle : 0.457 9.353 26740 Z= 0.226 Chirality : 0.037 0.202 3056 Planarity : 0.003 0.035 3488 Dihedral : 3.170 15.422 2718 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.78 % Allowed : 10.90 % Favored : 87.32 % 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: 3.13 (0.14), residues: 1450 sheet: 0.39 (0.34), residues: 240 loop : -1.16 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 128 HIS 0.002 0.000 HIS H 216 PHE 0.020 0.001 PHE D 886 TYR 0.022 0.001 TYR G 74 ARG 0.004 0.000 ARG H 51 *********************** 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 123 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 86 time to evaluate : 2.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 29 residues processed: 120 average time/residue: 1.2044 time to fit residues: 166.9125 Evaluate side-chains 109 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 80 time to evaluate : 2.207 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 28 residues processed: 1 average time/residue: 0.3211 time to fit residues: 3.5905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 213 optimal weight: 0.0770 chunk 128 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 167 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 202 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 GLN G 57 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19792 Z= 0.194 Angle : 0.478 10.419 26740 Z= 0.238 Chirality : 0.038 0.239 3056 Planarity : 0.004 0.036 3488 Dihedral : 3.188 14.783 2718 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.63 % Allowed : 11.19 % Favored : 87.18 % 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: 3.13 (0.14), residues: 1452 sheet: 0.43 (0.35), residues: 240 loop : -1.14 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 128 HIS 0.002 0.000 HIS C1061 PHE 0.018 0.001 PHE D 886 TYR 0.020 0.001 TYR G 74 ARG 0.006 0.000 ARG G 125 *********************** 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 115 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 81 time to evaluate : 2.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 28 residues processed: 112 average time/residue: 1.0794 time to fit residues: 140.5038 Evaluate side-chains 107 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 79 time to evaluate : 2.035 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 28 residues processed: 0 time to fit residues: 2.6666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 157 optimal weight: 5.9990 chunk 237 optimal weight: 0.9980 chunk 218 optimal weight: 20.0000 chunk 188 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 145 optimal weight: 0.9980 chunk 115 optimal weight: 0.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 GLN G 57 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 19792 Z= 0.171 Angle : 0.476 12.095 26740 Z= 0.236 Chirality : 0.038 0.199 3056 Planarity : 0.003 0.035 3488 Dihedral : 3.170 14.925 2718 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.54 % Allowed : 11.38 % Favored : 87.08 % 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: 3.15 (0.14), residues: 1450 sheet: 0.44 (0.35), residues: 240 loop : -1.17 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 128 HIS 0.002 0.000 HIS C1061 PHE 0.018 0.001 PHE D 886 TYR 0.020 0.001 TYR G 74 ARG 0.006 0.000 ARG G 125 ********************** 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 112 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 80 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 30 residues processed: 110 average time/residue: 1.2216 time to fit residues: 155.4372 Evaluate side-chains 109 residues out of total 2088 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 79 time to evaluate : 2.298 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 28 residues processed: 2 average time/residue: 1.1547 time to fit residues: 5.9284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 201 optimal weight: 0.9980 chunk 57 optimal weight: 0.0370 chunk 174 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 52 optimal weight: 0.9980 chunk 189 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 194 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 GLN F 110 GLN G 57 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 170 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.093507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063304 restraints weight = 52615.262| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.48 r_work: 0.2939 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 19792 Z= 0.146 Angle : 0.483 12.858 26740 Z= 0.236 Chirality : 0.037 0.150 3056 Planarity : 0.003 0.036 3488 Dihedral : 3.113 14.960 2718 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.49 % Allowed : 11.48 % Favored : 87.03 % 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: 2.59 (0.18), residues: 2390 helix: 3.18 (0.14), residues: 1450 sheet: 0.47 (0.35), residues: 240 loop : -1.16 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 128 HIS 0.003 0.000 HIS G 196 PHE 0.018 0.001 PHE D 886 TYR 0.020 0.001 TYR G 74 ARG 0.006 0.000 ARG G 125 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4798.36 seconds wall clock time: 88 minutes 26.25 seconds (5306.25 seconds total)