Starting phenix.real_space_refine on Thu Jan 15 04:53:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fw5_29497/01_2026/8fw5_29497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fw5_29497/01_2026/8fw5_29497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fw5_29497/01_2026/8fw5_29497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fw5_29497/01_2026/8fw5_29497.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fw5_29497/01_2026/8fw5_29497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fw5_29497/01_2026/8fw5_29497.map" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.009 sd= 0.125 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 4 5.49 5 Mg 1 5.21 5 S 120 5.16 5 C 14608 2.51 5 N 3845 2.21 5 O 4271 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22853 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 8488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1036, 8488 Classifications: {'peptide': 1036} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 42, 'TRANS': 993} Chain breaks: 10 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2928 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Chain: "C" Number of atoms: 3198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 400, 3198 Classifications: {'peptide': 400} Link IDs: {'PTRANS': 20, 'TRANS': 379} Chain breaks: 5 Chain: "D" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2409 Classifications: {'peptide': 301} Link IDs: {'PTRANS': 6, 'TRANS': 294} Chain: "E" Number of atoms: 2275 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2275 Classifications: {'peptide': 285} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Chain: "F" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 757 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "G" Number of atoms: 1225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 1225 Classifications: {'peptide': 160} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 152} Chain: "H" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 886 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "I" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 626 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 5 Unusual residues: {' MG': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.60, per 1000 atoms: 0.20 Number of scatterers: 22853 At special positions: 0 Unit cell: (112.88, 151.89, 195.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 120 16.00 P 4 15.00 Al 1 13.00 Mg 1 11.99 F 3 9.00 O 4271 8.00 N 3845 7.00 C 14608 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: 1.69 Conformation dependent library (CDL) restraints added in 1.1 seconds 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5446 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 24 sheets defined 40.9% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 71 through 77 Processing helix chain 'A' and resid 110 through 121 Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.741A pdb=" N TRP A 182 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 211 removed outlier: 3.708A pdb=" N LEU A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N ALA A 201 " --> pdb=" O ASN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 268 No H-bonds generated for 'chain 'A' and resid 266 through 268' Processing helix chain 'A' and resid 269 through 280 removed outlier: 4.569A pdb=" N THR A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N GLN A 280 " --> pdb=" O LYS A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 285 Processing helix chain 'A' and resid 305 through 319 removed outlier: 4.063A pdb=" N LYS A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.854A pdb=" N ASP A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN A 360 " --> pdb=" O ARG A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 659 through 670 Processing helix chain 'A' and resid 743 through 749 Processing helix chain 'A' and resid 762 through 769 removed outlier: 3.605A pdb=" N ASP A 769 " --> pdb=" O GLY A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 810 removed outlier: 3.750A pdb=" N GLN A 809 " --> pdb=" O GLN A 805 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLY A 810 " --> pdb=" O ARG A 806 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 927 Processing helix chain 'A' and resid 931 through 940 removed outlier: 4.218A pdb=" N SER A 934 " --> pdb=" O GLU A 931 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLU A 937 " --> pdb=" O SER A 934 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N SER A 938 " --> pdb=" O LEU A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 962 Processing helix chain 'A' and resid 978 through 994 removed outlier: 3.621A pdb=" N LEU A 982 " --> pdb=" O ASP A 978 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 983 " --> pdb=" O GLU A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1185 Processing helix chain 'A' and resid 1207 through 1217 removed outlier: 3.589A pdb=" N ASN A1216 " --> pdb=" O HIS A1212 " (cutoff:3.500A) Processing helix chain 'A' and resid 1223 through 1237 removed outlier: 3.707A pdb=" N ALA A1227 " --> pdb=" O THR A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1394 through 1412 Processing helix chain 'A' and resid 1464 through 1480 Processing helix chain 'A' and resid 1567 through 1581 removed outlier: 3.508A pdb=" N ARG A1571 " --> pdb=" O LYS A1567 " (cutoff:3.500A) Processing helix chain 'A' and resid 1582 through 1584 No H-bonds generated for 'chain 'A' and resid 1582 through 1584' Processing helix chain 'A' and resid 1585 through 1596 removed outlier: 3.785A pdb=" N SER A1593 " --> pdb=" O THR A1589 " (cutoff:3.500A) Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 98 through 117 Processing helix chain 'B' and resid 121 through 126 removed outlier: 3.756A pdb=" N GLN B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 141 removed outlier: 3.813A pdb=" N ASN B 140 " --> pdb=" O LEU B 136 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 185 through 189 removed outlier: 3.532A pdb=" N GLN B 188 " --> pdb=" O PHE B 185 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N TRP B 189 " --> pdb=" O ASN B 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 185 through 189' Processing helix chain 'B' and resid 190 through 197 Processing helix chain 'B' and resid 198 through 200 No H-bonds generated for 'chain 'B' and resid 198 through 200' Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 216 through 230 Processing helix chain 'B' and resid 251 through 256 removed outlier: 3.836A pdb=" N VAL B 255 " --> pdb=" O VAL B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 268 Processing helix chain 'B' and resid 277 through 287 removed outlier: 3.514A pdb=" N VAL B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 301 Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 361 through 370 Processing helix chain 'C' and resid 65 through 74 removed outlier: 3.549A pdb=" N ALA C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 removed outlier: 3.599A pdb=" N CYS C 80 " --> pdb=" O SER C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 135 through 161 Processing helix chain 'C' and resid 161 through 173 removed outlier: 3.530A pdb=" N LEU C 173 " --> pdb=" O LEU C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 3.669A pdb=" N LYS C 197 " --> pdb=" O HIS C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 213 Processing helix chain 'C' and resid 266 through 274 Processing helix chain 'C' and resid 279 through 289 removed outlier: 3.554A pdb=" N VAL C 283 " --> pdb=" O SER C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 302 Processing helix chain 'C' and resid 305 through 319 removed outlier: 3.557A pdb=" N TRP C 319 " --> pdb=" O HIS C 315 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 356 Processing helix chain 'C' and resid 360 through 368 Processing helix chain 'C' and resid 374 through 378 removed outlier: 3.728A pdb=" N ARG C 378 " --> pdb=" O LEU C 374 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 374 through 378' Processing helix chain 'C' and resid 383 through 400 Processing helix chain 'C' and resid 481 through 488 Processing helix chain 'C' and resid 491 through 501 removed outlier: 3.547A pdb=" N VAL C 501 " --> pdb=" O ALA C 497 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 506 through 516 removed outlier: 3.768A pdb=" N LEU C 510 " --> pdb=" O ASN C 506 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ARG C 511 " --> pdb=" O PRO C 507 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) Processing helix chain 'C' and resid 525 through 533 Processing helix chain 'C' and resid 536 through 547 removed outlier: 3.620A pdb=" N LEU C 540 " --> pdb=" O ARG C 536 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 23 Processing helix chain 'D' and resid 28 through 34 removed outlier: 3.575A pdb=" N THR D 31 " --> pdb=" O ALA D 28 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG D 32 " --> pdb=" O LYS D 29 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG D 33 " --> pdb=" O ASP D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 69 removed outlier: 3.572A pdb=" N ASN D 67 " --> pdb=" O ALA D 63 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU D 69 " --> pdb=" O MET D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 77 Processing helix chain 'D' and resid 93 through 112 removed outlier: 3.670A pdb=" N VAL D 99 " --> pdb=" O GLU D 95 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR D 100 " --> pdb=" O ARG D 96 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 127 Processing helix chain 'D' and resid 128 through 132 Processing helix chain 'D' and resid 135 through 147 removed outlier: 3.702A pdb=" N ILE D 142 " --> pdb=" O GLU D 138 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 176 removed outlier: 4.047A pdb=" N THR D 174 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU D 175 " --> pdb=" O ILE D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 178 through 193 Processing helix chain 'D' and resid 223 through 242 removed outlier: 3.680A pdb=" N LYS D 227 " --> pdb=" O HIS D 223 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 279 through 301 removed outlier: 3.706A pdb=" N THR D 283 " --> pdb=" O GLU D 279 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET D 285 " --> pdb=" O ALA D 281 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLN D 288 " --> pdb=" O LEU D 284 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ALA D 290 " --> pdb=" O ASN D 286 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA D 300 " --> pdb=" O ALA D 296 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 23 Processing helix chain 'E' and resid 69 through 76 removed outlier: 3.514A pdb=" N THR E 75 " --> pdb=" O GLU E 71 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN E 76 " --> pdb=" O SER E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 108 Processing helix chain 'E' and resid 124 through 147 removed outlier: 3.987A pdb=" N ILE E 129 " --> pdb=" O ASP E 125 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASP E 130 " --> pdb=" O GLU E 126 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP E 141 " --> pdb=" O GLN E 137 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU E 142 " --> pdb=" O ARG E 138 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA E 144 " --> pdb=" O GLN E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 177 removed outlier: 3.714A pdb=" N LYS E 175 " --> pdb=" O ARG E 171 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N LEU E 176 " --> pdb=" O VAL E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 195 Processing helix chain 'E' and resid 218 through 240 removed outlier: 3.745A pdb=" N ILE E 224 " --> pdb=" O GLN E 220 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE E 229 " --> pdb=" O CYS E 225 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP E 230 " --> pdb=" O SER E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 291 through 310 removed outlier: 3.662A pdb=" N ILE E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 60 Processing helix chain 'F' and resid 81 through 88 removed outlier: 4.026A pdb=" N GLU F 85 " --> pdb=" O ASN F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 125 removed outlier: 3.629A pdb=" N GLY F 117 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL F 118 " --> pdb=" O ARG F 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 13 removed outlier: 4.082A pdb=" N GLN G 13 " --> pdb=" O SER G 9 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 68 removed outlier: 3.845A pdb=" N LEU G 49 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASN G 62 " --> pdb=" O ALA G 58 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N TYR G 67 " --> pdb=" O MET G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 76 removed outlier: 3.766A pdb=" N VAL G 76 " --> pdb=" O SER G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 86 Processing helix chain 'G' and resid 134 through 153 removed outlier: 3.725A pdb=" N ASN G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 154 through 156 No H-bonds generated for 'chain 'G' and resid 154 through 156' Processing helix chain 'H' and resid 2 through 10 Processing helix chain 'H' and resid 38 through 54 removed outlier: 3.590A pdb=" N GLN H 42 " --> pdb=" O THR H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 57 No H-bonds generated for 'chain 'H' and resid 55 through 57' Processing helix chain 'H' and resid 96 through 101 removed outlier: 3.547A pdb=" N LEU H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG H 101 " --> pdb=" O HIS H 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 96 through 101' Processing helix chain 'H' and resid 103 through 117 removed outlier: 3.683A pdb=" N SER H 107 " --> pdb=" O ALA H 103 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N VAL H 113 " --> pdb=" O ALA H 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 13 Processing helix chain 'I' and resid 40 through 45 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.503A pdb=" N LYS A 8 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL A 69 " --> pdb=" O LYS A 8 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N VAL A 10 " --> pdb=" O VAL A 69 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ILE A 38 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 131 through 134 removed outlier: 4.393A pdb=" N LEU A 144 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 131 through 134 removed outlier: 5.881A pdb=" N ALA A 141 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR A 103 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU A 143 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU A 99 " --> pdb=" O TRP A 145 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 242 through 244 removed outlier: 4.089A pdb=" N PHE A 250 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL A 218 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N MET A 170 " --> pdb=" O MET A 332 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N VAL A 334 " --> pdb=" O MET A 170 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR A 172 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N ILE A 336 " --> pdb=" O TYR A 172 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE A 174 " --> pdb=" O ILE A 336 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N VAL A 364 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N SER A 333 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N LEU A 366 " --> pdb=" O SER A 333 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VAL A 335 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 406 " --> pdb=" O ASP A 365 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 297 through 298 removed outlier: 6.637A pdb=" N VAL A 218 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N PHE A 250 " --> pdb=" O TYR A 226 " (cutoff:3.500A) removed outlier: 9.253A pdb=" N TYR A 251 " --> pdb=" O THR A 889 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N SER A 891 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N ASP A 253 " --> pdb=" O SER A 891 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N CYS A 893 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR A 255 " --> pdb=" O CYS A 893 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 342 through 344 removed outlier: 6.558A pdb=" N PHE A 343 " --> pdb=" O LYS A 381 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 756 through 757 removed outlier: 4.591A pdb=" N TRP A 853 " --> pdb=" O ILE A 814 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1351 through 1357 removed outlier: 6.564A pdb=" N GLU A1385 " --> pdb=" O HIS A1375 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ARG A 945 " --> pdb=" O VAL A1419 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1204 through 1206 Processing sheet with id=AB1, first strand: chain 'A' and resid 1254 through 1255 removed outlier: 6.739A pdb=" N ALA A1297 " --> pdb=" O PHE A1378 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1439 through 1442 removed outlier: 6.006A pdb=" N VAL A1509 " --> pdb=" O HIS A1504 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLN A1501 " --> pdb=" O ASP A1485 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 21 through 26 removed outlier: 5.366A pdb=" N ILE B 23 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU B 14 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 25 " --> pdb=" O PHE B 12 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLU C 85 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER C 9 " --> pdb=" O ALA C 129 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N VAL C 10 " --> pdb=" O ARG C 25 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N ARG C 25 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N LEU C 12 " --> pdb=" O LEU C 23 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 21 through 26 removed outlier: 5.366A pdb=" N ILE B 23 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU B 14 " --> pdb=" O ILE B 23 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR B 25 " --> pdb=" O PHE B 12 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N GLU C 85 " --> pdb=" O THR B 58 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 144 through 148 Processing sheet with id=AB6, first strand: chain 'B' and resid 174 through 177 Processing sheet with id=AB7, first strand: chain 'B' and resid 244 through 247 removed outlier: 4.433A pdb=" N VAL B 244 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN B 327 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 260 through 263 Processing sheet with id=AB9, first strand: chain 'C' and resid 372 through 373 removed outlier: 3.613A pdb=" N VAL C 372 " --> pdb=" O TYR C 334 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL C 333 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 40 through 46 removed outlier: 6.429A pdb=" N LYS D 3 " --> pdb=" O ASN D 54 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N TRP D 56 " --> pdb=" O LYS D 3 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N VAL D 5 " --> pdb=" O TRP D 56 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N CYS D 58 " --> pdb=" O VAL D 5 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LEU D 7 " --> pdb=" O CYS D 58 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N VAL D 82 " --> pdb=" O ARG D 2 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LYS D 4 " --> pdb=" O VAL D 82 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N ILE D 84 " --> pdb=" O LYS D 4 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N LEU D 6 " --> pdb=" O ILE D 84 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL D 86 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N MET D 8 " --> pdb=" O VAL D 86 " (cutoff:3.500A) removed outlier: 8.472A pdb=" N ASP D 88 " --> pdb=" O MET D 8 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 208 through 213 removed outlier: 7.056A pdb=" N VAL D 208 " --> pdb=" O GLU D 202 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU D 202 " --> pdb=" O VAL D 208 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 258 " --> pdb=" O LEU D 251 " (cutoff:3.500A) removed outlier: 9.872A pdb=" N THR D 247 " --> pdb=" O PRO D 262 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LEU E 267 " --> pdb=" O LEU E 263 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ALA E 199 " --> pdb=" O THR E 212 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N THR E 212 " --> pdb=" O ALA E 199 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N LEU E 201 " --> pdb=" O VAL E 210 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE E 208 " --> pdb=" O ASP E 203 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 54 through 56 removed outlier: 6.328A pdb=" N ILE E 6 " --> pdb=" O TRP E 55 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS E 5 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA E 79 " --> pdb=" O LYS E 5 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 100 through 102 removed outlier: 3.517A pdb=" N VAL I 54 " --> pdb=" O ALA F 102 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N ARG I 24 " --> pdb=" O PRO I 28 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 31 through 34 removed outlier: 6.885A pdb=" N VAL G 24 " --> pdb=" O LEU G 32 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N TYR G 34 " --> pdb=" O ILE G 22 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ILE G 22 " --> pdb=" O TYR G 34 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU G 123 " --> pdb=" O ILE G 108 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER H 64 " --> pdb=" O GLU G 97 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE H 94 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N VAL H 17 " --> pdb=" O ILE H 94 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 80 through 81 1040 hydrogen bonds defined for protein. 2961 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: 4.86 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7137 1.34 - 1.46: 4039 1.46 - 1.58: 11965 1.58 - 1.69: 9 1.69 - 1.81: 177 Bond restraints: 23327 Sorted by residual: bond pdb=" C VAL B 27 " pdb=" N PRO B 28 " ideal model delta sigma weight residual 1.334 1.388 -0.054 2.34e-02 1.83e+03 5.39e+00 bond pdb=" C VAL A 377 " pdb=" N PRO A 378 " ideal model delta sigma weight residual 1.334 1.386 -0.052 2.34e-02 1.83e+03 5.01e+00 bond pdb=" C VAL B 129 " pdb=" N PRO B 130 " ideal model delta sigma weight residual 1.335 1.361 -0.027 1.28e-02 6.10e+03 4.41e+00 bond pdb=" C TYR C 26 " pdb=" N PRO C 27 " ideal model delta sigma weight residual 1.334 1.380 -0.046 2.34e-02 1.83e+03 3.82e+00 bond pdb=" C LEU C 361 " pdb=" N PRO C 362 " ideal model delta sigma weight residual 1.336 1.358 -0.023 1.23e-02 6.61e+03 3.44e+00 ... (remaining 23322 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.56: 31330 3.56 - 7.11: 238 7.11 - 10.67: 40 10.67 - 14.23: 2 14.23 - 17.78: 2 Bond angle restraints: 31612 Sorted by residual: angle pdb=" C LEU A 414 " pdb=" N PHE A 415 " pdb=" CA PHE A 415 " ideal model delta sigma weight residual 122.41 133.70 -11.29 2.09e+00 2.29e-01 2.92e+01 angle pdb=" N VAL A 231 " pdb=" CA VAL A 231 " pdb=" C VAL A 231 " ideal model delta sigma weight residual 112.96 107.58 5.38 1.00e+00 1.00e+00 2.90e+01 angle pdb=" C ALA C 302 " pdb=" N ASP C 303 " pdb=" CA ASP C 303 " ideal model delta sigma weight residual 122.46 129.54 -7.08 1.41e+00 5.03e-01 2.52e+01 angle pdb=" C LYS A 866 " pdb=" N ASP A 867 " pdb=" CA ASP A 867 " ideal model delta sigma weight residual 121.54 131.12 -9.58 1.91e+00 2.74e-01 2.52e+01 angle pdb=" C LYS F 98 " pdb=" N TYR F 99 " pdb=" CA TYR F 99 " ideal model delta sigma weight residual 121.54 130.91 -9.37 1.91e+00 2.74e-01 2.41e+01 ... (remaining 31607 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.35: 13161 22.35 - 44.69: 822 44.69 - 67.04: 62 67.04 - 89.39: 19 89.39 - 111.73: 3 Dihedral angle restraints: 14067 sinusoidal: 5714 harmonic: 8353 Sorted by residual: dihedral pdb=" C5' GDP D 501 " pdb=" O5' GDP D 501 " pdb=" PA GDP D 501 " pdb=" O3A GDP D 501 " ideal model delta sinusoidal sigma weight residual 179.98 68.25 111.73 1 2.00e+01 2.50e-03 3.29e+01 dihedral pdb=" CA LEU A 414 " pdb=" C LEU A 414 " pdb=" N PHE A 415 " pdb=" CA PHE A 415 " ideal model delta harmonic sigma weight residual 180.00 156.30 23.70 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ILE A 362 " pdb=" C ILE A 362 " pdb=" N GLY A 363 " pdb=" CA GLY A 363 " ideal model delta harmonic sigma weight residual -180.00 -156.32 -23.68 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 14064 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 3229 0.087 - 0.173: 351 0.173 - 0.260: 20 0.260 - 0.347: 0 0.347 - 0.434: 1 Chirality restraints: 3601 Sorted by residual: chirality pdb=" CB VAL A1218 " pdb=" CA VAL A1218 " pdb=" CG1 VAL A1218 " pdb=" CG2 VAL A1218 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" CB VAL F 86 " pdb=" CA VAL F 86 " pdb=" CG1 VAL F 86 " pdb=" CG2 VAL F 86 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CB ILE G 110 " pdb=" CA ILE G 110 " pdb=" CG1 ILE G 110 " pdb=" CG2 ILE G 110 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 3598 not shown) Planarity restraints: 4019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 469 " -0.054 5.00e-02 4.00e+02 8.05e-02 1.04e+01 pdb=" N PRO A 470 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 470 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 470 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 31 " 0.052 5.00e-02 4.00e+02 7.83e-02 9.81e+00 pdb=" N PRO H 32 " -0.135 5.00e-02 4.00e+02 pdb=" CA PRO H 32 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO H 32 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 248 " -0.049 5.00e-02 4.00e+02 7.59e-02 9.22e+00 pdb=" N PRO B 249 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 249 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO B 249 " -0.042 5.00e-02 4.00e+02 ... (remaining 4016 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.13: 5 2.13 - 2.82: 6529 2.82 - 3.51: 28654 3.51 - 4.21: 53885 4.21 - 4.90: 94391 Nonbonded interactions: 183464 Sorted by model distance: nonbonded pdb=" O1B GDP D 501 " pdb=" F2 AF3 D 502 " model vdw 1.432 2.990 nonbonded pdb=" O1B GDP D 501 " pdb="AL AF3 D 502 " model vdw 1.693 2.760 nonbonded pdb=" F2 AF3 D 502 " pdb="MG MG D 503 " model vdw 2.042 2.120 nonbonded pdb=" OG SER D 16 " pdb="MG MG D 503 " model vdw 2.085 2.170 nonbonded pdb=" OG1 THR D 37 " pdb="MG MG D 503 " model vdw 2.119 2.170 ... (remaining 183459 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: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.260 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 23327 Z= 0.197 Angle : 0.815 17.783 31612 Z= 0.434 Chirality : 0.051 0.434 3601 Planarity : 0.006 0.081 4019 Dihedral : 13.955 111.732 8621 Min Nonbonded Distance : 1.432 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.72 % Favored : 94.24 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.50 (0.14), residues: 2780 helix: -2.28 (0.11), residues: 1063 sheet: 0.10 (0.23), residues: 549 loop : -1.79 (0.16), residues: 1168 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 422 TYR 0.027 0.002 TYR F 99 PHE 0.041 0.002 PHE A1286 TRP 0.024 0.001 TRP B 379 HIS 0.008 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00384 (23327) covalent geometry : angle 0.81547 (31612) hydrogen bonds : bond 0.17978 ( 1004) hydrogen bonds : angle 7.23338 ( 2961) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 272 time to evaluate : 0.928 Fit side-chains REVERT: C 482 MET cc_start: 0.6139 (ptt) cc_final: 0.4918 (tpp) REVERT: E 90 TYR cc_start: 0.7635 (p90) cc_final: 0.7081 (p90) REVERT: E 188 ASN cc_start: 0.8765 (m-40) cc_final: 0.8558 (m-40) REVERT: E 266 ASP cc_start: 0.7327 (t0) cc_final: 0.6882 (t0) REVERT: G 155 THR cc_start: 0.7395 (p) cc_final: 0.7046 (t) REVERT: H 14 GLU cc_start: 0.6065 (pm20) cc_final: 0.5532 (mp0) outliers start: 0 outliers final: 0 residues processed: 272 average time/residue: 0.1772 time to fit residues: 73.9179 Evaluate side-chains 171 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 171 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 0.0980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 417 ASN ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 ASN B 188 GLN B 301 HIS C 222 ASN D 61 GLN D 114 GLN E 137 GLN E 163 HIS H 51 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.104741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.073725 restraints weight = 49803.602| |-----------------------------------------------------------------------------| r_work (start): 0.3193 rms_B_bonded: 2.57 r_work: 0.3028 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2893 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 23327 Z= 0.160 Angle : 0.556 11.076 31612 Z= 0.288 Chirality : 0.043 0.170 3601 Planarity : 0.004 0.061 4019 Dihedral : 5.926 135.554 3078 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 0.75 % Allowed : 5.62 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.15), residues: 2780 helix: -0.28 (0.14), residues: 1091 sheet: 0.04 (0.23), residues: 532 loop : -1.39 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 24 TYR 0.022 0.001 TYR F 99 PHE 0.021 0.001 PHE F 111 TRP 0.017 0.001 TRP A1548 HIS 0.005 0.001 HIS B 156 Details of bonding type rmsd covalent geometry : bond 0.00375 (23327) covalent geometry : angle 0.55614 (31612) hydrogen bonds : bond 0.03894 ( 1004) hydrogen bonds : angle 4.82352 ( 2961) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 190 time to evaluate : 1.016 Fit side-chains revert: symmetry clash REVERT: B 205 HIS cc_start: 0.7719 (OUTLIER) cc_final: 0.7205 (m170) REVERT: C 222 ASN cc_start: 0.6244 (OUTLIER) cc_final: 0.5653 (m110) REVERT: C 224 TRP cc_start: 0.5814 (m-90) cc_final: 0.5612 (m100) REVERT: F 123 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8298 (mm) REVERT: I 22 LEU cc_start: 0.7527 (mt) cc_final: 0.7088 (mt) outliers start: 19 outliers final: 11 residues processed: 203 average time/residue: 0.1787 time to fit residues: 55.6084 Evaluate side-chains 178 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 1188 SER Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain B residue 23 ILE Chi-restraints excluded: chain B residue 30 ASP Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain C residue 222 ASN Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain H residue 108 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 204 optimal weight: 5.9990 chunk 215 optimal weight: 9.9990 chunk 47 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 277 optimal weight: 2.9990 chunk 131 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 219 optimal weight: 20.0000 chunk 85 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 417 ASN A 633 HIS ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN C 222 ASN D 114 GLN E 163 HIS E 188 ASN G 151 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.104119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.072869 restraints weight = 49651.401| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.44 r_work: 0.3023 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2889 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23327 Z= 0.141 Angle : 0.525 14.286 31612 Z= 0.270 Chirality : 0.043 0.152 3601 Planarity : 0.004 0.064 4019 Dihedral : 5.728 129.591 3078 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.98 % Allowed : 7.54 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.39 (0.16), residues: 2780 helix: 0.58 (0.15), residues: 1080 sheet: 0.04 (0.22), residues: 547 loop : -1.16 (0.18), residues: 1153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 669 TYR 0.020 0.001 TYR F 99 PHE 0.017 0.001 PHE F 111 TRP 0.014 0.001 TRP A1548 HIS 0.004 0.001 HIS A1186 Details of bonding type rmsd covalent geometry : bond 0.00330 (23327) covalent geometry : angle 0.52514 (31612) hydrogen bonds : bond 0.03405 ( 1004) hydrogen bonds : angle 4.48292 ( 2961) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.855 Fit side-chains REVERT: B 205 HIS cc_start: 0.7750 (OUTLIER) cc_final: 0.7187 (m170) REVERT: C 222 ASN cc_start: 0.6064 (OUTLIER) cc_final: 0.5691 (m110) REVERT: C 335 MET cc_start: 0.7961 (tpt) cc_final: 0.7132 (tpt) REVERT: F 123 ILE cc_start: 0.8683 (OUTLIER) cc_final: 0.8403 (mm) REVERT: G 48 ASP cc_start: 0.7936 (p0) cc_final: 0.7716 (p0) REVERT: I 22 LEU cc_start: 0.7563 (mt) cc_final: 0.7163 (mt) REVERT: I 68 THR cc_start: 0.8603 (p) cc_final: 0.8296 (t) outliers start: 25 outliers final: 17 residues processed: 192 average time/residue: 0.1615 time to fit residues: 48.7709 Evaluate side-chains 181 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 670 HIS Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain C residue 222 ASN Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain I residue 52 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 272 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 7 optimal weight: 0.4980 chunk 170 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 235 optimal weight: 3.9990 chunk 128 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 118 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN C 222 ASN D 114 GLN E 108 ASN E 163 HIS E 188 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.103018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.071694 restraints weight = 49624.615| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 2.46 r_work: 0.2996 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23327 Z= 0.160 Angle : 0.534 14.937 31612 Z= 0.274 Chirality : 0.043 0.183 3601 Planarity : 0.004 0.066 4019 Dihedral : 5.707 127.322 3078 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.00 % Favored : 94.96 % Rotamer: Outliers : 1.10 % Allowed : 8.92 % Favored : 89.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.16), residues: 2780 helix: 1.02 (0.16), residues: 1070 sheet: -0.08 (0.22), residues: 531 loop : -0.99 (0.18), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 101 TYR 0.017 0.001 TYR F 99 PHE 0.015 0.001 PHE A 199 TRP 0.019 0.001 TRP C 224 HIS 0.004 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00381 (23327) covalent geometry : angle 0.53373 (31612) hydrogen bonds : bond 0.03303 ( 1004) hydrogen bonds : angle 4.35649 ( 2961) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 165 time to evaluate : 0.985 Fit side-chains REVERT: A 365 ASP cc_start: 0.8698 (OUTLIER) cc_final: 0.7616 (t0) REVERT: A 414 LEU cc_start: 0.1811 (OUTLIER) cc_final: 0.1070 (tp) REVERT: B 205 HIS cc_start: 0.7863 (OUTLIER) cc_final: 0.7293 (m90) REVERT: C 335 MET cc_start: 0.7985 (tpt) cc_final: 0.6996 (tpt) REVERT: F 123 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8481 (mm) REVERT: I 22 LEU cc_start: 0.7662 (mt) cc_final: 0.7273 (mt) REVERT: I 68 THR cc_start: 0.8604 (p) cc_final: 0.8303 (t) outliers start: 28 outliers final: 20 residues processed: 188 average time/residue: 0.1627 time to fit residues: 48.0062 Evaluate side-chains 176 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 152 time to evaluate : 0.816 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 670 HIS Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 123 ILE Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain I residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 40 optimal weight: 0.0980 chunk 57 optimal weight: 6.9990 chunk 254 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 203 optimal weight: 7.9990 chunk 94 optimal weight: 0.7980 chunk 210 optimal weight: 10.0000 chunk 126 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN D 114 GLN E 188 ASN H 77 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.104586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.074698 restraints weight = 49478.280| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.47 r_work: 0.3038 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 23327 Z= 0.101 Angle : 0.495 15.706 31612 Z= 0.252 Chirality : 0.042 0.156 3601 Planarity : 0.003 0.057 4019 Dihedral : 5.509 126.203 3078 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.64 % Favored : 95.32 % Rotamer: Outliers : 0.83 % Allowed : 9.74 % Favored : 89.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.16), residues: 2780 helix: 1.36 (0.16), residues: 1075 sheet: -0.01 (0.23), residues: 526 loop : -0.85 (0.19), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 997 TYR 0.014 0.001 TYR F 99 PHE 0.015 0.001 PHE E 270 TRP 0.013 0.001 TRP D 168 HIS 0.003 0.001 HIS H 97 Details of bonding type rmsd covalent geometry : bond 0.00230 (23327) covalent geometry : angle 0.49503 (31612) hydrogen bonds : bond 0.02847 ( 1004) hydrogen bonds : angle 4.13666 ( 2961) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: C 335 MET cc_start: 0.7949 (tpt) cc_final: 0.7158 (tpt) REVERT: F 123 ILE cc_start: 0.8699 (tt) cc_final: 0.8465 (mm) REVERT: G 48 ASP cc_start: 0.7931 (p0) cc_final: 0.7712 (p0) REVERT: G 155 THR cc_start: 0.7492 (p) cc_final: 0.7113 (t) REVERT: I 22 LEU cc_start: 0.7664 (mt) cc_final: 0.7255 (mt) REVERT: I 68 THR cc_start: 0.8574 (p) cc_final: 0.8252 (t) outliers start: 21 outliers final: 16 residues processed: 187 average time/residue: 0.1659 time to fit residues: 48.4371 Evaluate side-chains 173 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 670 HIS Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 17 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 58 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 220 optimal weight: 20.0000 chunk 259 optimal weight: 9.9990 chunk 201 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 174 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 118 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 188 ASN H 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.103396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.071684 restraints weight = 49993.067| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.55 r_work: 0.2996 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23327 Z= 0.140 Angle : 0.518 15.884 31612 Z= 0.263 Chirality : 0.042 0.156 3601 Planarity : 0.004 0.063 4019 Dihedral : 5.531 122.621 3078 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.93 % Favored : 95.04 % Rotamer: Outliers : 1.26 % Allowed : 10.14 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.16), residues: 2780 helix: 1.52 (0.16), residues: 1068 sheet: 0.04 (0.23), residues: 520 loop : -0.82 (0.19), residues: 1192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 997 TYR 0.017 0.001 TYR A 759 PHE 0.016 0.001 PHE A1286 TRP 0.014 0.001 TRP A1548 HIS 0.004 0.001 HIS H 97 Details of bonding type rmsd covalent geometry : bond 0.00332 (23327) covalent geometry : angle 0.51794 (31612) hydrogen bonds : bond 0.03013 ( 1004) hydrogen bonds : angle 4.16099 ( 2961) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: A 365 ASP cc_start: 0.8573 (OUTLIER) cc_final: 0.7466 (t0) REVERT: A 414 LEU cc_start: 0.2023 (OUTLIER) cc_final: 0.1450 (tp) REVERT: A 1473 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8430 (mt0) REVERT: B 205 HIS cc_start: 0.7784 (OUTLIER) cc_final: 0.7266 (m90) REVERT: C 335 MET cc_start: 0.7981 (tpt) cc_final: 0.7277 (tpt) REVERT: F 123 ILE cc_start: 0.8719 (tt) cc_final: 0.8517 (mm) REVERT: G 155 THR cc_start: 0.7411 (p) cc_final: 0.7038 (t) REVERT: I 22 LEU cc_start: 0.7539 (mt) cc_final: 0.7253 (mt) REVERT: I 68 THR cc_start: 0.8590 (p) cc_final: 0.8269 (t) outliers start: 32 outliers final: 20 residues processed: 190 average time/residue: 0.1594 time to fit residues: 47.7193 Evaluate side-chains 181 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 670 HIS Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain A residue 1473 GLN Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain G residue 160 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain I residue 52 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 41 optimal weight: 8.9990 chunk 237 optimal weight: 4.9990 chunk 198 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 chunk 215 optimal weight: 9.9990 chunk 133 optimal weight: 0.9990 chunk 71 optimal weight: 6.9990 chunk 85 optimal weight: 0.7980 chunk 197 optimal weight: 0.9990 chunk 127 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN B 273 HIS D 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.101389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.071444 restraints weight = 49612.787| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.44 r_work: 0.2961 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 23327 Z= 0.213 Angle : 0.577 14.173 31612 Z= 0.296 Chirality : 0.045 0.155 3601 Planarity : 0.004 0.075 4019 Dihedral : 5.841 123.443 3078 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.76 % Favored : 94.21 % Rotamer: Outliers : 1.45 % Allowed : 10.18 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.16), residues: 2780 helix: 1.37 (0.16), residues: 1068 sheet: -0.08 (0.23), residues: 515 loop : -0.92 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1363 TYR 0.018 0.001 TYR E 209 PHE 0.017 0.002 PHE A 199 TRP 0.016 0.001 TRP A1548 HIS 0.006 0.001 HIS B 205 Details of bonding type rmsd covalent geometry : bond 0.00509 (23327) covalent geometry : angle 0.57659 (31612) hydrogen bonds : bond 0.03527 ( 1004) hydrogen bonds : angle 4.36033 ( 2961) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.875 Fit side-chains REVERT: A 365 ASP cc_start: 0.8753 (OUTLIER) cc_final: 0.7853 (t0) REVERT: A 414 LEU cc_start: 0.2364 (OUTLIER) cc_final: 0.1811 (tp) REVERT: B 205 HIS cc_start: 0.8079 (OUTLIER) cc_final: 0.7389 (m90) REVERT: C 335 MET cc_start: 0.8042 (tpt) cc_final: 0.7349 (tpt) REVERT: F 123 ILE cc_start: 0.8719 (tt) cc_final: 0.8505 (mm) REVERT: G 48 ASP cc_start: 0.8037 (p0) cc_final: 0.7764 (p0) REVERT: G 155 THR cc_start: 0.7343 (p) cc_final: 0.6998 (t) REVERT: I 22 LEU cc_start: 0.7438 (mt) cc_final: 0.7127 (mt) REVERT: I 68 THR cc_start: 0.8604 (p) cc_final: 0.8295 (t) outliers start: 37 outliers final: 24 residues processed: 195 average time/residue: 0.1592 time to fit residues: 48.5055 Evaluate side-chains 182 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 670 HIS Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 72 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 64 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 151 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 134 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 41 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1470 HIS B 226 ASN C 222 ASN D 67 ASN D 114 GLN E 188 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.102189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.072597 restraints weight = 49569.777| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.39 r_work: 0.2994 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23327 Z= 0.154 Angle : 0.539 14.190 31612 Z= 0.275 Chirality : 0.043 0.156 3601 Planarity : 0.004 0.069 4019 Dihedral : 5.722 123.257 3078 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.11 % Favored : 94.86 % Rotamer: Outliers : 1.22 % Allowed : 10.77 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.16), residues: 2780 helix: 1.49 (0.16), residues: 1070 sheet: -0.08 (0.23), residues: 513 loop : -0.86 (0.18), residues: 1197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 997 TYR 0.017 0.001 TYR A 759 PHE 0.014 0.001 PHE E 270 TRP 0.014 0.001 TRP A1548 HIS 0.004 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00368 (23327) covalent geometry : angle 0.53868 (31612) hydrogen bonds : bond 0.03159 ( 1004) hydrogen bonds : angle 4.25824 ( 2961) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 163 time to evaluate : 0.877 Fit side-chains REVERT: A 365 ASP cc_start: 0.8632 (OUTLIER) cc_final: 0.7612 (t0) REVERT: A 414 LEU cc_start: 0.2163 (OUTLIER) cc_final: 0.1781 (tp) REVERT: B 205 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7352 (m170) REVERT: C 335 MET cc_start: 0.8032 (tpt) cc_final: 0.7436 (tpt) REVERT: F 123 ILE cc_start: 0.8718 (tt) cc_final: 0.8505 (mm) REVERT: G 155 THR cc_start: 0.7340 (p) cc_final: 0.6997 (t) REVERT: I 22 LEU cc_start: 0.7482 (mt) cc_final: 0.7091 (mt) REVERT: I 68 THR cc_start: 0.8597 (p) cc_final: 0.8287 (t) outliers start: 31 outliers final: 24 residues processed: 189 average time/residue: 0.1652 time to fit residues: 48.7788 Evaluate side-chains 184 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 670 HIS Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 66 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 204 optimal weight: 5.9990 chunk 65 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 155 optimal weight: 6.9990 chunk 143 optimal weight: 0.9980 chunk 136 optimal weight: 7.9990 chunk 152 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 201 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1478 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.103338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.073676 restraints weight = 49674.236| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.46 r_work: 0.3011 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23327 Z= 0.115 Angle : 0.516 14.452 31612 Z= 0.263 Chirality : 0.042 0.157 3601 Planarity : 0.003 0.063 4019 Dihedral : 5.577 121.391 3078 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.89 % Favored : 95.07 % Rotamer: Outliers : 1.18 % Allowed : 10.96 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.16), residues: 2780 helix: 1.69 (0.16), residues: 1069 sheet: -0.01 (0.23), residues: 513 loop : -0.79 (0.19), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 138 TYR 0.015 0.001 TYR G 64 PHE 0.016 0.001 PHE E 270 TRP 0.012 0.001 TRP D 168 HIS 0.003 0.001 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00269 (23327) covalent geometry : angle 0.51603 (31612) hydrogen bonds : bond 0.02912 ( 1004) hydrogen bonds : angle 4.13559 ( 2961) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: A 414 LEU cc_start: 0.1974 (OUTLIER) cc_final: 0.1760 (tp) REVERT: B 205 HIS cc_start: 0.7803 (OUTLIER) cc_final: 0.7320 (m170) REVERT: C 335 MET cc_start: 0.8018 (tpt) cc_final: 0.7487 (tpt) REVERT: F 123 ILE cc_start: 0.8721 (tt) cc_final: 0.8513 (mm) REVERT: G 155 THR cc_start: 0.7334 (p) cc_final: 0.7007 (t) REVERT: I 22 LEU cc_start: 0.7394 (mt) cc_final: 0.7046 (mt) REVERT: I 68 THR cc_start: 0.8586 (p) cc_final: 0.8263 (t) outliers start: 30 outliers final: 27 residues processed: 196 average time/residue: 0.1735 time to fit residues: 52.6729 Evaluate side-chains 192 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 414 LEU Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 670 HIS Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain C residue 222 ASN Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 134 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 101 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 56 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 178 optimal weight: 5.9990 chunk 127 optimal weight: 3.9990 chunk 277 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 154 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 114 GLN E 188 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.103510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.073866 restraints weight = 49762.761| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.46 r_work: 0.3016 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23327 Z= 0.114 Angle : 0.517 14.905 31612 Z= 0.263 Chirality : 0.042 0.156 3601 Planarity : 0.004 0.061 4019 Dihedral : 5.507 119.367 3078 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.82 % Favored : 95.14 % Rotamer: Outliers : 1.18 % Allowed : 11.08 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.16), residues: 2780 helix: 1.76 (0.16), residues: 1072 sheet: 0.04 (0.23), residues: 513 loop : -0.76 (0.19), residues: 1195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 997 TYR 0.017 0.001 TYR A 759 PHE 0.016 0.001 PHE E 270 TRP 0.013 0.001 TRP D 168 HIS 0.004 0.001 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00267 (23327) covalent geometry : angle 0.51710 (31612) hydrogen bonds : bond 0.02857 ( 1004) hydrogen bonds : angle 4.09039 ( 2961) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5560 Ramachandran restraints generated. 2780 Oldfield, 0 Emsley, 2780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: B 205 HIS cc_start: 0.7751 (OUTLIER) cc_final: 0.7305 (m90) REVERT: C 335 MET cc_start: 0.8009 (tpt) cc_final: 0.7483 (tpt) REVERT: G 48 ASP cc_start: 0.7924 (p0) cc_final: 0.7628 (p0) REVERT: H 6 GLN cc_start: 0.8271 (pt0) cc_final: 0.7101 (mm-40) REVERT: H 83 LYS cc_start: 0.5201 (mptt) cc_final: 0.4903 (mttt) REVERT: I 22 LEU cc_start: 0.7455 (mt) cc_final: 0.7068 (mt) REVERT: I 68 THR cc_start: 0.8565 (p) cc_final: 0.8258 (t) outliers start: 30 outliers final: 26 residues processed: 195 average time/residue: 0.1662 time to fit residues: 50.1602 Evaluate side-chains 194 residues out of total 2546 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 167 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 171 VAL Chi-restraints excluded: chain A residue 219 VAL Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 412 SER Chi-restraints excluded: chain A residue 415 PHE Chi-restraints excluded: chain A residue 633 HIS Chi-restraints excluded: chain A residue 670 HIS Chi-restraints excluded: chain A residue 732 VAL Chi-restraints excluded: chain A residue 1566 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 205 HIS Chi-restraints excluded: chain C residue 222 ASN Chi-restraints excluded: chain C residue 285 VAL Chi-restraints excluded: chain C residue 490 LEU Chi-restraints excluded: chain D residue 182 LEU Chi-restraints excluded: chain D residue 246 PHE Chi-restraints excluded: chain E residue 188 ASN Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 97 HIS Chi-restraints excluded: chain I residue 6 SER Chi-restraints excluded: chain I residue 13 VAL Chi-restraints excluded: chain I residue 66 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 281 random chunks: chunk 93 optimal weight: 3.9990 chunk 170 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 159 optimal weight: 6.9990 chunk 172 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 95 optimal weight: 6.9990 chunk 33 optimal weight: 0.0010 overall best weight: 1.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 634 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 56 HIS ** 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 = 0.3763 r_free = 0.3763 target = 0.103365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.073648 restraints weight = 49827.096| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.45 r_work: 0.3013 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.142 23327 Z= 0.171 Angle : 0.669 59.199 31612 Z= 0.376 Chirality : 0.045 0.808 3601 Planarity : 0.004 0.061 4019 Dihedral : 5.552 119.399 3078 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.86 % Favored : 95.07 % Rotamer: Outliers : 1.10 % Allowed : 11.08 % Favored : 87.82 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.16), residues: 2780 helix: 1.74 (0.16), residues: 1072 sheet: 0.03 (0.23), residues: 514 loop : -0.76 (0.19), residues: 1194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 997 TYR 0.013 0.001 TYR F 99 PHE 0.016 0.001 PHE E 270 TRP 0.013 0.001 TRP D 168 HIS 0.004 0.001 HIS B 16 Details of bonding type rmsd covalent geometry : bond 0.00361 (23327) covalent geometry : angle 0.66897 (31612) hydrogen bonds : bond 0.03015 ( 1004) hydrogen bonds : angle 4.10921 ( 2961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6613.72 seconds wall clock time: 113 minutes 44.20 seconds (6824.20 seconds total)