Starting phenix.real_space_refine on Fri Mar 6 16:58:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t3c_25654/03_2026/7t3c_25654.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3c_25654/03_2026/7t3c_25654.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7t3c_25654/03_2026/7t3c_25654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3c_25654/03_2026/7t3c_25654.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7t3c_25654/03_2026/7t3c_25654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3c_25654/03_2026/7t3c_25654.map" } resolution = 4.0 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= 0.002 sd= 0.028 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: 7 Type Number sf(0) Gaussians Al 3 5.89 5 P 6 5.49 5 S 183 5.16 5 C 20694 2.51 5 N 5489 2.21 5 O 6068 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 47 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32452 Number of models: 1 Model: "" Number of chains: 23 Chain: "B" Number of atoms: 2918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2918 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 8120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 990, 8120 Classifications: {'peptide': 990} Link IDs: {'PTRANS': 41, 'TRANS': 948} Chain breaks: 7 Chain: "H" Number of atoms: 939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 939 Classifications: {'peptide': 121} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 114} Chain: "G" Number of atoms: 944 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 944 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "J" Number of atoms: 672 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 91, 666 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Conformer: "B" Number of residues, atoms: 91, 666 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} bond proxies already assigned to first conformer: 665 Chain: "I" Number of atoms: 647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 647 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain breaks: 1 Chain: "F" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 861 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 6, 'TRANS': 104} Chain: "C" Number of atoms: 3242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 3242 Classifications: {'peptide': 406} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 385} Chain breaks: 5 Chain: "D" Number of atoms: 2429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2429 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 5, 'TRANS': 290} Chain: "E" Number of atoms: 2471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2471 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 7, 'TRANS': 298} Chain: "O" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 934 Classifications: {'peptide': 120} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 113} Chain: "N" Number of atoms: 936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 936 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 2, 'TRANS': 121} Chain: "Q" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 666 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "P" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 738 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "M" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 892 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 6, 'TRANS': 108} Chain: "K" Number of atoms: 2459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2459 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 6, 'TRANS': 293} Chain: "L" Number of atoms: 2488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2488 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 8, 'TRANS': 298} 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'AF3': 1} Classifications: {'undetermined': 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} Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'AF3': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'GDP': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'AF3': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS J 23 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS J 23 " occ=0.50 Time building chain proxies: 6.81, per 1000 atoms: 0.21 Number of scatterers: 32452 At special positions: 0 Unit cell: (168.49, 200.86, 208.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 183 16.00 P 6 15.00 Al 3 13.00 F 9 9.00 O 6068 8.00 N 5489 7.00 C 20694 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.4 seconds 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7752 Finding SS restraints... Secondary structure from input PDB file: 143 helices and 31 sheets defined 40.9% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.98 Creating SS restraints... Processing helix chain 'B' and resid 35 through 41 Processing helix chain 'B' and resid 98 through 117 removed outlier: 3.596A pdb=" N GLU B 115 " --> pdb=" O THR B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 124 through 140 Proline residue: B 130 - end of helix Processing helix chain 'B' and resid 180 through 184 removed outlier: 3.938A pdb=" N PHE B 184 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix 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 231 removed outlier: 3.753A pdb=" N VAL B 220 " --> pdb=" O GLU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 268 Processing helix chain 'B' and resid 277 through 287 removed outlier: 3.675A pdb=" N VAL B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 301 removed outlier: 3.620A pdb=" N LEU B 297 " --> pdb=" O THR B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 removed outlier: 3.743A pdb=" N ILE B 314 " --> pdb=" O GLU B 310 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 358 Processing helix chain 'B' and resid 362 through 370 removed outlier: 4.047A pdb=" N GLU B 367 " --> pdb=" O HIS B 363 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ARG B 368 " --> pdb=" O GLU B 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 78 Processing helix chain 'A' and resid 110 through 121 Processing helix chain 'A' and resid 146 through 149 Processing helix chain 'A' and resid 178 through 182 removed outlier: 3.621A pdb=" N TRP A 182 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 198 Processing helix chain 'A' and resid 198 through 210 Processing helix chain 'A' and resid 268 through 281 removed outlier: 4.035A pdb=" N VAL A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR A 273 " --> pdb=" O SER A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 286 Processing helix chain 'A' and resid 306 through 318 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 346 through 360 removed outlier: 3.619A pdb=" N ASP A 359 " --> pdb=" O GLN A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 743 through 749 Processing helix chain 'A' and resid 763 through 769 Processing helix chain 'A' and resid 795 through 809 removed outlier: 3.595A pdb=" N PHE A 799 " --> pdb=" O ALA A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 927 removed outlier: 4.115A pdb=" N LEU A 921 " --> pdb=" O LYS A 917 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 940 removed outlier: 3.893A pdb=" N LYS A 940 " --> pdb=" O GLU A 937 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 961 removed outlier: 3.565A pdb=" N THR A 956 " --> pdb=" O CYS A 952 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ARG A 958 " --> pdb=" O THR A 954 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE A 959 " --> pdb=" O ALA A 955 " (cutoff:3.500A) Processing helix chain 'A' and resid 975 through 994 removed outlier: 3.570A pdb=" N TRP A 980 " --> pdb=" O ASP A 976 " (cutoff:3.500A) Processing helix chain 'A' and resid 1178 through 1186 Processing helix chain 'A' and resid 1207 through 1218 Processing helix chain 'A' and resid 1224 through 1236 removed outlier: 4.557A pdb=" N ILE A1228 " --> pdb=" O GLN A1224 " (cutoff:3.500A) Processing helix chain 'A' and resid 1286 through 1291 Processing helix chain 'A' and resid 1394 through 1411 Processing helix chain 'A' and resid 1444 through 1449 removed outlier: 3.592A pdb=" N CYS A1447 " --> pdb=" O ASN A1444 " (cutoff:3.500A) Processing helix chain 'A' and resid 1464 through 1480 Processing helix chain 'A' and resid 1555 through 1559 Processing helix chain 'A' and resid 1565 through 1581 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 1595 Processing helix chain 'H' and resid 3 through 12 Processing helix chain 'H' and resid 13 through 16 Processing helix chain 'H' and resid 41 through 45 Processing helix chain 'H' and resid 46 through 62 removed outlier: 4.652A pdb=" N THR H 52 " --> pdb=" O GLY H 48 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N PHE H 53 " --> pdb=" O PHE H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 110 Processing helix chain 'H' and resid 110 through 118 Processing helix chain 'G' and resid 3 through 14 removed outlier: 3.903A pdb=" N ALA G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 64 removed outlier: 4.109A pdb=" N ILE G 48 " --> pdb=" O VAL G 44 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLN G 62 " --> pdb=" O ARG G 58 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N PHE G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 114 Processing helix chain 'G' and resid 116 through 125 Processing helix chain 'J' and resid 2 through 13 Processing helix chain 'J' and resid 41 through 56 removed outlier: 3.585A pdb=" N LEU J 55 " --> pdb=" O GLN J 51 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR J 56 " --> pdb=" O ALA J 52 " (cutoff:3.500A) Processing helix chain 'I' and resid 36 through 52 Processing helix chain 'F' and resid 50 through 62 removed outlier: 3.937A pdb=" N SER F 56 " --> pdb=" O ALA F 52 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ILE F 57 " --> pdb=" O LEU F 53 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU F 58 " --> pdb=" O LEU F 54 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA F 62 " --> pdb=" O LEU F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 98 Processing helix chain 'F' and resid 114 through 119 removed outlier: 4.060A pdb=" N VAL F 118 " --> pdb=" O GLN F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 125 through 146 removed outlier: 3.627A pdb=" N SER F 144 " --> pdb=" O TYR F 140 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 73 removed outlier: 4.299A pdb=" N LEU C 69 " --> pdb=" O SER C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 135 through 160 Processing helix chain 'C' and resid 161 through 174 removed outlier: 3.882A pdb=" N ARG C 165 " --> pdb=" O GLN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 198 through 213 removed outlier: 3.730A pdb=" N THR C 213 " --> pdb=" O ASP C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 226 removed outlier: 3.613A pdb=" N LEU C 225 " --> pdb=" O ASN C 222 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU C 226 " --> pdb=" O SER C 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 222 through 226' Processing helix chain 'C' and resid 266 through 274 Processing helix chain 'C' and resid 279 through 289 removed outlier: 3.888A 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 Processing helix chain 'C' and resid 347 through 356 Processing helix chain 'C' and resid 360 through 368 Processing helix chain 'C' and resid 374 through 378 Processing helix chain 'C' and resid 383 through 400 removed outlier: 3.608A pdb=" N GLU C 387 " --> pdb=" O PRO C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 481 through 488 Processing helix chain 'C' and resid 491 through 499 Processing helix chain 'C' and resid 507 through 515 Processing helix chain 'C' and resid 526 through 534 Processing helix chain 'C' and resid 536 through 547 Processing helix chain 'C' and resid 558 through 564 removed outlier: 3.515A pdb=" N ALA C 562 " --> pdb=" O ASP C 558 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 29 Processing helix chain 'D' and resid 32 through 37 Processing helix chain 'D' and resid 66 through 76 Processing helix chain 'D' and resid 77 through 83 Processing helix chain 'D' and resid 98 through 117 Processing helix chain 'D' and resid 136 through 151 Processing helix chain 'D' and resid 167 through 181 Processing helix chain 'D' and resid 183 through 198 Processing helix chain 'D' and resid 225 through 244 removed outlier: 3.960A pdb=" N GLU D 229 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ILE D 231 " --> pdb=" O ARG D 227 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 299 removed outlier: 3.970A pdb=" N LYS D 295 " --> pdb=" O ARG D 291 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N HIS D 296 " --> pdb=" O ASN D 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 82 Processing helix chain 'E' and resid 88 through 93 removed outlier: 3.726A pdb=" N LEU E 91 " --> pdb=" O ASN E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 135 removed outlier: 4.234A pdb=" N ILE E 133 " --> pdb=" O ASP E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 168 Processing helix chain 'E' and resid 179 through 183 removed outlier: 3.926A pdb=" N GLY E 182 " --> pdb=" O LYS E 179 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU E 183 " --> pdb=" O VAL E 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 179 through 183' Processing helix chain 'E' and resid 184 through 205 Processing helix chain 'E' and resid 223 through 237 Processing helix chain 'E' and resid 239 through 255 removed outlier: 3.802A pdb=" N ASN E 253 " --> pdb=" O ILE E 249 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER E 254 " --> pdb=" O PHE E 250 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY E 255 " --> pdb=" O ILE E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 279 through 300 removed outlier: 3.544A pdb=" N LEU E 284 " --> pdb=" O GLN E 280 " (cutoff:3.500A) Processing helix chain 'E' and resid 348 through 367 Processing helix chain 'O' and resid 4 through 12 Processing helix chain 'O' and resid 41 through 45 Processing helix chain 'O' and resid 46 through 51 Processing helix chain 'O' and resid 51 through 61 Processing helix chain 'O' and resid 99 through 110 Processing helix chain 'O' and resid 110 through 117 Processing helix chain 'O' and resid 117 through 122 removed outlier: 4.456A pdb=" N VAL O 121 " --> pdb=" O LEU O 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 4 through 16 removed outlier: 3.673A pdb=" N LEU N 12 " --> pdb=" O LEU N 8 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN N 16 " --> pdb=" O LEU N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 48 No H-bonds generated for 'chain 'N' and resid 46 through 48' Processing helix chain 'N' and resid 49 through 58 Processing helix chain 'N' and resid 101 through 115 Processing helix chain 'Q' and resid 2 through 14 Processing helix chain 'Q' and resid 41 through 52 Processing helix chain 'P' and resid 2 through 10 removed outlier: 4.047A pdb=" N GLY P 8 " --> pdb=" O ALA P 4 " (cutoff:3.500A) Processing helix chain 'P' and resid 36 through 51 Processing helix chain 'M' and resid 47 through 64 Processing helix chain 'M' and resid 78 through 95 Processing helix chain 'M' and resid 114 through 119 Processing helix chain 'M' and resid 125 through 139 Processing helix chain 'K' and resid 19 through 29 removed outlier: 4.435A pdb=" N ARG K 24 " --> pdb=" O LYS K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 39 removed outlier: 3.891A pdb=" N ARG K 37 " --> pdb=" O ARG K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 66 through 75 Processing helix chain 'K' and resid 77 through 82 Processing helix chain 'K' and resid 98 through 117 Processing helix chain 'K' and resid 133 through 152 Processing helix chain 'K' and resid 167 through 181 Processing helix chain 'K' and resid 184 through 198 Processing helix chain 'K' and resid 225 through 245 removed outlier: 4.173A pdb=" N GLU K 229 " --> pdb=" O VAL K 225 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU K 245 " --> pdb=" O SER K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 298 removed outlier: 4.260A pdb=" N HIS K 296 " --> pdb=" O ASN K 292 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 85 removed outlier: 3.620A pdb=" N LYS L 74 " --> pdb=" O ARG L 70 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN L 75 " --> pdb=" O ARG L 71 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N SER L 76 " --> pdb=" O SER L 72 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ILE L 77 " --> pdb=" O GLY L 73 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 89 Processing helix chain 'L' and resid 101 through 111 removed outlier: 3.524A pdb=" N SER L 105 " --> pdb=" O LYS L 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.821A pdb=" N MET L 132 " --> pdb=" O PHE L 128 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 168 removed outlier: 3.783A pdb=" N ILE L 159 " --> pdb=" O THR L 155 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS L 163 " --> pdb=" O ILE L 159 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 199 removed outlier: 3.588A pdb=" N ILE L 189 " --> pdb=" O ASP L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 205 removed outlier: 3.946A pdb=" N ASP L 205 " --> pdb=" O ASP L 201 " (cutoff:3.500A) Processing helix chain 'L' and resid 224 through 235 removed outlier: 4.362A pdb=" N ALA L 228 " --> pdb=" O SER L 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 240 through 251 Processing helix chain 'L' and resid 281 through 299 removed outlier: 3.550A pdb=" N ILE L 298 " --> pdb=" O ASP L 294 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR L 299 " --> pdb=" O VAL L 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 352 through 367 Processing sheet with id=AA1, first strand: chain 'B' and resid 7 through 14 removed outlier: 8.495A pdb=" N ILE B 7 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ASP B 90 " --> pdb=" O ILE B 7 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N GLU C 85 " --> pdb=" O THR B 58 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ARG C 131 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 144 through 147 Processing sheet with id=AA3, first strand: chain 'B' and resid 174 through 177 Processing sheet with id=AA4, first strand: chain 'B' and resid 244 through 247 removed outlier: 4.383A pdb=" N VAL B 244 " --> pdb=" O LEU B 326 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 327 " --> pdb=" O LYS B 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 23 through 24 removed outlier: 8.706A pdb=" N ILE A 67 " --> pdb=" O VAL A 6 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LYS A 8 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N VAL A 69 " --> pdb=" O LYS A 8 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N VAL A 10 " --> pdb=" O VAL A 69 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 96 through 97 removed outlier: 4.049A pdb=" N SER A 157 " --> pdb=" O LEU A 97 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR A 124 " --> pdb=" O ILE A 156 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 131 through 133 removed outlier: 4.476A pdb=" N GLU A 101 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N VAL A 100 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ARG A 165 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N LEU A 102 " --> pdb=" O ARG A 165 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 364 through 367 removed outlier: 3.803A pdb=" N THR A 224 " --> pdb=" O GLU A 252 " (cutoff:3.500A) removed outlier: 8.657A pdb=" N TYR A 251 " --> pdb=" O THR A 889 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N SER A 891 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ASP A 253 " --> pdb=" O SER A 891 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N CYS A 893 " --> pdb=" O ASP A 253 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TYR A 255 " --> pdb=" O CYS A 893 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 380 through 381 Processing sheet with id=AB1, first strand: chain 'A' and resid 770 through 777 Processing sheet with id=AB2, first strand: chain 'A' and resid 1351 through 1357 removed outlier: 6.332A pdb=" N GLU A1385 " --> pdb=" O HIS A1375 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1240 through 1241 Processing sheet with id=AB4, first strand: chain 'A' and resid 1297 through 1298 removed outlier: 7.399A pdb=" N ALA A1297 " --> pdb=" O PHE A1378 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 1439 through 1441 Processing sheet with id=AB6, first strand: chain 'A' and resid 1482 through 1485 Processing sheet with id=AB7, first strand: chain 'H' and resid 33 through 36 removed outlier: 7.128A pdb=" N LEU H 19 " --> pdb=" O SER H 95 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N SER H 95 " --> pdb=" O LEU H 19 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N TYR H 78 " --> pdb=" O TYR H 75 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LYS G 70 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N ARG G 85 " --> pdb=" O LYS G 70 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 21 through 24 removed outlier: 3.685A pdb=" N LEU J 22 " --> pdb=" O ALA J 85 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY I 17 " --> pdb=" O LYS I 88 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 372 through 373 removed outlier: 4.074A pdb=" N VAL C 333 " --> pdb=" O LEU C 406 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR C 408 " --> pdb=" O HIS C 524 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N HIS C 524 " --> pdb=" O THR C 408 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N VAL C 410 " --> pdb=" O GLY C 522 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 372 through 373 removed outlier: 4.074A pdb=" N VAL C 333 " --> pdb=" O LEU C 406 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 46 through 52 removed outlier: 7.927A pdb=" N GLU D 86 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N LYS D 9 " --> pdb=" O GLU D 86 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU D 88 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N LEU D 11 " --> pdb=" O LEU D 88 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLU D 86 " --> pdb=" O LYS D 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 91 through 92 removed outlier: 6.690A pdb=" N PHE D 92 " --> pdb=" O HIS D 127 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL D 126 " --> pdb=" O THR D 162 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'D' and resid 213 through 218 removed outlier: 6.785A pdb=" N LEU D 205 " --> pdb=" O ILE D 214 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N HIS D 216 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL D 203 " --> pdb=" O HIS D 216 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER D 251 " --> pdb=" O LYS E 319 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 100 through 102 Processing sheet with id=AC6, first strand: chain 'E' and resid 140 through 145 removed outlier: 6.096A pdb=" N LEU E 140 " --> pdb=" O GLU E 174 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE E 176 " --> pdb=" O LEU E 140 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR E 142 " --> pdb=" O PHE E 176 " (cutoff:3.500A) removed outlier: 7.547A pdb=" N HIS E 178 " --> pdb=" O TYR E 142 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ILE E 144 " --> pdb=" O HIS E 178 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N TYR E 216 " --> pdb=" O PHE E 173 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL E 175 " --> pdb=" O TYR E 216 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'O' and resid 31 through 36 removed outlier: 6.901A pdb=" N VAL O 24 " --> pdb=" O VAL O 32 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N LYS O 34 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE O 22 " --> pdb=" O LYS O 34 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N ALA O 36 " --> pdb=" O HIS O 20 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N HIS O 20 " --> pdb=" O ALA O 36 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ILE O 93 " --> pdb=" O HIS O 20 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ILE O 22 " --> pdb=" O SER O 91 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N SER O 91 " --> pdb=" O ILE O 22 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL O 24 " --> pdb=" O VAL O 89 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N VAL O 89 " --> pdb=" O VAL O 24 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG O 85 " --> pdb=" O LEU O 88 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL O 90 " --> pdb=" O PHE O 83 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR O 78 " --> pdb=" O TYR O 75 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'N' and resid 32 through 35 removed outlier: 7.145A pdb=" N LEU N 25 " --> pdb=" O LEU N 33 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR N 35 " --> pdb=" O THR N 23 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR N 23 " --> pdb=" O TYR N 35 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA N 96 " --> pdb=" O ARG N 81 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG N 81 " --> pdb=" O ALA N 96 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Q' and resid 34 through 35 removed outlier: 3.677A pdb=" N ARG Q 34 " --> pdb=" O VAL Q 21 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU Q 22 " --> pdb=" O ALA Q 85 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ALA Q 85 " --> pdb=" O LEU Q 22 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLY P 17 " --> pdb=" O LYS P 88 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N GLN P 90 " --> pdb=" O GLN P 15 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N GLN P 15 " --> pdb=" O GLN P 90 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N LEU P 16 " --> pdb=" O GLY P 31 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLY P 31 " --> pdb=" O LEU P 16 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N TYR P 18 " --> pdb=" O SER P 29 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N SER P 29 " --> pdb=" O TYR P 18 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VAL P 20 " --> pdb=" O LEU P 27 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 45 through 47 removed outlier: 7.472A pdb=" N LYS K 8 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N TRP K 61 " --> pdb=" O LYS K 8 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL K 10 " --> pdb=" O TRP K 61 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N CYS K 63 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU K 12 " --> pdb=" O CYS K 63 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS K 9 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE K 89 " --> pdb=" O LYS K 9 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU K 11 " --> pdb=" O ILE K 89 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLU K 86 " --> pdb=" O LYS K 121 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE K 123 " --> pdb=" O GLU K 86 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU K 88 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU K 125 " --> pdb=" O LEU K 88 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR K 90 " --> pdb=" O LEU K 125 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS K 127 " --> pdb=" O TYR K 90 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N PHE K 92 " --> pdb=" O HIS K 127 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 50 through 52 removed outlier: 7.472A pdb=" N LYS K 8 " --> pdb=" O ASN K 59 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N TRP K 61 " --> pdb=" O LYS K 8 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL K 10 " --> pdb=" O TRP K 61 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N CYS K 63 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU K 12 " --> pdb=" O CYS K 63 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LYS K 9 " --> pdb=" O VAL K 87 " (cutoff:3.500A) removed outlier: 7.970A pdb=" N ILE K 89 " --> pdb=" O LYS K 9 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU K 11 " --> pdb=" O ILE K 89 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLU K 86 " --> pdb=" O LYS K 121 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE K 123 " --> pdb=" O GLU K 86 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N LEU K 88 " --> pdb=" O PHE K 123 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU K 125 " --> pdb=" O LEU K 88 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N TYR K 90 " --> pdb=" O LEU K 125 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N HIS K 127 " --> pdb=" O TYR K 90 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 213 through 218 removed outlier: 6.765A pdb=" N THR K 270 " --> pdb=" O PHE K 266 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'L' and resid 64 through 65 removed outlier: 3.635A pdb=" N ILE L 141 " --> pdb=" O LEU L 65 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU L 140 " --> pdb=" O GLU L 174 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N PHE L 176 " --> pdb=" O LEU L 140 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N TYR L 142 " --> pdb=" O PHE L 176 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N VAL L 175 " --> pdb=" O SER L 214 " (cutoff:3.500A) 1466 hydrogen bonds defined for protein. 4138 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: 7.24 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9301 1.33 - 1.46: 7620 1.46 - 1.58: 15886 1.58 - 1.71: 16 1.71 - 1.83: 285 Bond restraints: 33108 Sorted by residual: bond pdb=" F2 AF3 K 502 " pdb="AL AF3 K 502 " ideal model delta sigma weight residual 1.637 1.710 -0.073 2.00e-02 2.50e+03 1.33e+01 bond pdb=" F2 AF3 E 502 " pdb="AL AF3 E 502 " ideal model delta sigma weight residual 1.637 1.708 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" F1 AF3 E 502 " pdb="AL AF3 E 502 " ideal model delta sigma weight residual 1.637 1.708 -0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" F3 AF3 K 502 " pdb="AL AF3 K 502 " ideal model delta sigma weight residual 1.637 1.707 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" F1 AF3 K 502 " pdb="AL AF3 K 502 " ideal model delta sigma weight residual 1.637 1.706 -0.069 2.00e-02 2.50e+03 1.21e+01 ... (remaining 33103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 43943 4.20 - 8.40: 767 8.40 - 12.59: 94 12.59 - 16.79: 21 16.79 - 20.99: 5 Bond angle restraints: 44830 Sorted by residual: angle pdb=" C GLN A 413 " pdb=" N LEU A 414 " pdb=" CA LEU A 414 " ideal model delta sigma weight residual 121.54 135.82 -14.28 1.91e+00 2.74e-01 5.59e+01 angle pdb=" CB MET A 369 " pdb=" CG MET A 369 " pdb=" SD MET A 369 " ideal model delta sigma weight residual 112.70 132.45 -19.75 3.00e+00 1.11e-01 4.33e+01 angle pdb=" CA GLU A 266 " pdb=" CB GLU A 266 " pdb=" CG GLU A 266 " ideal model delta sigma weight residual 114.10 126.95 -12.85 2.00e+00 2.50e-01 4.13e+01 angle pdb=" CB MET A 114 " pdb=" CG MET A 114 " pdb=" SD MET A 114 " ideal model delta sigma weight residual 112.70 131.11 -18.41 3.00e+00 1.11e-01 3.77e+01 angle pdb=" C ASP D 93 " pdb=" N VAL D 94 " pdb=" CA VAL D 94 " ideal model delta sigma weight residual 122.66 116.83 5.83 9.70e-01 1.06e+00 3.61e+01 ... (remaining 44825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.71: 18456 23.71 - 47.43: 1393 47.43 - 71.14: 99 71.14 - 94.85: 26 94.85 - 118.56: 3 Dihedral angle restraints: 19977 sinusoidal: 8064 harmonic: 11913 Sorted by residual: dihedral pdb=" CA TYR E 269 " pdb=" C TYR E 269 " pdb=" N ILE E 270 " pdb=" CA ILE E 270 " ideal model delta harmonic sigma weight residual -180.00 -118.37 -61.63 0 5.00e+00 4.00e-02 1.52e+02 dihedral pdb=" CA VAL A 258 " pdb=" C VAL A 258 " pdb=" N VAL A 259 " pdb=" CA VAL A 259 " ideal model delta harmonic sigma weight residual -180.00 -122.55 -57.45 0 5.00e+00 4.00e-02 1.32e+02 dihedral pdb=" CA ILE B 23 " pdb=" C ILE B 23 " pdb=" N THR B 24 " pdb=" CA THR B 24 " ideal model delta harmonic sigma weight residual -180.00 -124.80 -55.20 0 5.00e+00 4.00e-02 1.22e+02 ... (remaining 19974 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.147: 4857 0.147 - 0.294: 214 0.294 - 0.442: 23 0.442 - 0.589: 1 0.589 - 0.736: 1 Chirality restraints: 5096 Sorted by residual: chirality pdb=" CB ILE L 225 " pdb=" CA ILE L 225 " pdb=" CG1 ILE L 225 " pdb=" CG2 ILE L 225 " both_signs ideal model delta sigma weight residual False 2.64 1.91 0.74 2.00e-01 2.50e+01 1.35e+01 chirality pdb=" CB VAL B 40 " pdb=" CA VAL B 40 " pdb=" CG1 VAL B 40 " pdb=" CG2 VAL B 40 " both_signs ideal model delta sigma weight residual False -2.63 -2.16 -0.47 2.00e-01 2.50e+01 5.60e+00 chirality pdb=" CB ILE L 237 " pdb=" CA ILE L 237 " pdb=" CG1 ILE L 237 " pdb=" CG2 ILE L 237 " both_signs ideal model delta sigma weight residual False 2.64 2.20 0.44 2.00e-01 2.50e+01 4.87e+00 ... (remaining 5093 not shown) Planarity restraints: 5714 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 27 " -0.079 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO B 28 " 0.209 5.00e-02 4.00e+02 pdb=" CA PRO B 28 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO B 28 " -0.068 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 344 " 0.022 2.00e-02 2.50e+03 4.56e-02 2.08e+01 pdb=" CD GLU A 344 " -0.079 2.00e-02 2.50e+03 pdb=" OE1 GLU A 344 " 0.028 2.00e-02 2.50e+03 pdb=" OE2 GLU A 344 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 216 " 0.033 2.00e-02 2.50e+03 3.09e-02 1.91e+01 pdb=" CG TYR L 216 " -0.077 2.00e-02 2.50e+03 pdb=" CD1 TYR L 216 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR L 216 " 0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR L 216 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR L 216 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR L 216 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR L 216 " 0.001 2.00e-02 2.50e+03 ... (remaining 5711 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 654 2.63 - 3.20: 28547 3.20 - 3.77: 56651 3.77 - 4.33: 72782 4.33 - 4.90: 113111 Nonbonded interactions: 271745 Sorted by model distance: nonbonded pdb=" O LEU A 9 " pdb=" CA TYR A 82 " model vdw 2.068 3.470 nonbonded pdb=" O PHE D 206 " pdb=" OG1 THR D 270 " model vdw 2.175 3.040 nonbonded pdb=" O2B GDP K 501 " pdb=" F3 AF3 K 502 " model vdw 2.219 2.990 nonbonded pdb=" OD2 ASP D 166 " pdb=" OG1 THR D 168 " model vdw 2.227 3.040 nonbonded pdb=" O ASP K 44 " pdb=" OH TYR K 73 " model vdw 2.233 3.040 ... (remaining 271740 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 Found NCS groups: ncs_group { reference = chain 'D' selection = (chain 'K' and resid 5 through 502) } ncs_group { reference = (chain 'E' and (resid 62 through 74 or resid 76 through 91 or resid 93 through 3 \ 67)) selection = (chain 'L' and (resid 62 through 74 or resid 76 through 91 or resid 93 through 3 \ 67)) } ncs_group { reference = chain 'F' selection = (chain 'M' and resid 49 through 159) } ncs_group { reference = (chain 'G' and resid 2 through 125) selection = chain 'N' } ncs_group { reference = (chain 'H' and resid 3 through 122) selection = chain 'O' } ncs_group { reference = chain 'I' selection = (chain 'P' and (resid 4 through 56 or resid 61 through 92)) } ncs_group { reference = (chain 'J' and (resid 1 through 22 or resid 24 through 91)) selection = (chain 'Q' and (resid 1 through 22 or resid 24 through 91)) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.760 Check model and map are aligned: 0.100 Set scattering table: 0.090 Process input model: 28.610 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.070 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6880 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 : 0.008 0.094 33112 Z= 0.354 Angle : 1.408 20.990 44830 Z= 0.746 Chirality : 0.075 0.736 5096 Planarity : 0.008 0.121 5714 Dihedral : 15.653 118.563 12225 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.07 % Favored : 88.86 % Rotamer: Outliers : 0.03 % Allowed : 0.92 % Favored : 99.06 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 2.08 % Twisted General : 0.85 % 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: -3.78 (0.11), residues: 3988 helix: -2.47 (0.10), residues: 1493 sheet: -1.76 (0.20), residues: 668 loop : -2.77 (0.13), residues: 1827 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG A 806 TYR 0.077 0.004 TYR L 216 PHE 0.066 0.004 PHE L 226 TRP 0.052 0.004 TRP A1558 HIS 0.014 0.003 HIS E 187 Details of bonding type rmsd covalent geometry : bond 0.00754 (33108) covalent geometry : angle 1.40769 (44830) hydrogen bonds : bond 0.13039 ( 1461) hydrogen bonds : angle 8.64066 ( 4138) Misc. bond : bond 0.00154 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 184 PHE cc_start: 0.8764 (p90) cc_final: 0.8509 (p90) REVERT: A 327 ASP cc_start: 0.8101 (p0) cc_final: 0.7785 (p0) REVERT: A 357 MET cc_start: 0.8354 (mmp) cc_final: 0.7964 (mmm) REVERT: A 808 MET cc_start: 0.7812 (mmm) cc_final: 0.7258 (mmt) REVERT: A 1256 TYR cc_start: 0.7298 (m-80) cc_final: 0.6990 (m-10) REVERT: A 1294 PHE cc_start: 0.8164 (m-80) cc_final: 0.7646 (m-80) REVERT: A 1403 GLN cc_start: 0.8530 (mm-40) cc_final: 0.8273 (mp10) REVERT: G 77 MET cc_start: 0.7910 (pmm) cc_final: 0.7279 (tmm) REVERT: J 1 MET cc_start: 0.7389 (mmp) cc_final: 0.6500 (tpp) REVERT: D 13 MET cc_start: 0.9148 (tmm) cc_final: 0.8839 (tmm) REVERT: D 23 MET cc_start: 0.8468 (mmt) cc_final: 0.8117 (mmt) REVERT: D 180 LEU cc_start: 0.9241 (tp) cc_final: 0.8932 (tt) REVERT: D 273 MET cc_start: 0.2805 (pmm) cc_final: 0.2282 (pmm) REVERT: D 276 MET cc_start: 0.6298 (tpp) cc_final: 0.5724 (tpp) REVERT: E 63 ARG cc_start: 0.8154 (mmp-170) cc_final: 0.7357 (tmm-80) REVERT: E 78 GLN cc_start: 0.9031 (tp-100) cc_final: 0.8803 (tp-100) REVERT: O 42 GLU cc_start: 0.8578 (pt0) cc_final: 0.8334 (pp20) REVERT: N 81 ARG cc_start: 0.7879 (ptt180) cc_final: 0.7201 (ppt170) REVERT: L 151 MET cc_start: 0.8010 (mmt) cc_final: 0.7595 (pmm) outliers start: 0 outliers final: 0 residues processed: 262 average time/residue: 0.2090 time to fit residues: 88.0785 Evaluate side-chains 206 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.9980 chunk 155 optimal weight: 30.0000 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 194 GLN B 207 GLN A 405 HIS A 413 GLN A 805 GLN A 861 HIS A1212 HIS ** A1484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN ** D 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 196 HIS ** N 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 HIS Q 27 GLN M 64 ASN M 114 GLN K 222 GLN L 192 GLN ** L 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 364 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.076184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.062406 restraints weight = 414665.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 82)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.063213 restraints weight = 311396.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.062859 restraints weight = 224670.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.062985 restraints weight = 191298.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.063191 restraints weight = 167161.745| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3905 r_free = 0.3905 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6478 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 33112 Z= 0.136 Angle : 0.751 10.639 44830 Z= 0.390 Chirality : 0.048 0.251 5096 Planarity : 0.005 0.087 5714 Dihedral : 8.045 137.400 4393 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.98 % Favored : 90.99 % Rotamer: Outliers : 0.75 % Allowed : 9.25 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.21 % 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: -2.92 (0.12), residues: 3988 helix: -1.34 (0.12), residues: 1538 sheet: -1.74 (0.19), residues: 685 loop : -2.49 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 80 TYR 0.031 0.002 TYR L 282 PHE 0.039 0.002 PHE L 226 TRP 0.018 0.001 TRP A1390 HIS 0.006 0.001 HIS L 364 Details of bonding type rmsd covalent geometry : bond 0.00285 (33108) covalent geometry : angle 0.75058 (44830) hydrogen bonds : bond 0.04392 ( 1461) hydrogen bonds : angle 6.72112 ( 4138) Misc. bond : bond 0.00097 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 234 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 170 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7945 (tmm) REVERT: A 193 GLU cc_start: 0.8883 (mp0) cc_final: 0.8677 (mm-30) REVERT: A 327 ASP cc_start: 0.7169 (p0) cc_final: 0.6798 (p0) REVERT: A 808 MET cc_start: 0.8286 (mmm) cc_final: 0.7351 (mmt) REVERT: A 1226 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.7706 (tpp) REVERT: A 1358 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8198 (p) REVERT: G 77 MET cc_start: 0.7467 (pmm) cc_final: 0.6875 (mtt) REVERT: F 86 ARG cc_start: 0.6614 (tpp-160) cc_final: 0.6380 (tmm160) REVERT: D 180 LEU cc_start: 0.8904 (tp) cc_final: 0.8623 (tt) REVERT: O 42 GLU cc_start: 0.8758 (pt0) cc_final: 0.8197 (pp20) REVERT: N 75 MET cc_start: 0.9059 (mmt) cc_final: 0.7613 (ppp) REVERT: K 13 MET cc_start: 0.4826 (mmt) cc_final: 0.3734 (mmt) outliers start: 26 outliers final: 11 residues processed: 248 average time/residue: 0.1970 time to fit residues: 79.5939 Evaluate side-chains 218 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1226 MET Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 247 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 137 optimal weight: 3.9990 chunk 268 optimal weight: 20.0000 chunk 135 optimal weight: 10.0000 chunk 179 optimal weight: 20.0000 chunk 221 optimal weight: 6.9990 chunk 162 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 315 optimal weight: 0.4980 chunk 312 optimal weight: 20.0000 chunk 215 optimal weight: 9.9990 chunk 84 optimal weight: 6.9990 overall best weight: 3.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 92 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 226 ASN A 107 GLN A 298 ASN A 331 GLN A 413 GLN ** A1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1403 GLN A1547 ASN ** H 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 74 GLN ** M 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.073582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.060895 restraints weight = 490770.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.061038 restraints weight = 365822.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.061257 restraints weight = 303000.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.061440 restraints weight = 231357.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.061452 restraints weight = 205684.391| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3822 r_free = 0.3822 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3822 r_free = 0.3822 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 33112 Z= 0.192 Angle : 0.763 9.878 44830 Z= 0.400 Chirality : 0.047 0.232 5096 Planarity : 0.005 0.075 5714 Dihedral : 7.788 140.622 4393 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 20.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.66 % Favored : 89.28 % Rotamer: Outliers : 1.72 % Allowed : 13.61 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.18 % 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: -2.59 (0.13), residues: 3988 helix: -0.92 (0.12), residues: 1539 sheet: -1.72 (0.19), residues: 692 loop : -2.40 (0.15), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 356 TYR 0.026 0.002 TYR L 327 PHE 0.030 0.002 PHE L 226 TRP 0.014 0.002 TRP A 145 HIS 0.007 0.001 HIS A1406 Details of bonding type rmsd covalent geometry : bond 0.00410 (33108) covalent geometry : angle 0.76332 (44830) hydrogen bonds : bond 0.04455 ( 1461) hydrogen bonds : angle 6.52356 ( 4138) Misc. bond : bond 0.00098 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 217 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 319 MET cc_start: 0.8604 (pmm) cc_final: 0.8363 (pmm) REVERT: A 193 GLU cc_start: 0.9020 (mp0) cc_final: 0.8778 (mm-30) REVERT: A 306 TYR cc_start: 0.7371 (OUTLIER) cc_final: 0.6048 (p90) REVERT: A 327 ASP cc_start: 0.7810 (p0) cc_final: 0.7404 (p0) REVERT: G 77 MET cc_start: 0.7624 (pmm) cc_final: 0.7090 (mtt) REVERT: D 180 LEU cc_start: 0.9135 (tp) cc_final: 0.8877 (tt) REVERT: E 364 HIS cc_start: 0.9152 (m90) cc_final: 0.8944 (m90) REVERT: O 42 GLU cc_start: 0.8873 (pt0) cc_final: 0.8239 (tm-30) REVERT: K 167 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7361 (pm20) REVERT: L 268 ILE cc_start: 0.8137 (mm) cc_final: 0.7851 (mm) outliers start: 61 outliers final: 32 residues processed: 257 average time/residue: 0.2013 time to fit residues: 84.8909 Evaluate side-chains 238 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 72 ASN Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain K residue 228 PHE Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 282 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 86 optimal weight: 7.9990 chunk 173 optimal weight: 7.9990 chunk 259 optimal weight: 50.0000 chunk 155 optimal weight: 20.0000 chunk 328 optimal weight: 20.0000 chunk 165 optimal weight: 30.0000 chunk 84 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 272 optimal weight: 5.9990 chunk 108 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 280 GLN A 355 GLN A 797 GLN ** A 805 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 809 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1224 GLN ** A1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN D 218 GLN D 258 ASN ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN ** E 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 41 HIS ** Q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN ** M 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 196 HIS ** L 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.070791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.058085 restraints weight = 493763.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.058322 restraints weight = 396103.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.058750 restraints weight = 305219.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.058947 restraints weight = 233793.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.059647 restraints weight = 210595.806| |-----------------------------------------------------------------------------| r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3758 r_free = 0.3758 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6679 moved from start: 0.2743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.126 33112 Z= 0.294 Angle : 0.887 12.221 44830 Z= 0.466 Chirality : 0.051 0.244 5096 Planarity : 0.006 0.070 5714 Dihedral : 8.288 149.899 4393 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 30.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.65 % Favored : 87.30 % Rotamer: Outliers : 3.22 % Allowed : 17.22 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.26 % 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: -2.84 (0.13), residues: 3988 helix: -1.07 (0.12), residues: 1517 sheet: -1.81 (0.20), residues: 651 loop : -2.61 (0.14), residues: 1820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 63 TYR 0.026 0.003 TYR L 327 PHE 0.037 0.003 PHE L 226 TRP 0.022 0.002 TRP A1390 HIS 0.011 0.002 HIS L 178 Details of bonding type rmsd covalent geometry : bond 0.00626 (33108) covalent geometry : angle 0.88719 (44830) hydrogen bonds : bond 0.05172 ( 1461) hydrogen bonds : angle 7.05237 ( 4138) Misc. bond : bond 0.00155 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 195 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 297 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8716 (mp) REVERT: A 170 MET cc_start: 0.8541 (OUTLIER) cc_final: 0.8012 (tmm) REVERT: A 177 MET cc_start: 0.8260 (OUTLIER) cc_final: 0.6676 (ppp) REVERT: A 193 GLU cc_start: 0.9018 (mp0) cc_final: 0.8786 (mm-30) REVERT: A 306 TYR cc_start: 0.7730 (OUTLIER) cc_final: 0.7041 (p90) REVERT: A 327 ASP cc_start: 0.7861 (p0) cc_final: 0.7349 (p0) REVERT: A 340 VAL cc_start: 0.7804 (t) cc_final: 0.7496 (p) REVERT: A 357 MET cc_start: 0.7332 (mmm) cc_final: 0.7046 (tpp) REVERT: A 369 MET cc_start: 0.6640 (tmm) cc_final: 0.6404 (tmm) REVERT: A 917 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7278 (ptmm) REVERT: G 77 MET cc_start: 0.7420 (pmm) cc_final: 0.6986 (pmm) REVERT: I 82 GLN cc_start: 0.3226 (OUTLIER) cc_final: 0.2889 (tp-100) REVERT: F 86 ARG cc_start: 0.6636 (tpp-160) cc_final: 0.6409 (tmm160) REVERT: D 165 TRP cc_start: 0.7061 (OUTLIER) cc_final: 0.4640 (m-90) REVERT: E 165 TYR cc_start: 0.8407 (t80) cc_final: 0.8107 (t80) REVERT: E 171 MET cc_start: 0.3734 (ttt) cc_final: 0.3532 (ttm) REVERT: E 318 ILE cc_start: 0.4836 (OUTLIER) cc_final: 0.4392 (mm) REVERT: E 364 HIS cc_start: 0.9180 (m90) cc_final: 0.8960 (m90) REVERT: O 42 GLU cc_start: 0.8955 (pt0) cc_final: 0.8342 (pp20) REVERT: N 4 ARG cc_start: 0.4383 (OUTLIER) cc_final: 0.2187 (ptp90) REVERT: N 75 MET cc_start: 0.8998 (mpp) cc_final: 0.7693 (ppp) REVERT: N 104 MET cc_start: 0.8796 (mmm) cc_final: 0.8553 (mmt) REVERT: K 12 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7222 (tt) REVERT: K 13 MET cc_start: 0.6380 (mmt) cc_final: 0.5675 (mtt) REVERT: K 167 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7529 (pm20) REVERT: L 359 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7449 (p90) outliers start: 115 outliers final: 64 residues processed: 291 average time/residue: 0.1944 time to fit residues: 93.6130 Evaluate side-chains 257 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 181 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 152 MET Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 794 THR Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 917 LYS Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1296 VAL Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1472 PHE Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1583 ARG Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain J residue 73 ASN Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain I residue 82 GLN Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 165 TRP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain N residue 4 ARG Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 43 ILE Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 72 ASN Chi-restraints excluded: chain K residue 167 GLU Chi-restraints excluded: chain K residue 228 PHE Chi-restraints excluded: chain K residue 250 GLN Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain K residue 287 LEU Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain L residue 196 HIS Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 357 HIS Chi-restraints excluded: chain L residue 359 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 24 optimal weight: 0.3980 chunk 10 optimal weight: 5.9990 chunk 139 optimal weight: 20.0000 chunk 64 optimal weight: 0.1980 chunk 391 optimal weight: 10.0000 chunk 367 optimal weight: 7.9990 chunk 245 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 344 optimal weight: 0.6980 chunk 219 optimal weight: 8.9990 chunk 138 optimal weight: 7.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN B 321 ASN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 GLN A 355 GLN A 805 GLN A 809 GLN ** A1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 ASN D 133 GLN D 258 ASN ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 116 HIS K 115 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.073866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.061115 restraints weight = 415119.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.061746 restraints weight = 308871.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.061829 restraints weight = 241904.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.062105 restraints weight = 196899.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.062129 restraints weight = 171230.578| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3836 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3836 r_free = 0.3836 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 33112 Z= 0.141 Angle : 0.722 10.327 44830 Z= 0.373 Chirality : 0.047 0.239 5096 Planarity : 0.005 0.065 5714 Dihedral : 7.565 161.084 4393 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.41 % Favored : 90.56 % Rotamer: Outliers : 2.69 % Allowed : 19.11 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -2.46 (0.13), residues: 3988 helix: -0.65 (0.13), residues: 1561 sheet: -1.67 (0.20), residues: 665 loop : -2.51 (0.14), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.023 0.002 TYR L 282 PHE 0.034 0.002 PHE L 226 TRP 0.016 0.001 TRP A1390 HIS 0.009 0.001 HIS L 196 Details of bonding type rmsd covalent geometry : bond 0.00308 (33108) covalent geometry : angle 0.72154 (44830) hydrogen bonds : bond 0.04118 ( 1461) hydrogen bonds : angle 6.29209 ( 4138) Misc. bond : bond 0.00091 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 221 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 ARG cc_start: 0.7575 (tpp-160) cc_final: 0.6678 (tpm170) REVERT: A 114 MET cc_start: 0.9155 (mpp) cc_final: 0.8915 (mpp) REVERT: A 177 MET cc_start: 0.7474 (OUTLIER) cc_final: 0.6848 (ppp) REVERT: A 306 TYR cc_start: 0.7473 (OUTLIER) cc_final: 0.6318 (p90) REVERT: A 327 ASP cc_start: 0.7395 (p0) cc_final: 0.6931 (p0) REVERT: A 332 MET cc_start: 0.4085 (ptt) cc_final: 0.3851 (ptt) REVERT: A 340 VAL cc_start: 0.7759 (t) cc_final: 0.7533 (p) REVERT: A 369 MET cc_start: 0.6285 (tmm) cc_final: 0.5957 (tmm) REVERT: A 812 GLN cc_start: 0.8524 (mp10) cc_final: 0.8043 (mp10) REVERT: A 856 MET cc_start: 0.7908 (ppp) cc_final: 0.7007 (ppp) REVERT: G 77 MET cc_start: 0.7440 (pmm) cc_final: 0.6804 (mtt) REVERT: F 86 ARG cc_start: 0.6361 (tpp-160) cc_final: 0.6134 (tmm160) REVERT: C 11 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8658 (mm) REVERT: C 530 MET cc_start: 0.8357 (ppp) cc_final: 0.8103 (ppp) REVERT: D 46 GLU cc_start: 0.6956 (mt-10) cc_final: 0.6637 (mt-10) REVERT: D 103 MET cc_start: 0.7780 (mmm) cc_final: 0.7577 (mmm) REVERT: D 165 TRP cc_start: 0.7230 (OUTLIER) cc_final: 0.5136 (m-90) REVERT: D 180 LEU cc_start: 0.9193 (tp) cc_final: 0.8968 (tt) REVERT: E 171 MET cc_start: 0.3872 (ttt) cc_final: 0.3582 (ttm) REVERT: E 318 ILE cc_start: 0.3851 (OUTLIER) cc_final: 0.3370 (mm) REVERT: E 364 HIS cc_start: 0.9167 (m90) cc_final: 0.8791 (m90) REVERT: O 42 GLU cc_start: 0.8867 (pt0) cc_final: 0.8165 (tm-30) REVERT: N 104 MET cc_start: 0.8736 (mmm) cc_final: 0.8461 (mmt) REVERT: P 59 MET cc_start: 0.2098 (mtm) cc_final: 0.1358 (ptt) REVERT: K 12 LEU cc_start: 0.7142 (OUTLIER) cc_final: 0.6833 (tt) REVERT: K 13 MET cc_start: 0.5781 (mmt) cc_final: 0.4622 (mmt) REVERT: L 226 PHE cc_start: 0.7102 (OUTLIER) cc_final: 0.6469 (p90) REVERT: L 359 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7584 (p90) outliers start: 96 outliers final: 48 residues processed: 299 average time/residue: 0.1837 time to fit residues: 91.5136 Evaluate side-chains 258 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 202 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1296 VAL Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1472 PHE Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1583 ARG Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 165 TRP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain O residue 43 HIS Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 72 ASN Chi-restraints excluded: chain K residue 228 PHE Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain L residue 196 HIS Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 359 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 292 optimal weight: 9.9990 chunk 125 optimal weight: 5.9990 chunk 392 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 284 optimal weight: 8.9990 chunk 316 optimal weight: 30.0000 chunk 343 optimal weight: 10.0000 chunk 59 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 355 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 overall best weight: 3.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 HIS ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.072912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.060072 restraints weight = 450336.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.060943 restraints weight = 325389.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.060954 restraints weight = 240053.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.061183 restraints weight = 196266.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.061297 restraints weight = 169891.107| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3806 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3806 r_free = 0.3806 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3806 r_free = 0.3806 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3806 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 33112 Z= 0.172 Angle : 0.740 11.306 44830 Z= 0.382 Chirality : 0.048 0.293 5096 Planarity : 0.005 0.072 5714 Dihedral : 7.482 160.290 4393 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 22.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.77 % Favored : 89.21 % Rotamer: Outliers : 2.86 % Allowed : 20.38 % Favored : 76.76 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.15 % 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: -2.37 (0.13), residues: 3988 helix: -0.49 (0.13), residues: 1554 sheet: -1.69 (0.20), residues: 663 loop : -2.50 (0.14), residues: 1771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.023 0.002 TYR L 282 PHE 0.033 0.002 PHE L 226 TRP 0.020 0.001 TRP A1390 HIS 0.005 0.001 HIS L 178 Details of bonding type rmsd covalent geometry : bond 0.00377 (33108) covalent geometry : angle 0.74037 (44830) hydrogen bonds : bond 0.04186 ( 1461) hydrogen bonds : angle 6.26816 ( 4138) Misc. bond : bond 0.00078 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 207 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 75 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8309 (tmmt) REVERT: A 177 MET cc_start: 0.7788 (OUTLIER) cc_final: 0.6654 (ppp) REVERT: A 306 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.6434 (p90) REVERT: A 327 ASP cc_start: 0.7554 (p0) cc_final: 0.7112 (p0) REVERT: A 340 VAL cc_start: 0.7835 (t) cc_final: 0.7548 (p) REVERT: A 792 GLN cc_start: 0.6732 (OUTLIER) cc_final: 0.6150 (mm-40) REVERT: A 856 MET cc_start: 0.8092 (ppp) cc_final: 0.7766 (ppp) REVERT: G 77 MET cc_start: 0.7435 (pmm) cc_final: 0.6742 (ttm) REVERT: F 82 MET cc_start: 0.6438 (tpp) cc_final: 0.6197 (ppp) REVERT: F 86 ARG cc_start: 0.6371 (tpp-160) cc_final: 0.6129 (tmm160) REVERT: D 46 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6798 (mt-10) REVERT: D 165 TRP cc_start: 0.7228 (OUTLIER) cc_final: 0.5075 (m-90) REVERT: D 180 LEU cc_start: 0.9183 (tp) cc_final: 0.8965 (tt) REVERT: E 178 HIS cc_start: 0.6768 (OUTLIER) cc_final: 0.6498 (m170) REVERT: E 315 MET cc_start: -0.0226 (OUTLIER) cc_final: -0.0543 (mmt) REVERT: E 318 ILE cc_start: 0.3967 (OUTLIER) cc_final: 0.3468 (mm) REVERT: E 364 HIS cc_start: 0.9192 (m90) cc_final: 0.8812 (m90) REVERT: O 42 GLU cc_start: 0.8910 (pt0) cc_final: 0.8219 (tm-30) REVERT: N 75 MET cc_start: 0.9133 (mpp) cc_final: 0.7809 (ppp) REVERT: P 59 MET cc_start: 0.2161 (mtm) cc_final: 0.1433 (ptt) REVERT: K 12 LEU cc_start: 0.7244 (OUTLIER) cc_final: 0.6658 (tt) REVERT: K 13 MET cc_start: 0.6009 (mmt) cc_final: 0.4995 (mtt) REVERT: L 151 MET cc_start: 0.8389 (mmt) cc_final: 0.7668 (pmm) REVERT: L 226 PHE cc_start: 0.7125 (OUTLIER) cc_final: 0.6412 (p90) REVERT: L 244 GLU cc_start: 0.2948 (OUTLIER) cc_final: 0.2550 (mt-10) REVERT: L 359 PHE cc_start: 0.8118 (OUTLIER) cc_final: 0.7531 (p90) outliers start: 102 outliers final: 60 residues processed: 295 average time/residue: 0.1871 time to fit residues: 91.7886 Evaluate side-chains 267 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 195 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1296 VAL Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1356 LEU Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1583 ARG Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 165 TRP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 178 HIS Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain O residue 43 HIS Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 72 ASN Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 228 PHE Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 244 GLU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 359 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 351 optimal weight: 8.9990 chunk 70 optimal weight: 1.9990 chunk 210 optimal weight: 5.9990 chunk 235 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 295 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 35 optimal weight: 7.9990 chunk 315 optimal weight: 0.0370 chunk 201 optimal weight: 30.0000 chunk 290 optimal weight: 8.9990 overall best weight: 2.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 ASN B 321 ASN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 289 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.073844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.061179 restraints weight = 501363.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.061796 restraints weight = 353881.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.062095 restraints weight = 249768.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.062124 restraints weight = 221607.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.062655 restraints weight = 189523.244| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3848 r_free = 0.3848 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.3071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 33112 Z= 0.142 Angle : 0.726 15.971 44830 Z= 0.370 Chirality : 0.047 0.292 5096 Planarity : 0.004 0.073 5714 Dihedral : 7.242 163.343 4393 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.56 % Favored : 90.41 % Rotamer: Outliers : 2.75 % Allowed : 20.99 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.13 % 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: -2.24 (0.13), residues: 3988 helix: -0.36 (0.13), residues: 1564 sheet: -1.63 (0.20), residues: 669 loop : -2.47 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG N 81 TYR 0.029 0.002 TYR E 165 PHE 0.032 0.002 PHE L 226 TRP 0.017 0.001 TRP A1390 HIS 0.005 0.001 HIS A 887 Details of bonding type rmsd covalent geometry : bond 0.00314 (33108) covalent geometry : angle 0.72566 (44830) hydrogen bonds : bond 0.03959 ( 1461) hydrogen bonds : angle 6.05231 ( 4138) Misc. bond : bond 0.00079 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 215 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8523 (mt) REVERT: A 177 MET cc_start: 0.7612 (OUTLIER) cc_final: 0.6580 (ppp) REVERT: A 306 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.6228 (p90) REVERT: A 327 ASP cc_start: 0.7567 (p0) cc_final: 0.7188 (p0) REVERT: A 369 MET cc_start: 0.5853 (tmm) cc_final: 0.5556 (tmm) REVERT: A 792 GLN cc_start: 0.6734 (OUTLIER) cc_final: 0.6207 (mm-40) REVERT: A 856 MET cc_start: 0.8058 (ppp) cc_final: 0.7709 (ppp) REVERT: G 77 MET cc_start: 0.7378 (pmm) cc_final: 0.6696 (ttm) REVERT: J 1 MET cc_start: 0.6217 (mmp) cc_final: 0.5933 (tpt) REVERT: I 64 LYS cc_start: 0.7815 (tppt) cc_final: 0.7584 (tptt) REVERT: F 82 MET cc_start: 0.6467 (tpp) cc_final: 0.6169 (ppp) REVERT: F 86 ARG cc_start: 0.6431 (tpp-160) cc_final: 0.6156 (tmm160) REVERT: C 397 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.5862 (mtt) REVERT: C 411 CYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7537 (t) REVERT: C 413 MET cc_start: 0.6807 (mmm) cc_final: 0.6313 (mmm) REVERT: D 165 TRP cc_start: 0.7240 (OUTLIER) cc_final: 0.5171 (m-90) REVERT: D 180 LEU cc_start: 0.9142 (tp) cc_final: 0.8906 (tt) REVERT: E 315 MET cc_start: -0.0432 (OUTLIER) cc_final: -0.0708 (mmt) REVERT: E 318 ILE cc_start: 0.3782 (OUTLIER) cc_final: 0.3385 (mm) REVERT: E 364 HIS cc_start: 0.9200 (m90) cc_final: 0.8891 (m90) REVERT: O 42 GLU cc_start: 0.8939 (pt0) cc_final: 0.8321 (tm-30) REVERT: N 75 MET cc_start: 0.9100 (mpp) cc_final: 0.7740 (ppp) REVERT: N 104 MET cc_start: 0.8717 (mmm) cc_final: 0.8389 (mmm) REVERT: P 59 MET cc_start: 0.2324 (mtm) cc_final: 0.1510 (ptt) REVERT: M 77 GLU cc_start: 0.8886 (tt0) cc_final: 0.8225 (tm-30) REVERT: K 12 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6854 (tt) REVERT: K 13 MET cc_start: 0.5847 (mmt) cc_final: 0.4826 (mmt) REVERT: L 226 PHE cc_start: 0.7094 (OUTLIER) cc_final: 0.6605 (p90) REVERT: L 359 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7544 (p90) outliers start: 98 outliers final: 60 residues processed: 298 average time/residue: 0.1907 time to fit residues: 95.2356 Evaluate side-chains 272 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 200 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 226 ASN Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1296 VAL Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1356 LEU Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1583 ARG Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain I residue 78 THR Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 165 TRP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain O residue 43 HIS Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 72 ASN Chi-restraints excluded: chain K residue 228 PHE Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 359 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 129 optimal weight: 1.9990 chunk 264 optimal weight: 20.0000 chunk 116 optimal weight: 7.9990 chunk 296 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 384 optimal weight: 9.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 375 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 HIS B 153 ASN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN A 83 GLN ** A1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 55 ASN ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 237 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.074171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.061298 restraints weight = 519603.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.061849 restraints weight = 401504.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.062335 restraints weight = 292254.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.062496 restraints weight = 216037.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.062582 restraints weight = 184093.270| |-----------------------------------------------------------------------------| r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3847 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3847 r_free = 0.3847 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3847 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6526 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 33112 Z= 0.135 Angle : 0.721 11.974 44830 Z= 0.367 Chirality : 0.047 0.252 5096 Planarity : 0.004 0.073 5714 Dihedral : 7.095 163.066 4393 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.84 % Favored : 90.14 % Rotamer: Outliers : 2.58 % Allowed : 21.61 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.14 (0.13), residues: 3988 helix: -0.25 (0.13), residues: 1563 sheet: -1.59 (0.20), residues: 672 loop : -2.42 (0.14), residues: 1753 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 221 TYR 0.024 0.002 TYR L 282 PHE 0.027 0.001 PHE L 226 TRP 0.011 0.001 TRP A 115 HIS 0.005 0.001 HIS A 887 Details of bonding type rmsd covalent geometry : bond 0.00299 (33108) covalent geometry : angle 0.72088 (44830) hydrogen bonds : bond 0.03844 ( 1461) hydrogen bonds : angle 5.91036 ( 4138) Misc. bond : bond 0.00080 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 213 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8328 (mt) REVERT: A 177 MET cc_start: 0.7629 (OUTLIER) cc_final: 0.6530 (ppp) REVERT: A 306 TYR cc_start: 0.7481 (OUTLIER) cc_final: 0.6251 (p90) REVERT: A 327 ASP cc_start: 0.7604 (p0) cc_final: 0.7163 (p0) REVERT: A 369 MET cc_start: 0.5916 (tmm) cc_final: 0.5569 (tmm) REVERT: A 747 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8519 (mm) REVERT: A 792 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6451 (mm-40) REVERT: A 856 MET cc_start: 0.8080 (OUTLIER) cc_final: 0.7759 (ppp) REVERT: A 1403 GLN cc_start: 0.8307 (tp40) cc_final: 0.7930 (mm110) REVERT: G 77 MET cc_start: 0.7313 (pmm) cc_final: 0.6653 (mtt) REVERT: J 1 MET cc_start: 0.6013 (mmp) cc_final: 0.5805 (tpt) REVERT: F 82 MET cc_start: 0.6546 (tpp) cc_final: 0.6223 (ppp) REVERT: F 86 ARG cc_start: 0.6405 (tpp-160) cc_final: 0.6120 (tmm160) REVERT: D 46 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6613 (mt-10) REVERT: D 165 TRP cc_start: 0.7167 (OUTLIER) cc_final: 0.5097 (m-90) REVERT: D 180 LEU cc_start: 0.9090 (tp) cc_final: 0.8848 (tt) REVERT: E 318 ILE cc_start: 0.3770 (OUTLIER) cc_final: 0.3392 (mm) REVERT: E 364 HIS cc_start: 0.9198 (m90) cc_final: 0.8914 (m90) REVERT: O 42 GLU cc_start: 0.8969 (pt0) cc_final: 0.8334 (tm-30) REVERT: N 104 MET cc_start: 0.8727 (mmm) cc_final: 0.8270 (mmt) REVERT: P 59 MET cc_start: 0.2156 (mtm) cc_final: 0.1364 (ptt) REVERT: M 77 GLU cc_start: 0.8869 (tt0) cc_final: 0.8171 (tm-30) REVERT: K 12 LEU cc_start: 0.7156 (OUTLIER) cc_final: 0.6863 (tt) REVERT: K 13 MET cc_start: 0.5957 (mmt) cc_final: 0.4872 (mtt) REVERT: K 222 GLN cc_start: 0.6887 (tp-100) cc_final: 0.6048 (tm-30) REVERT: L 226 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.6369 (p90) REVERT: L 359 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7567 (p90) outliers start: 92 outliers final: 62 residues processed: 289 average time/residue: 0.1990 time to fit residues: 95.6135 Evaluate side-chains 276 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 203 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain B residue 319 MET Chi-restraints excluded: chain B residue 321 ASN Chi-restraints excluded: chain B residue 369 LEU Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 324 ARG Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 856 MET Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1296 VAL Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1356 LEU Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1583 ARG Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 165 TRP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 285 CYS Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain O residue 43 HIS Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 72 ASN Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 228 PHE Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 359 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 271 optimal weight: 8.9990 chunk 214 optimal weight: 9.9990 chunk 57 optimal weight: 6.9990 chunk 185 optimal weight: 3.9990 chunk 265 optimal weight: 30.0000 chunk 165 optimal weight: 20.0000 chunk 242 optimal weight: 9.9990 chunk 292 optimal weight: 20.0000 chunk 252 optimal weight: 20.0000 chunk 208 optimal weight: 30.0000 chunk 371 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 162 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 GLN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN ** A1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 8 HIS ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN D 258 ASN ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 364 HIS O 79 GLN ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 226 HIS K 289 ASN L 196 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.069578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.053174 restraints weight = 352648.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.052842 restraints weight = 306515.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.052993 restraints weight = 266433.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.052881 restraints weight = 247577.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.052918 restraints weight = 243612.451| |-----------------------------------------------------------------------------| r_work (final): 0.3743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.129 33112 Z= 0.306 Angle : 0.920 12.617 44830 Z= 0.477 Chirality : 0.052 0.256 5096 Planarity : 0.006 0.077 5714 Dihedral : 7.979 165.528 4393 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 32.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 12.65 % Favored : 87.28 % Rotamer: Outliers : 2.58 % Allowed : 22.49 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.63 (0.13), residues: 3988 helix: -0.75 (0.13), residues: 1539 sheet: -1.86 (0.20), residues: 662 loop : -2.58 (0.14), residues: 1787 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG I 65 TYR 0.032 0.003 TYR E 165 PHE 0.033 0.003 PHE L 226 TRP 0.024 0.002 TRP A 145 HIS 0.011 0.002 HIS A1504 Details of bonding type rmsd covalent geometry : bond 0.00659 (33108) covalent geometry : angle 0.91957 (44830) hydrogen bonds : bond 0.05095 ( 1461) hydrogen bonds : angle 6.78315 ( 4138) Misc. bond : bond 0.00134 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 196 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8753 (mm) REVERT: A 177 MET cc_start: 0.8172 (OUTLIER) cc_final: 0.6188 (ppp) REVERT: A 306 TYR cc_start: 0.7626 (OUTLIER) cc_final: 0.6547 (p90) REVERT: A 327 ASP cc_start: 0.8101 (p0) cc_final: 0.7417 (p0) REVERT: A 340 VAL cc_start: 0.7966 (t) cc_final: 0.7660 (p) REVERT: A 342 VAL cc_start: 0.8593 (m) cc_final: 0.8377 (p) REVERT: A 357 MET cc_start: 0.8100 (mmm) cc_final: 0.7895 (tpp) REVERT: A 792 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.6369 (mm-40) REVERT: A 856 MET cc_start: 0.7445 (ppp) cc_final: 0.7069 (ppp) REVERT: A 907 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7787 (mm-30) REVERT: G 77 MET cc_start: 0.7777 (pmm) cc_final: 0.7540 (pmm) REVERT: D 165 TRP cc_start: 0.7724 (OUTLIER) cc_final: 0.5568 (m-90) REVERT: D 273 MET cc_start: 0.4176 (pmm) cc_final: 0.3808 (pmm) REVERT: O 42 GLU cc_start: 0.8924 (pt0) cc_final: 0.8399 (tm-30) REVERT: N 104 MET cc_start: 0.8835 (mmm) cc_final: 0.8422 (mmm) REVERT: P 54 ARG cc_start: 0.7291 (mmp-170) cc_final: 0.6641 (ttp80) REVERT: M 77 GLU cc_start: 0.8701 (tt0) cc_final: 0.8320 (tm-30) REVERT: K 12 LEU cc_start: 0.6495 (OUTLIER) cc_final: 0.6246 (tt) REVERT: K 13 MET cc_start: 0.6764 (mmt) cc_final: 0.6392 (mtt) REVERT: L 226 PHE cc_start: 0.7439 (OUTLIER) cc_final: 0.6875 (p90) REVERT: L 244 GLU cc_start: 0.3331 (OUTLIER) cc_final: 0.2990 (mt-10) outliers start: 92 outliers final: 70 residues processed: 277 average time/residue: 0.1880 time to fit residues: 87.3483 Evaluate side-chains 265 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 186 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 238 ILE Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 225 PHE Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 907 GLU Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 989 PHE Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1221 ILE Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1296 VAL Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1356 LEU Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1583 ARG Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain C residue 499 LEU Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 59 ASN Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 165 TRP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain O residue 43 HIS Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 72 ASN Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 228 PHE Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 244 GLU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 325 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 142 optimal weight: 2.9990 chunk 120 optimal weight: 0.0770 chunk 269 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 347 optimal weight: 2.9990 chunk 164 optimal weight: 9.9990 chunk 300 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 384 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 176 GLN A 355 GLN ** A1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1403 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 GLN D 258 ASN ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 178 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.073641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.060663 restraints weight = 502362.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.061073 restraints weight = 373250.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.061323 restraints weight = 303523.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.061642 restraints weight = 224136.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.061774 restraints weight = 188328.678| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3830 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3830 r_free = 0.3830 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3830 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6605 moved from start: 0.3526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 33112 Z= 0.145 Angle : 0.772 18.187 44830 Z= 0.391 Chirality : 0.048 0.283 5096 Planarity : 0.005 0.071 5714 Dihedral : 7.350 169.982 4393 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 9.23 % Favored : 90.74 % Rotamer: Outliers : 2.25 % Allowed : 23.16 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.29 (0.13), residues: 3988 helix: -0.38 (0.13), residues: 1554 sheet: -1.73 (0.20), residues: 673 loop : -2.48 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG N 81 TYR 0.025 0.002 TYR L 282 PHE 0.035 0.002 PHE E 124 TRP 0.022 0.001 TRP A1390 HIS 0.006 0.001 HIS A 887 Details of bonding type rmsd covalent geometry : bond 0.00323 (33108) covalent geometry : angle 0.77249 (44830) hydrogen bonds : bond 0.04059 ( 1461) hydrogen bonds : angle 6.14206 ( 4138) Misc. bond : bond 0.00094 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7976 Ramachandran restraints generated. 3988 Oldfield, 0 Emsley, 3988 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 207 time to evaluate : 1.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8629 (mt) REVERT: A 177 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.6318 (ppp) REVERT: A 306 TYR cc_start: 0.7460 (OUTLIER) cc_final: 0.6238 (p90) REVERT: A 327 ASP cc_start: 0.7486 (p0) cc_final: 0.7163 (p0) REVERT: A 792 GLN cc_start: 0.6929 (OUTLIER) cc_final: 0.6314 (mm-40) REVERT: A 856 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7682 (ppp) REVERT: G 77 MET cc_start: 0.7491 (pmm) cc_final: 0.6876 (mtt) REVERT: C 397 MET cc_start: 0.6367 (OUTLIER) cc_final: 0.5928 (mpt) REVERT: D 165 TRP cc_start: 0.7210 (OUTLIER) cc_final: 0.5072 (m-90) REVERT: D 180 LEU cc_start: 0.9129 (tp) cc_final: 0.8889 (tt) REVERT: E 208 LEU cc_start: 0.8339 (mt) cc_final: 0.7886 (tt) REVERT: O 42 GLU cc_start: 0.9001 (pt0) cc_final: 0.8418 (tm-30) REVERT: N 104 MET cc_start: 0.8735 (mmm) cc_final: 0.8290 (mmm) REVERT: P 59 MET cc_start: 0.2081 (mtm) cc_final: 0.1268 (ppp) REVERT: M 77 GLU cc_start: 0.8839 (tt0) cc_final: 0.8235 (tm-30) REVERT: K 12 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6896 (tt) REVERT: K 13 MET cc_start: 0.6359 (mmt) cc_final: 0.5377 (mtt) REVERT: L 226 PHE cc_start: 0.7015 (OUTLIER) cc_final: 0.6467 (p90) REVERT: L 359 PHE cc_start: 0.8163 (OUTLIER) cc_final: 0.7615 (p90) outliers start: 80 outliers final: 61 residues processed: 270 average time/residue: 0.1897 time to fit residues: 85.6917 Evaluate side-chains 270 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 199 time to evaluate : 1.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 196 ILE Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 306 TYR Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 420 THR Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 771 THR Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 852 TYR Chi-restraints excluded: chain A residue 856 MET Chi-restraints excluded: chain A residue 873 THR Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1203 TYR Chi-restraints excluded: chain A residue 1212 HIS Chi-restraints excluded: chain A residue 1252 ILE Chi-restraints excluded: chain A residue 1296 VAL Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1313 LEU Chi-restraints excluded: chain A residue 1356 LEU Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1403 GLN Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain I residue 61 VAL Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 397 MET Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 123 PHE Chi-restraints excluded: chain D residue 165 TRP Chi-restraints excluded: chain D residue 184 VAL Chi-restraints excluded: chain D residue 286 THR Chi-restraints excluded: chain E residue 142 TYR Chi-restraints excluded: chain E residue 217 LEU Chi-restraints excluded: chain E residue 233 VAL Chi-restraints excluded: chain E residue 264 VAL Chi-restraints excluded: chain E residue 315 MET Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain O residue 43 HIS Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 12 LEU Chi-restraints excluded: chain K residue 47 HIS Chi-restraints excluded: chain K residue 50 VAL Chi-restraints excluded: chain K residue 57 VAL Chi-restraints excluded: chain K residue 72 ASN Chi-restraints excluded: chain K residue 127 HIS Chi-restraints excluded: chain K residue 228 PHE Chi-restraints excluded: chain K residue 272 VAL Chi-restraints excluded: chain L residue 181 ASP Chi-restraints excluded: chain L residue 225 ILE Chi-restraints excluded: chain L residue 226 PHE Chi-restraints excluded: chain L residue 236 LEU Chi-restraints excluded: chain L residue 247 LEU Chi-restraints excluded: chain L residue 282 TYR Chi-restraints excluded: chain L residue 325 VAL Chi-restraints excluded: chain L residue 359 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 296 optimal weight: 10.0000 chunk 389 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 164 optimal weight: 30.0000 chunk 102 optimal weight: 6.9990 chunk 284 optimal weight: 7.9990 chunk 320 optimal weight: 10.0000 chunk 315 optimal weight: 0.9990 chunk 33 optimal weight: 20.0000 chunk 311 optimal weight: 0.0670 chunk 205 optimal weight: 30.0000 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 357 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 87 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.073558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.061043 restraints weight = 489760.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.061096 restraints weight = 363674.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.061370 restraints weight = 320138.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.061844 restraints weight = 222125.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.061955 restraints weight = 183604.164| |-----------------------------------------------------------------------------| r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3831 r_free = 0.3831 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6564 moved from start: 0.3535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.320 33112 Z= 0.202 Angle : 0.865 59.191 44830 Z= 0.457 Chirality : 0.050 0.979 5096 Planarity : 0.005 0.070 5714 Dihedral : 7.335 169.858 4393 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 21.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.56 % Favored : 90.39 % Rotamer: Outliers : 2.17 % Allowed : 23.49 % Favored : 74.34 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.29 (0.13), residues: 3988 helix: -0.38 (0.13), residues: 1554 sheet: -1.72 (0.20), residues: 673 loop : -2.47 (0.14), residues: 1761 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A1583 TYR 0.025 0.002 TYR L 282 PHE 0.029 0.002 PHE L 226 TRP 0.025 0.001 TRP A1390 HIS 0.005 0.001 HIS A 887 Details of bonding type rmsd covalent geometry : bond 0.00455 (33108) covalent geometry : angle 0.86541 (44830) hydrogen bonds : bond 0.04104 ( 1461) hydrogen bonds : angle 6.14406 ( 4138) Misc. bond : bond 0.00067 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7694.85 seconds wall clock time: 133 minutes 34.59 seconds (8014.59 seconds total)