Starting phenix.real_space_refine on Sat Jun 28 06:15:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t3c_25654/06_2025/7t3c_25654.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t3c_25654/06_2025/7t3c_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7t3c_25654/06_2025/7t3c_25654.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t3c_25654/06_2025/7t3c_25654.map" model { file = "/net/cci-nas-00/data/ceres_data/7t3c_25654/06_2025/7t3c_25654.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t3c_25654/06_2025/7t3c_25654.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 21.33, per 1000 atoms: 0.66 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: 8.48 Conformation dependent library (CDL) restraints added in 4.5 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: 4.01 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: 15.76 Time building geometry restraints manager: 9.94 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 300 or resid 501 or resid 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: 6.240 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: 0.030 Extract box with map and model: 1.560 Check model and map are aligned: 0.240 Set scattering table: 0.320 Process input model: 79.680 Find NCS groups from input model: 1.090 Set up NCS constraints: 0.230 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:3.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.620 ------------------------------------------------------------------------------- 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 : 11.89 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.052 0.004 TRP A1558 HIS 0.014 0.003 HIS E 187 PHE 0.066 0.004 PHE L 226 TYR 0.077 0.004 TYR L 216 ARG 0.024 0.001 ARG A 806 Details of bonding type rmsd hydrogen bonds : bond 0.13039 ( 1461) hydrogen bonds : angle 8.64066 ( 4138) covalent geometry : bond 0.00754 (33108) covalent geometry : angle 1.40769 (44830) 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 : 3.583 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: 0.8840 (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: 0.4809 time to fit residues: 202.6565 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 : 3.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 336 optimal weight: 10.0000 chunk 302 optimal weight: 6.9990 chunk 167 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 203 optimal weight: 8.9990 chunk 161 optimal weight: 7.9990 chunk 312 optimal weight: 20.0000 chunk 121 optimal weight: 0.0030 chunk 190 optimal weight: 1.9990 chunk 232 optimal weight: 0.8980 chunk 362 optimal weight: 1.9990 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 GLN A 805 GLN ** A 861 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1212 HIS ** A1484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN E 196 HIS ** E 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 8 HIS Q 27 GLN M 64 ASN M 114 GLN K 222 GLN ** L 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 355 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 364 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.074608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.061440 restraints weight = 474459.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.061642 restraints weight = 361702.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.061890 restraints weight = 290261.306| |-----------------------------------------------------------------------------| 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) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-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: 0.6618 moved from start: 0.1401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 33112 Z= 0.160 Angle : 0.788 11.106 44830 Z= 0.410 Chirality : 0.048 0.267 5096 Planarity : 0.006 0.094 5714 Dihedral : 8.350 135.700 4393 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.99 % Favored : 89.96 % Rotamer: Outliers : 0.86 % Allowed : 9.41 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.12), residues: 3988 helix: -1.46 (0.12), residues: 1539 sheet: -1.79 (0.19), residues: 689 loop : -2.51 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A1390 HIS 0.006 0.001 HIS Q 87 PHE 0.038 0.002 PHE L 226 TYR 0.031 0.002 TYR L 282 ARG 0.006 0.000 ARG G 80 Details of bonding type rmsd hydrogen bonds : bond 0.04759 ( 1461) hydrogen bonds : angle 6.99505 ( 4138) covalent geometry : bond 0.00338 (33108) covalent geometry : angle 0.78751 (44830) Misc. bond : bond 0.00091 ( 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 250 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 220 time to evaluate : 3.815 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: 0.8372 (OUTLIER) cc_final: 0.8105 (tmm) REVERT: A 193 GLU cc_start: 0.9029 (mp0) cc_final: 0.8753 (mm-30) REVERT: A 327 ASP cc_start: 0.7642 (p0) cc_final: 0.7275 (p0) REVERT: A 369 MET cc_start: 0.6126 (tmm) cc_final: 0.5868 (tmm) REVERT: A 808 MET cc_start: 0.8455 (mmm) cc_final: 0.7589 (mmt) REVERT: A 1358 VAL cc_start: 0.8822 (OUTLIER) cc_final: 0.8239 (m) REVERT: A 1435 LEU cc_start: 0.7388 (mt) cc_final: 0.7138 (mt) REVERT: A 1596 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8262 (pm20) REVERT: G 77 MET cc_start: 0.7626 (pmm) cc_final: 0.7132 (mtt) REVERT: D 180 LEU cc_start: 0.9142 (tp) cc_final: 0.8894 (tt) REVERT: O 42 GLU cc_start: 0.8790 (pt0) cc_final: 0.8203 (pp20) REVERT: K 13 MET cc_start: 0.5009 (mmt) cc_final: 0.3897 (mmt) REVERT: K 276 MET cc_start: 0.5936 (ppp) cc_final: 0.5657 (ppp) outliers start: 30 outliers final: 17 residues processed: 236 average time/residue: 0.4523 time to fit residues: 173.7832 Evaluate side-chains 220 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 200 time to evaluate : 3.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain A residue 170 MET Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 1181 LEU Chi-restraints excluded: chain A residue 1311 PHE Chi-restraints excluded: chain A residue 1358 VAL Chi-restraints excluded: chain A residue 1596 GLU 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 C residue 133 ASN 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 K residue 228 PHE 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 182 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 53 optimal weight: 3.9990 chunk 136 optimal weight: 40.0000 chunk 202 optimal weight: 0.1980 chunk 244 optimal weight: 7.9990 chunk 125 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 140 optimal weight: 7.9990 chunk 186 optimal weight: 9.9990 chunk 174 optimal weight: 20.0000 overall best weight: 3.4186 ------------------------------------------------------------------------------- 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 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN B 226 ASN A 331 GLN A 405 HIS ** 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 72 ASN ** 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** M 87 GLN M 114 GLN ** M 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 84 ASN ** L 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.073672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.061068 restraints weight = 434787.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.061136 restraints weight = 341348.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.061544 restraints weight = 281938.558| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3801 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3801 r_free = 0.3801 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 = 0.3801 r_free = 0.3801 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3801 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6621 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 33112 Z= 0.178 Angle : 0.749 9.953 44830 Z= 0.392 Chirality : 0.047 0.234 5096 Planarity : 0.005 0.081 5714 Dihedral : 7.841 141.769 4393 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 20.43 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.46 % Favored : 89.49 % Rotamer: Outliers : 1.83 % Allowed : 13.47 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 1.39 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.13), residues: 3988 helix: -0.96 (0.12), residues: 1540 sheet: -1.79 (0.19), residues: 702 loop : -2.44 (0.15), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP D 61 HIS 0.006 0.001 HIS A1406 PHE 0.031 0.002 PHE L 226 TYR 0.026 0.002 TYR L 327 ARG 0.006 0.001 ARG A 356 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 1461) hydrogen bonds : angle 6.56887 ( 4138) covalent geometry : bond 0.00381 (33108) covalent geometry : angle 0.74909 (44830) Misc. bond : bond 0.00085 ( 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 288 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 223 time to evaluate : 4.121 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: 0.8569 (pmm) cc_final: 0.8337 (pmm) REVERT: A 193 GLU cc_start: 0.9077 (mp0) cc_final: 0.8852 (mm-30) REVERT: A 306 TYR cc_start: 0.7193 (OUTLIER) cc_final: 0.5545 (p90) REVERT: A 327 ASP cc_start: 0.7651 (p0) cc_final: 0.7239 (p0) REVERT: A 991 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.7609 (pp20) REVERT: A 1435 LEU cc_start: 0.7529 (mt) cc_final: 0.7284 (mt) REVERT: G 77 MET cc_start: 0.7494 (pmm) cc_final: 0.6899 (mtt) REVERT: J 1 MET cc_start: 0.6210 (mmp) cc_final: 0.5891 (tpt) REVERT: D 180 LEU cc_start: 0.9207 (tp) cc_final: 0.8965 (tt) REVERT: E 364 HIS cc_start: 0.9132 (m90) cc_final: 0.8921 (m90) REVERT: O 42 GLU cc_start: 0.8868 (pt0) cc_final: 0.8238 (tm-30) REVERT: K 167 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7248 (pm20) REVERT: K 276 MET cc_start: 0.5867 (ppp) cc_final: 0.5654 (ppp) outliers start: 65 outliers final: 34 residues processed: 270 average time/residue: 0.5169 time to fit residues: 231.2726 Evaluate side-chains 242 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 4.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 41 GLN Chi-restraints excluded: chain B residue 109 LEU Chi-restraints excluded: chain B residue 168 VAL 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 873 THR Chi-restraints excluded: chain A residue 914 GLU Chi-restraints excluded: chain A residue 991 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 1505 VAL Chi-restraints excluded: chain A residue 1511 LEU 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 141 CYS 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 M residue 87 GLN 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 173 optimal weight: 7.9990 chunk 326 optimal weight: 20.0000 chunk 371 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 393 optimal weight: 30.0000 chunk 27 optimal weight: 10.0000 chunk 245 optimal weight: 4.9990 chunk 210 optimal weight: 2.9990 chunk 355 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 234 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 194 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** 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 114 GLN ** M 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 192 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.071640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.059242 restraints weight = 436136.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.059160 restraints weight = 343798.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.059468 restraints weight = 302774.313| |-----------------------------------------------------------------------------| r_work (final): 0.3744 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 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 = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 33112 Z= 0.247 Angle : 0.831 11.526 44830 Z= 0.434 Chirality : 0.049 0.257 5096 Planarity : 0.006 0.077 5714 Dihedral : 8.055 149.730 4393 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 26.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.32 % Favored : 87.63 % Rotamer: Outliers : 2.75 % Allowed : 17.33 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.13), residues: 3988 helix: -0.96 (0.12), residues: 1535 sheet: -1.78 (0.20), residues: 657 loop : -2.57 (0.14), residues: 1796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 145 HIS 0.009 0.002 HIS L 178 PHE 0.031 0.002 PHE L 226 TYR 0.026 0.003 TYR L 282 ARG 0.006 0.001 ARG A1291 Details of bonding type rmsd hydrogen bonds : bond 0.04843 ( 1461) hydrogen bonds : angle 6.84013 ( 4138) covalent geometry : bond 0.00527 (33108) covalent geometry : angle 0.83116 (44830) Misc. bond : bond 0.00132 ( 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 301 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 203 time to evaluate : 4.246 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 147 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7890 (tp) REVERT: A 306 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.6823 (p90) REVERT: A 327 ASP cc_start: 0.7798 (p0) cc_final: 0.7294 (p0) REVERT: A 340 VAL cc_start: 0.7819 (t) cc_final: 0.7551 (p) REVERT: A 357 MET cc_start: 0.7517 (mmm) cc_final: 0.7247 (tpp) REVERT: A 369 MET cc_start: 0.6462 (tmm) cc_final: 0.6234 (tmm) REVERT: A 1291 ARG cc_start: 0.6633 (ttt-90) cc_final: 0.5090 (ttp-170) REVERT: G 77 MET cc_start: 0.7531 (pmm) cc_final: 0.7153 (pmm) REVERT: F 86 ARG cc_start: 0.6645 (tpp-160) cc_final: 0.6388 (tmm160) REVERT: D 165 TRP cc_start: 0.7032 (OUTLIER) cc_final: 0.4717 (m-90) REVERT: E 165 TYR cc_start: 0.8396 (t80) cc_final: 0.8171 (t80) REVERT: E 318 ILE cc_start: 0.4511 (OUTLIER) cc_final: 0.4011 (mm) REVERT: E 364 HIS cc_start: 0.9182 (m90) cc_final: 0.8976 (m90) REVERT: O 42 GLU cc_start: 0.8979 (pt0) cc_final: 0.8332 (tm-30) REVERT: N 104 MET cc_start: 0.8758 (mmm) cc_final: 0.8520 (mmm) REVERT: K 13 MET cc_start: 0.6235 (mmt) cc_final: 0.5445 (mtt) REVERT: K 167 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7303 (pm20) REVERT: K 276 MET cc_start: 0.5700 (ppp) cc_final: 0.5375 (ppp) REVERT: L 359 PHE cc_start: 0.7991 (OUTLIER) cc_final: 0.7406 (p90) outliers start: 98 outliers final: 61 residues processed: 283 average time/residue: 0.4639 time to fit residues: 217.0147 Evaluate side-chains 256 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 189 time to evaluate : 3.965 ------------------------------------------------------------------------------- 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 111 THR Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 268 VAL Chi-restraints excluded: chain A residue 152 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 374 LEU Chi-restraints excluded: chain A residue 420 THR 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 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 1313 LEU 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 1511 LEU 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 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 33 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain Q residue 22 LEU 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 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 287 LEU Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 181 ASP 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 56 optimal weight: 7.9990 chunk 376 optimal weight: 9.9990 chunk 67 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 116 optimal weight: 6.9990 chunk 167 optimal weight: 40.0000 chunk 227 optimal weight: 10.0000 chunk 108 optimal weight: 0.6980 chunk 135 optimal weight: 1.9990 chunk 343 optimal weight: 6.9990 chunk 300 optimal weight: 20.0000 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 186 ASN B 194 GLN B 226 ASN B 321 ASN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** A1403 GLN ** 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 47 HIS ** 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 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 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 ** both conformations clash, **PLEASE CHECK MANUALLY** K 115 GLN L 192 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.072627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.060227 restraints weight = 505070.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.060504 restraints weight = 371610.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.061254 restraints weight = 284512.483| |-----------------------------------------------------------------------------| r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3798 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3798 r_free = 0.3798 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 = 0.3798 r_free = 0.3798 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3798 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.2660 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= 0.180 Angle : 0.752 10.376 44830 Z= 0.391 Chirality : 0.047 0.248 5096 Planarity : 0.005 0.069 5714 Dihedral : 7.745 156.464 4393 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 10.92 % Favored : 89.03 % Rotamer: Outliers : 3.08 % Allowed : 18.99 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.13), residues: 3988 helix: -0.74 (0.13), residues: 1550 sheet: -1.77 (0.20), residues: 658 loop : -2.54 (0.14), residues: 1780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A1390 HIS 0.006 0.001 HIS A 887 PHE 0.034 0.002 PHE L 226 TYR 0.025 0.002 TYR L 282 ARG 0.005 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.04357 ( 1461) hydrogen bonds : angle 6.52434 ( 4138) covalent geometry : bond 0.00392 (33108) covalent geometry : angle 0.75235 (44830) Misc. bond : bond 0.00080 ( 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 321 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 211 time to evaluate : 4.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 306 TYR cc_start: 0.7486 (OUTLIER) cc_final: 0.6588 (p90) REVERT: A 327 ASP cc_start: 0.7816 (p0) cc_final: 0.7463 (p0) REVERT: A 340 VAL cc_start: 0.7769 (t) cc_final: 0.7495 (p) REVERT: A 369 MET cc_start: 0.6458 (tmm) cc_final: 0.6220 (tmm) REVERT: A 792 GLN cc_start: 0.6451 (OUTLIER) cc_final: 0.5813 (mm-40) REVERT: G 77 MET cc_start: 0.7396 (pmm) cc_final: 0.6668 (ttm) REVERT: I 82 GLN cc_start: 0.3231 (OUTLIER) cc_final: 0.2940 (tp-100) REVERT: F 82 MET cc_start: 0.6470 (tpp) cc_final: 0.6245 (ppp) REVERT: F 86 ARG cc_start: 0.6653 (tpp-160) cc_final: 0.6391 (tmm160) REVERT: C 530 MET cc_start: 0.8255 (ppp) cc_final: 0.8010 (ppp) REVERT: D 103 MET cc_start: 0.7672 (mmm) cc_final: 0.7434 (mmm) REVERT: D 165 TRP cc_start: 0.7221 (OUTLIER) cc_final: 0.5038 (m-90) REVERT: E 63 ARG cc_start: 0.7141 (mmp-170) cc_final: 0.6694 (mmp-170) REVERT: E 165 TYR cc_start: 0.8392 (t80) cc_final: 0.8133 (t80) REVERT: E 171 MET cc_start: 0.4068 (ttt) cc_final: 0.2776 (tmm) REVERT: E 318 ILE cc_start: 0.4115 (OUTLIER) cc_final: 0.3700 (mm) REVERT: E 364 HIS cc_start: 0.9185 (m90) cc_final: 0.8835 (m90) REVERT: O 42 GLU cc_start: 0.8963 (pt0) cc_final: 0.8335 (tm-30) REVERT: N 104 MET cc_start: 0.8786 (mmm) cc_final: 0.8483 (mmt) REVERT: P 59 MET cc_start: 0.2115 (mtm) cc_final: 0.1238 (ptt) REVERT: K 13 MET cc_start: 0.6115 (mmt) cc_final: 0.5199 (mtt) REVERT: K 167 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7472 (pm20) REVERT: K 276 MET cc_start: 0.5595 (ppp) cc_final: 0.5243 (ppp) REVERT: L 226 PHE cc_start: 0.7256 (OUTLIER) cc_final: 0.6548 (p90) REVERT: L 359 PHE cc_start: 0.8055 (OUTLIER) cc_final: 0.7493 (p90) outliers start: 110 outliers final: 58 residues processed: 302 average time/residue: 0.5529 time to fit residues: 279.4005 Evaluate side-chains 260 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 194 time to evaluate : 4.201 ------------------------------------------------------------------------------- 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 226 ASN 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 362 ILE Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 399 ILE 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 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 1356 LEU Chi-restraints excluded: chain A residue 1393 VAL Chi-restraints excluded: chain A residue 1505 VAL Chi-restraints excluded: chain A residue 1511 LEU 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 I residue 82 GLN 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 43 HIS Chi-restraints excluded: chain O residue 121 VAL 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 43 ILE 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 167 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 399 random chunks: chunk 308 optimal weight: 2.9990 chunk 209 optimal weight: 6.9990 chunk 46 optimal weight: 0.5980 chunk 247 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 61 optimal weight: 0.8980 chunk 262 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 245 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 309 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 GLN ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 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 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 HIS ** 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** ** M 116 HIS ** 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 = 0.4200 r_free = 0.4200 target = 0.073219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.060670 restraints weight = 566613.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.061351 restraints weight = 399134.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.062031 restraints weight = 280596.439| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3829 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3829 r_free = 0.3829 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 = 0.3829 r_free = 0.3829 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3829 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6516 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 33112 Z= 0.157 Angle : 0.733 9.861 44830 Z= 0.379 Chirality : 0.048 0.290 5096 Planarity : 0.005 0.070 5714 Dihedral : 7.471 159.123 4393 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 20.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.59 % Favored : 89.39 % Rotamer: Outliers : 2.80 % Allowed : 20.58 % Favored : 76.62 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.69 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.13), residues: 3988 helix: -0.53 (0.13), residues: 1556 sheet: -1.77 (0.20), residues: 670 loop : -2.49 (0.15), residues: 1762 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1390 HIS 0.006 0.001 HIS A 887 PHE 0.032 0.002 PHE L 226 TYR 0.025 0.002 TYR L 282 ARG 0.004 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 1461) hydrogen bonds : angle 6.28469 ( 4138) covalent geometry : bond 0.00344 (33108) covalent geometry : angle 0.73275 (44830) Misc. bond : bond 0.00074 ( 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 312 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 212 time to evaluate : 4.225 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: B 319 MET cc_start: 0.8448 (pmm) cc_final: 0.8229 (pmm) REVERT: A 306 TYR cc_start: 0.7445 (OUTLIER) cc_final: 0.6336 (p90) REVERT: A 327 ASP cc_start: 0.7761 (p0) cc_final: 0.7335 (p0) REVERT: G 77 MET cc_start: 0.7299 (pmm) cc_final: 0.6546 (ttm) REVERT: I 82 GLN cc_start: 0.3317 (OUTLIER) cc_final: 0.3046 (tp-100) REVERT: F 82 MET cc_start: 0.6411 (tpp) cc_final: 0.6147 (ppp) REVERT: F 86 ARG cc_start: 0.6425 (tpp-160) cc_final: 0.6165 (tmm160) REVERT: C 397 MET cc_start: 0.6455 (OUTLIER) cc_final: 0.5866 (mtt) REVERT: D 46 GLU cc_start: 0.6977 (mt-10) cc_final: 0.6725 (mt-10) REVERT: D 165 TRP cc_start: 0.7142 (OUTLIER) cc_final: 0.5018 (m-90) REVERT: E 63 ARG cc_start: 0.7128 (mmp-170) cc_final: 0.6175 (mmp-170) REVERT: E 165 TYR cc_start: 0.8395 (t80) cc_final: 0.8128 (t80) REVERT: E 171 MET cc_start: 0.4447 (ttt) cc_final: 0.4018 (ttm) REVERT: E 178 HIS cc_start: 0.7004 (OUTLIER) cc_final: 0.6666 (m170) REVERT: E 318 ILE cc_start: 0.4070 (OUTLIER) cc_final: 0.3579 (mm) REVERT: E 364 HIS cc_start: 0.9167 (m90) cc_final: 0.8791 (m90) REVERT: O 42 GLU cc_start: 0.8959 (pt0) cc_final: 0.8214 (tm-30) REVERT: N 75 MET cc_start: 0.9057 (mpp) cc_final: 0.7461 (ppp) REVERT: P 59 MET cc_start: 0.2269 (mtm) cc_final: 0.1391 (ptt) REVERT: K 13 MET cc_start: 0.6168 (mmt) cc_final: 0.5251 (mtt) REVERT: K 167 GLU cc_start: 0.7652 (OUTLIER) cc_final: 0.7178 (pm20) REVERT: K 276 MET cc_start: 0.5363 (ppp) cc_final: 0.5061 (ppp) REVERT: L 151 MET cc_start: 0.8390 (mmt) cc_final: 0.7631 (pmm) REVERT: L 226 PHE cc_start: 0.7112 (OUTLIER) cc_final: 0.6499 (p90) REVERT: L 244 GLU cc_start: 0.2971 (OUTLIER) cc_final: 0.2467 (mt-10) REVERT: L 359 PHE cc_start: 0.8048 (OUTLIER) cc_final: 0.7489 (p90) outliers start: 100 outliers final: 59 residues processed: 296 average time/residue: 0.5358 time to fit residues: 263.4132 Evaluate side-chains 265 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 196 time to evaluate : 3.520 ------------------------------------------------------------------------------- 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 226 ASN Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 268 VAL 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 374 LEU Chi-restraints excluded: chain A residue 420 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 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 1356 LEU Chi-restraints excluded: chain A residue 1403 GLN 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 I residue 82 GLN 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 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 315 MET Chi-restraints excluded: chain E residue 318 ILE Chi-restraints excluded: chain O residue 43 HIS Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 73 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 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 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 337 optimal weight: 0.5980 chunk 353 optimal weight: 10.0000 chunk 91 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 345 optimal weight: 3.9990 chunk 8 optimal weight: 8.9990 chunk 380 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 391 optimal weight: 2.9990 chunk 272 optimal weight: 10.0000 chunk 190 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- 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 226 ASN B 321 ASN ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 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 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** ** M 116 HIS ** 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 = 0.4197 r_free = 0.4197 target = 0.073116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.061026 restraints weight = 594034.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.061389 restraints weight = 403661.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.061770 restraints weight = 302610.075| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3820 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3820 r_free = 0.3820 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 = 0.3820 r_free = 0.3820 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3820 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6532 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 33112 Z= 0.162 Angle : 0.755 16.075 44830 Z= 0.384 Chirality : 0.048 0.265 5096 Planarity : 0.005 0.069 5714 Dihedral : 7.370 160.179 4393 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 21.63 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.72 % Favored : 89.26 % Rotamer: Outliers : 2.86 % Allowed : 21.52 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.13), residues: 3988 helix: -0.43 (0.13), residues: 1554 sheet: -1.77 (0.20), residues: 669 loop : -2.47 (0.15), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP A1558 HIS 0.007 0.001 HIS D 49 PHE 0.031 0.002 PHE L 226 TYR 0.025 0.002 TYR L 282 ARG 0.004 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.04124 ( 1461) hydrogen bonds : angle 6.22561 ( 4138) covalent geometry : bond 0.00358 (33108) covalent geometry : angle 0.75493 (44830) 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 303 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 201 time to evaluate : 3.710 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 151 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8057 (tm-30) REVERT: B 319 MET cc_start: 0.8470 (pmm) cc_final: 0.8212 (pmm) REVERT: A 306 TYR cc_start: 0.7430 (OUTLIER) cc_final: 0.6298 (p90) REVERT: A 327 ASP cc_start: 0.7829 (p0) cc_final: 0.7449 (p0) REVERT: A 369 MET cc_start: 0.6090 (tmm) cc_final: 0.5802 (tmm) REVERT: A 792 GLN cc_start: 0.6863 (OUTLIER) cc_final: 0.6205 (mm-40) REVERT: G 77 MET cc_start: 0.7339 (pmm) cc_final: 0.6640 (ttm) REVERT: I 54 ARG cc_start: 0.4969 (mmp-170) cc_final: 0.4767 (mmp-170) REVERT: I 82 GLN cc_start: 0.3156 (OUTLIER) cc_final: 0.2920 (tp-100) REVERT: F 82 MET cc_start: 0.6467 (tpp) cc_final: 0.6129 (ppp) REVERT: F 86 ARG cc_start: 0.6458 (tpp-160) cc_final: 0.6187 (tmm160) REVERT: C 397 MET cc_start: 0.6456 (OUTLIER) cc_final: 0.5855 (mtt) REVERT: D 46 GLU cc_start: 0.7037 (mt-10) cc_final: 0.6762 (mt-10) REVERT: D 165 TRP cc_start: 0.7369 (OUTLIER) cc_final: 0.5321 (m-90) REVERT: E 63 ARG cc_start: 0.7072 (mmp-170) cc_final: 0.6061 (mmp-170) REVERT: E 165 TYR cc_start: 0.8407 (t80) cc_final: 0.8107 (t80) REVERT: E 171 MET cc_start: 0.4501 (ttt) cc_final: 0.4172 (ttm) REVERT: E 364 HIS cc_start: 0.9222 (m90) cc_final: 0.8834 (m90) REVERT: O 42 GLU cc_start: 0.8996 (pt0) cc_final: 0.8344 (tm-30) REVERT: N 104 MET cc_start: 0.8751 (mmm) cc_final: 0.8316 (mmt) REVERT: P 59 MET cc_start: 0.2253 (mtm) cc_final: 0.1355 (ptt) REVERT: M 77 GLU cc_start: 0.8951 (tt0) cc_final: 0.8248 (tm-30) REVERT: K 13 MET cc_start: 0.6320 (mmt) cc_final: 0.5435 (mtt) REVERT: K 167 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7178 (pm20) REVERT: K 276 MET cc_start: 0.5368 (ppp) cc_final: 0.5111 (ppp) REVERT: L 226 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.6490 (p90) REVERT: L 244 GLU cc_start: 0.2946 (OUTLIER) cc_final: 0.2418 (mt-10) REVERT: L 359 PHE cc_start: 0.8064 (OUTLIER) cc_final: 0.7498 (p90) outliers start: 102 outliers final: 67 residues processed: 288 average time/residue: 0.4428 time to fit residues: 210.4997 Evaluate side-chains 274 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 197 time to evaluate : 3.904 ------------------------------------------------------------------------------- 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 151 GLU Chi-restraints excluded: chain B residue 168 VAL 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 369 LEU Chi-restraints excluded: chain A residue 107 GLN 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 374 LEU Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 420 THR 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 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 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 1403 GLN 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 I residue 82 GLN 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 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 285 CYS Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain O residue 43 HIS Chi-restraints excluded: chain O residue 121 VAL 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 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 167 GLU 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 267 LYS Chi-restraints excluded: chain L residue 282 TYR 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 362 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 143 optimal weight: 9.9990 chunk 124 optimal weight: 6.9990 chunk 388 optimal weight: 1.9990 chunk 321 optimal weight: 6.9990 chunk 261 optimal weight: 8.9990 chunk 286 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 206 optimal weight: 7.9990 chunk 264 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN ** 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 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 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** ** M 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 222 GLN K 226 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.072489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.059818 restraints weight = 565238.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.060352 restraints weight = 408850.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.060542 restraints weight = 305091.045| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 33112 Z= 0.185 Angle : 0.772 13.251 44830 Z= 0.394 Chirality : 0.048 0.269 5096 Planarity : 0.005 0.072 5714 Dihedral : 7.442 162.810 4393 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 23.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 11.14 % Favored : 88.81 % Rotamer: Outliers : 3.03 % Allowed : 22.08 % Favored : 74.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.13), residues: 3988 helix: -0.47 (0.13), residues: 1552 sheet: -1.80 (0.20), residues: 661 loop : -2.50 (0.14), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A1558 HIS 0.006 0.001 HIS A1406 PHE 0.029 0.002 PHE L 226 TYR 0.026 0.002 TYR L 282 ARG 0.005 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.04238 ( 1461) hydrogen bonds : angle 6.30352 ( 4138) covalent geometry : bond 0.00405 (33108) covalent geometry : angle 0.77205 (44830) Misc. bond : bond 0.00086 ( 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 306 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 198 time to evaluate : 3.895 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: B 151 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: B 319 MET cc_start: 0.8464 (pmm) cc_final: 0.8185 (pmm) REVERT: A 306 TYR cc_start: 0.7437 (OUTLIER) cc_final: 0.6335 (p90) REVERT: A 327 ASP cc_start: 0.7832 (p0) cc_final: 0.7377 (p0) REVERT: A 369 MET cc_start: 0.5937 (tmm) cc_final: 0.5717 (tmm) REVERT: A 792 GLN cc_start: 0.6967 (OUTLIER) cc_final: 0.6345 (mm-40) REVERT: A 1212 HIS cc_start: 0.7805 (OUTLIER) cc_final: 0.7183 (t-90) REVERT: G 77 MET cc_start: 0.7460 (pmm) cc_final: 0.6802 (ttm) REVERT: I 82 GLN cc_start: 0.3316 (OUTLIER) cc_final: 0.3056 (tp-100) REVERT: F 82 MET cc_start: 0.6467 (tpp) cc_final: 0.6161 (ppp) REVERT: F 86 ARG cc_start: 0.6441 (tpp-160) cc_final: 0.6180 (tmm160) REVERT: C 411 CYS cc_start: 0.8481 (OUTLIER) cc_final: 0.7804 (t) REVERT: D 165 TRP cc_start: 0.7280 (OUTLIER) cc_final: 0.5125 (m-90) REVERT: E 63 ARG cc_start: 0.7297 (mmp-170) cc_final: 0.6217 (mmp-170) REVERT: E 165 TYR cc_start: 0.8431 (t80) cc_final: 0.8154 (t80) REVERT: E 171 MET cc_start: 0.4395 (ttt) cc_final: 0.4134 (ttm) REVERT: E 364 HIS cc_start: 0.9261 (m90) cc_final: 0.8864 (m90) REVERT: O 42 GLU cc_start: 0.9002 (pt0) cc_final: 0.8370 (tm-30) REVERT: N 104 MET cc_start: 0.8747 (mmm) cc_final: 0.8374 (mmm) REVERT: P 59 MET cc_start: 0.2224 (mtm) cc_final: 0.1450 (ptt) REVERT: M 77 GLU cc_start: 0.8909 (tt0) cc_final: 0.8302 (tm-30) REVERT: K 13 MET cc_start: 0.6476 (mmt) cc_final: 0.5760 (mtt) REVERT: K 167 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7237 (pm20) REVERT: K 276 MET cc_start: 0.5301 (ppp) cc_final: 0.5029 (ppp) REVERT: L 226 PHE cc_start: 0.7177 (OUTLIER) cc_final: 0.6481 (p90) REVERT: L 244 GLU cc_start: 0.2836 (OUTLIER) cc_final: 0.2584 (mt-10) REVERT: L 346 PHE cc_start: -0.2529 (OUTLIER) cc_final: -0.3958 (p90) REVERT: L 359 PHE cc_start: 0.8223 (OUTLIER) cc_final: 0.7647 (p90) outliers start: 108 outliers final: 74 residues processed: 292 average time/residue: 0.4322 time to fit residues: 209.0015 Evaluate side-chains 280 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 194 time to evaluate : 3.850 ------------------------------------------------------------------------------- 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 151 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 LEU 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 369 LEU Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 225 PHE 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 362 ILE Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 420 THR 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 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 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 1403 GLN 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 I residue 82 GLN Chi-restraints excluded: chain F residue 118 VAL Chi-restraints excluded: chain C residue 141 CYS 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 285 CYS Chi-restraints excluded: chain E residue 311 ASP Chi-restraints excluded: chain E residue 325 VAL Chi-restraints excluded: chain O residue 43 HIS Chi-restraints excluded: chain O residue 121 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 99 THR 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 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 167 GLU 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 346 PHE 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 76 optimal weight: 0.5980 chunk 266 optimal weight: 7.9990 chunk 313 optimal weight: 40.0000 chunk 159 optimal weight: 10.0000 chunk 371 optimal weight: 9.9990 chunk 109 optimal weight: 7.9990 chunk 102 optimal weight: 0.8980 chunk 251 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 321 optimal weight: 9.9990 chunk 280 optimal weight: 0.5980 overall best weight: 3.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 16 HIS B 226 ASN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 303 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 355 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN ** 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 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** ** M 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 237 GLN ** L 178 HIS ** 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 = 0.4184 r_free = 0.4184 target = 0.072543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.059978 restraints weight = 504367.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.060197 restraints weight = 375921.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.060498 restraints weight = 291379.975| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 33112 Z= 0.180 Angle : 0.779 12.759 44830 Z= 0.397 Chirality : 0.048 0.259 5096 Planarity : 0.005 0.071 5714 Dihedral : 7.460 169.694 4393 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 23.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 11.07 % Favored : 88.91 % Rotamer: Outliers : 2.78 % Allowed : 22.72 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.13), residues: 3988 helix: -0.47 (0.13), residues: 1552 sheet: -1.75 (0.20), residues: 664 loop : -2.53 (0.14), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A1558 HIS 0.006 0.001 HIS L 178 PHE 0.035 0.002 PHE E 229 TYR 0.025 0.002 TYR L 282 ARG 0.005 0.000 ARG A 223 Details of bonding type rmsd hydrogen bonds : bond 0.04225 ( 1461) hydrogen bonds : angle 6.29028 ( 4138) covalent geometry : bond 0.00399 (33108) covalent geometry : angle 0.77927 (44830) Misc. bond : bond 0.00083 ( 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 297 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 198 time to evaluate : 3.591 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 151 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8025 (tm-30) REVERT: B 319 MET cc_start: 0.8438 (pmm) cc_final: 0.8108 (pmm) REVERT: A 306 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.6459 (p90) REVERT: A 327 ASP cc_start: 0.7762 (p0) cc_final: 0.7327 (p0) REVERT: A 369 MET cc_start: 0.5849 (tmm) cc_final: 0.5639 (tmm) REVERT: A 792 GLN cc_start: 0.6977 (OUTLIER) cc_final: 0.6376 (mm-40) REVERT: A 907 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7576 (mm-30) REVERT: A 1212 HIS cc_start: 0.7772 (OUTLIER) cc_final: 0.7149 (t-90) REVERT: G 77 MET cc_start: 0.7512 (pmm) cc_final: 0.6878 (ttm) REVERT: I 82 GLN cc_start: 0.3366 (OUTLIER) cc_final: 0.3109 (tp-100) REVERT: F 82 MET cc_start: 0.6513 (tpp) cc_final: 0.6230 (ppp) REVERT: F 86 ARG cc_start: 0.6366 (tpp-160) cc_final: 0.6121 (tmm160) REVERT: C 397 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6114 (mtt) REVERT: C 411 CYS cc_start: 0.8563 (OUTLIER) cc_final: 0.8133 (t) REVERT: D 165 TRP cc_start: 0.7376 (OUTLIER) cc_final: 0.5232 (m-90) REVERT: E 63 ARG cc_start: 0.7381 (mmp-170) cc_final: 0.6931 (mmp-170) REVERT: E 165 TYR cc_start: 0.8403 (t80) cc_final: 0.8156 (t80) REVERT: E 208 LEU cc_start: 0.8302 (mt) cc_final: 0.7808 (tt) REVERT: E 364 HIS cc_start: 0.9266 (m90) cc_final: 0.8864 (m90) REVERT: O 42 GLU cc_start: 0.9016 (pt0) cc_final: 0.8407 (tm-30) REVERT: N 81 ARG cc_start: 0.8806 (ptt180) cc_final: 0.8441 (tmm-80) REVERT: N 104 MET cc_start: 0.8727 (mmm) cc_final: 0.8299 (mmt) REVERT: M 77 GLU cc_start: 0.8896 (tt0) cc_final: 0.8296 (tm-30) REVERT: K 13 MET cc_start: 0.6407 (mmt) cc_final: 0.5694 (mtt) REVERT: K 167 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7266 (pm20) REVERT: K 276 MET cc_start: 0.5263 (ppp) cc_final: 0.4987 (ppp) REVERT: L 226 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.6401 (p90) REVERT: L 244 GLU cc_start: 0.2880 (OUTLIER) cc_final: 0.2565 (mt-10) REVERT: L 346 PHE cc_start: -0.2635 (OUTLIER) cc_final: -0.3814 (p90) REVERT: L 359 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.7520 (p90) outliers start: 99 outliers final: 79 residues processed: 280 average time/residue: 0.4481 time to fit residues: 206.0138 Evaluate side-chains 288 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 195 time to evaluate : 3.814 ------------------------------------------------------------------------------- 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 151 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 219 LEU 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 369 LEU Chi-restraints excluded: chain A residue 107 GLN Chi-restraints excluded: chain A residue 211 ASN Chi-restraints excluded: chain A residue 225 PHE 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 362 ILE Chi-restraints excluded: chain A residue 365 ASP Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 399 ILE Chi-restraints excluded: chain A residue 420 THR 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 991 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 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 I residue 82 GLN 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 6 MET Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 20 LYS 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 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 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 O residue 121 VAL Chi-restraints excluded: chain N residue 33 LEU Chi-restraints excluded: chain N residue 49 ILE Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain M residue 83 ASP Chi-restraints excluded: chain K residue 10 VAL 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 167 GLU 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 346 PHE 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 117 optimal weight: 2.9990 chunk 266 optimal weight: 0.5980 chunk 215 optimal weight: 6.9990 chunk 362 optimal weight: 7.9990 chunk 341 optimal weight: 0.9980 chunk 119 optimal weight: 0.0050 chunk 66 optimal weight: 0.9980 chunk 127 optimal weight: 0.3980 chunk 2 optimal weight: 3.9990 chunk 176 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 207 GLN B 321 ASN A 83 GLN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 355 GLN ** A1351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 82 GLN ** 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 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** 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** M 116 HIS K 289 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.075144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.062385 restraints weight = 541748.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.063047 restraints weight = 399543.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.063394 restraints weight = 275332.970| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3853 r_free = 0.3853 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 = 0.3853 r_free = 0.3853 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 33112 Z= 0.129 Angle : 0.740 14.013 44830 Z= 0.371 Chirality : 0.047 0.254 5096 Planarity : 0.004 0.069 5714 Dihedral : 7.044 175.540 4393 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.78 % Favored : 91.19 % Rotamer: Outliers : 1.94 % Allowed : 23.72 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.13), residues: 3988 helix: -0.18 (0.13), residues: 1552 sheet: -1.63 (0.20), residues: 681 loop : -2.41 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1558 HIS 0.005 0.001 HIS A 887 PHE 0.039 0.002 PHE E 124 TYR 0.023 0.001 TYR L 282 ARG 0.005 0.000 ARG N 81 Details of bonding type rmsd hydrogen bonds : bond 0.03795 ( 1461) hydrogen bonds : angle 5.86340 ( 4138) covalent geometry : bond 0.00284 (33108) covalent geometry : angle 0.73993 (44830) Misc. bond : bond 0.00169 ( 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 292 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 223 time to evaluate : 3.722 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 151 GLU cc_start: 0.8596 (OUTLIER) cc_final: 0.8066 (tm-30) REVERT: A 78 ARG cc_start: 0.7388 (tpp-160) cc_final: 0.6801 (tpm170) REVERT: A 306 TYR cc_start: 0.7256 (OUTLIER) cc_final: 0.6067 (p90) REVERT: A 327 ASP cc_start: 0.7556 (p0) cc_final: 0.7255 (p0) REVERT: A 369 MET cc_start: 0.5739 (tmm) cc_final: 0.5538 (tmm) REVERT: A 792 GLN cc_start: 0.7354 (OUTLIER) cc_final: 0.6836 (mm-40) REVERT: A 856 MET cc_start: 0.7819 (ppp) cc_final: 0.7340 (ppp) REVERT: A 1212 HIS cc_start: 0.7720 (OUTLIER) cc_final: 0.7242 (t-90) REVERT: A 1403 GLN cc_start: 0.8417 (tp40) cc_final: 0.8088 (mm110) REVERT: A 1553 MET cc_start: 0.6093 (mtt) cc_final: 0.5809 (mmt) REVERT: G 77 MET cc_start: 0.7487 (pmm) cc_final: 0.6853 (mtt) REVERT: J 1 MET cc_start: 0.5846 (mmp) cc_final: 0.5413 (tpt) REVERT: I 54 ARG cc_start: 0.5282 (mmp-170) cc_final: 0.5056 (mmm160) REVERT: I 65 ARG cc_start: 0.5585 (ptt180) cc_final: 0.5335 (ttm110) REVERT: F 82 MET cc_start: 0.6618 (tpp) cc_final: 0.6289 (ppp) REVERT: F 86 ARG cc_start: 0.6318 (tpp-160) cc_final: 0.6094 (tmt170) REVERT: C 397 MET cc_start: 0.6320 (OUTLIER) cc_final: 0.5823 (mtt) REVERT: C 411 CYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8323 (t) REVERT: D 165 TRP cc_start: 0.7090 (OUTLIER) cc_final: 0.5341 (m-90) REVERT: D 252 MET cc_start: 0.3752 (tpt) cc_final: 0.2920 (tpp) REVERT: E 63 ARG cc_start: 0.7063 (mmp-170) cc_final: 0.6576 (mmp-170) REVERT: E 208 LEU cc_start: 0.8563 (mt) cc_final: 0.8080 (tt) REVERT: E 364 HIS cc_start: 0.9171 (m90) cc_final: 0.8897 (m90) REVERT: O 42 GLU cc_start: 0.8980 (pt0) cc_final: 0.8184 (tm-30) REVERT: N 104 MET cc_start: 0.8672 (mmm) cc_final: 0.8266 (mmm) REVERT: Q 27 GLN cc_start: 0.4956 (mm110) cc_final: 0.3822 (tt0) REVERT: P 12 ILE cc_start: 0.2899 (mm) cc_final: 0.2653 (mm) REVERT: P 59 MET cc_start: 0.2172 (mtm) cc_final: 0.1247 (ppp) REVERT: M 77 GLU cc_start: 0.8812 (tt0) cc_final: 0.8124 (tm-30) REVERT: K 13 MET cc_start: 0.5860 (mmt) cc_final: 0.4950 (mtt) REVERT: K 276 MET cc_start: 0.5342 (ppp) cc_final: 0.5037 (ppp) REVERT: L 359 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7595 (p90) outliers start: 69 outliers final: 51 residues processed: 280 average time/residue: 0.4455 time to fit residues: 207.8482 Evaluate side-chains 264 residues out of total 3601 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 205 time to evaluate : 3.805 ------------------------------------------------------------------------------- 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 151 GLU Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain A residue 183 ASP 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 771 THR Chi-restraints excluded: chain A residue 792 GLN Chi-restraints excluded: chain A residue 873 THR 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 1393 VAL Chi-restraints excluded: chain A residue 1557 THR Chi-restraints excluded: chain A residue 1583 ARG 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 397 MET Chi-restraints excluded: chain C residue 411 CYS Chi-restraints excluded: chain D residue 12 LEU Chi-restraints excluded: chain D residue 20 LYS 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 264 VAL Chi-restraints excluded: chain E residue 285 CYS 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 N residue 73 ILE Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain P residue 45 GLU Chi-restraints excluded: chain M residue 83 ASP 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 167 GLU Chi-restraints excluded: chain K residue 228 PHE Chi-restraints excluded: chain K residue 272 VAL 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 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 218 optimal weight: 20.0000 chunk 272 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 136 optimal weight: 10.0000 chunk 252 optimal weight: 20.0000 chunk 204 optimal weight: 1.9990 chunk 167 optimal weight: 9.9990 chunk 170 optimal weight: 30.0000 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 105 optimal weight: 9.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 ASN B 162 GLN ** B 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 ASN ** A 303 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1403 GLN I 82 GLN F 74 GLN ** 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 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 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.072783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.060042 restraints weight = 486026.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.060508 restraints weight = 360963.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.060596 restraints weight = 291397.431| |-----------------------------------------------------------------------------| r_work (final): 0.3777 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3778 r_free = 0.3778 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6668 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 : 0.004 0.066 33112 Z= 0.188 Angle : 0.790 12.309 44830 Z= 0.401 Chirality : 0.048 0.264 5096 Planarity : 0.005 0.074 5714 Dihedral : 7.229 174.504 4393 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.03 % Allowed : 10.64 % Favored : 89.34 % Rotamer: Outliers : 2.30 % Allowed : 23.99 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.13), residues: 3988 helix: -0.22 (0.13), residues: 1543 sheet: -1.70 (0.20), residues: 671 loop : -2.40 (0.14), residues: 1774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1558 HIS 0.007 0.001 HIS A1406 PHE 0.033 0.002 PHE E 229 TYR 0.024 0.002 TYR L 282 ARG 0.005 0.000 ARG D 51 Details of bonding type rmsd hydrogen bonds : bond 0.04136 ( 1461) hydrogen bonds : angle 6.08691 ( 4138) covalent geometry : bond 0.00415 (33108) covalent geometry : angle 0.78988 (44830) Misc. bond : bond 0.00138 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14377.50 seconds wall clock time: 255 minutes 43.93 seconds (15343.93 seconds total)