Starting phenix.real_space_refine on Sat Mar 7 10:10:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qv9_14171/03_2026/7qv9_14171.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qv9_14171/03_2026/7qv9_14171.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qv9_14171/03_2026/7qv9_14171.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qv9_14171/03_2026/7qv9_14171.map" model { file = "/net/cci-nas-00/data/ceres_data/7qv9_14171/03_2026/7qv9_14171.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qv9_14171/03_2026/7qv9_14171.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 4 5.89 5 P 82 5.49 5 S 160 5.16 5 C 25844 2.51 5 N 7325 2.21 5 O 8064 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 166 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 41491 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2322 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 6, 'PHE:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 53 Chain: "B" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1676 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 214} Chain breaks: 1 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 10125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1341, 10125 Classifications: {'peptide': 1341} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 56, 'TRANS': 1284} Unresolved non-hydrogen bonds: 461 Unresolved non-hydrogen angles: 557 Unresolved non-hydrogen dihedrals: 394 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'TYR:plan': 4, 'ASP:plan': 13, 'GLU:plan': 24, 'ASN:plan1': 4, 'ARG:plan': 14, 'HIS:plan': 3, 'PHE:plan': 2, 'GLN:plan1': 3, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 293 Chain: "D" Number of atoms: 9634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 9634 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 207} Link IDs: {'PTRANS': 53, 'TRANS': 1280} Chain breaks: 5 Unresolved non-hydrogen bonds: 782 Unresolved non-hydrogen angles: 963 Unresolved non-hydrogen dihedrals: 648 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLU:plan': 29, 'PHE:plan': 10, 'ARG:plan': 25, 'ASP:plan': 22, 'ASN:plan1': 7, 'HIS:plan': 2, 'GLN:plan1': 10, 'TYR:plan': 3, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 477 Chain: "E" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 546 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 2, 'TRANS': 71} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'GLU:plan': 5, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 45 Chain: "N" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 738 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "a" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2052 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 243} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "b" Number of atoms: 2052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2052 Classifications: {'peptide': 258} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 243} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "c" Number of atoms: 2000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2000 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 14, 'TRANS': 241} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 60 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 2, 'HIS:plan': 2, 'GLU:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "d" Number of atoms: 2041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2041 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 241} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2053 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 243} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "e" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2062 Classifications: {'peptide': 259} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 243} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "M" Number of atoms: 3301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3301 Classifications: {'peptide': 417} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 399} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "a" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLY M 166 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 166 " occ=0.20 residue: pdb=" N GLY M 171 " occ=0.20 ... (2 atoms not shown) pdb=" O GLY M 171 " occ=0.20 Time building chain proxies: 8.11, per 1000 atoms: 0.20 Number of scatterers: 41491 At special positions: 0 Unit cell: (210.1, 204.6, 163.9, 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 160 16.00 P 82 15.00 Al 4 13.00 F 12 9.00 O 8064 8.00 N 7325 7.00 C 25844 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.41 Conformation dependent library (CDL) restraints added in 1.7 seconds 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9748 Finding SS restraints... Secondary structure from input PDB file: 187 helices and 53 sheets defined 40.1% alpha, 9.3% beta 34 base pairs and 59 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 77 through 87 removed outlier: 3.595A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 160 removed outlier: 3.612A pdb=" N ILE A 159 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N HIS A 160 " --> pdb=" O THR A 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 156 through 160' Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.264A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 232 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ASP A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 273 Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 296 through 312 removed outlier: 3.957A pdb=" N ARG A 310 " --> pdb=" O VAL A 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 50 removed outlier: 3.823A pdb=" N THR B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.708A pdb=" N GLY B 87 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 115 No H-bonds generated for 'chain 'B' and resid 113 through 115' Processing helix chain 'B' and resid 212 through 229 Processing helix chain 'C' and resid 28 through 39 removed outlier: 3.916A pdb=" N LEU C 32 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N SER C 34 " --> pdb=" O ILE C 30 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE C 35 " --> pdb=" O GLN C 31 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ILE C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 48 through 57 removed outlier: 3.672A pdb=" N ARG C 54 " --> pdb=" O GLU C 50 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 Processing helix chain 'C' and resid 137 through 141 Processing helix chain 'C' and resid 162 through 166 Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.573A pdb=" N LEU C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 Processing helix chain 'C' and resid 270 through 280 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.820A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS C 295 " --> pdb=" O TYR C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 295' Processing helix chain 'C' and resid 318 through 328 removed outlier: 3.970A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 352 removed outlier: 4.088A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 371 removed outlier: 3.646A pdb=" N VAL C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE C 366 " --> pdb=" O ALA C 362 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYR C 367 " --> pdb=" O LEU C 363 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 389 removed outlier: 3.724A pdb=" N SER C 383 " --> pdb=" O GLU C 379 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 408 removed outlier: 3.588A pdb=" N ARG C 402 " --> pdb=" O SER C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 438 Processing helix chain 'C' and resid 455 through 481 removed outlier: 3.760A pdb=" N MET C 459 " --> pdb=" O SER C 455 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 507 removed outlier: 4.710A pdb=" N ILE C 498 " --> pdb=" O ASN C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 664 through 668 Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.930A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 703 through 712 removed outlier: 4.284A pdb=" N ALA C 707 " --> pdb=" O GLY C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 860 through 865 removed outlier: 3.808A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 Processing helix chain 'C' and resid 945 through 979 removed outlier: 3.844A pdb=" N GLU C 949 " --> pdb=" O ALA C 945 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU C 962 " --> pdb=" O LYS C 958 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) Processing helix chain 'C' and resid 985 through 992 removed outlier: 4.120A pdb=" N LEU C 989 " --> pdb=" O GLU C 985 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 998 removed outlier: 4.287A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) Processing helix chain 'C' and resid 1006 through 1037 Processing helix chain 'C' and resid 1102 through 1107 Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 3.899A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 removed outlier: 3.708A pdb=" N LEU C1141 " --> pdb=" O GLU C1137 " (cutoff:3.500A) Processing helix chain 'C' and resid 1167 through 1176 removed outlier: 3.882A pdb=" N ARG C1171 " --> pdb=" O GLU C1167 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1202 removed outlier: 3.638A pdb=" N LYS C1200 " --> pdb=" O LYS C1196 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N LEU C1201 " --> pdb=" O GLU C1197 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLY C1202 " --> pdb=" O LEU C1198 " (cutoff:3.500A) Processing helix chain 'C' and resid 1238 through 1243 removed outlier: 3.825A pdb=" N LYS C1242 " --> pdb=" O LEU C1238 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N MET C1243 " --> pdb=" O VAL C1239 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1238 through 1243' Processing helix chain 'C' and resid 1271 through 1282 Processing helix chain 'C' and resid 1283 through 1293 Processing helix chain 'C' and resid 1297 through 1311 removed outlier: 4.220A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N LYS C1303 " --> pdb=" O ASN C1299 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 3.989A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 6 through 12 removed outlier: 3.530A pdb=" N GLN D 11 " --> pdb=" O PHE D 7 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N THR D 12 " --> pdb=" O LEU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 26 through 34 Processing helix chain 'D' and resid 95 through 101 removed outlier: 3.841A pdb=" N ARG D 101 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 Processing helix chain 'D' and resid 131 through 139 Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'D' and resid 181 through 191 removed outlier: 4.097A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.919A pdb=" N GLU D 197 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 230 Processing helix chain 'D' and resid 233 through 238 Processing helix chain 'D' and resid 246 through 250 Processing helix chain 'D' and resid 266 through 284 removed outlier: 3.953A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 403 Processing helix chain 'D' and resid 405 through 416 Processing helix chain 'D' and resid 430 through 432 No H-bonds generated for 'chain 'D' and resid 430 through 432' Processing helix chain 'D' and resid 450 through 458 removed outlier: 3.973A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ALA D 456 " --> pdb=" O LEU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 473 through 483 Processing helix chain 'D' and resid 504 through 514 removed outlier: 3.905A pdb=" N LEU D 508 " --> pdb=" O GLN D 504 " (cutoff:3.500A) Processing helix chain 'D' and resid 530 through 538 removed outlier: 4.155A pdb=" N GLU D 534 " --> pdb=" O PRO D 530 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG D 538 " --> pdb=" O GLU D 534 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.811A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 593 Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.895A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 613 through 635 removed outlier: 3.576A pdb=" N THR D 617 " --> pdb=" O GLY D 613 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA D 633 " --> pdb=" O PHE D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 702 Processing helix chain 'D' and resid 720 through 729 Processing helix chain 'D' and resid 733 through 739 removed outlier: 3.549A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 775 Processing helix chain 'D' and resid 776 through 804 removed outlier: 4.864A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 875 Processing helix chain 'D' and resid 895 through 899 removed outlier: 3.691A pdb=" N CYS D 898 " --> pdb=" O CYS D 895 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N TYR D 899 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 895 through 899' Processing helix chain 'D' and resid 914 through 919 Processing helix chain 'D' and resid 1137 through 1146 Processing helix chain 'D' and resid 1216 through 1224 Processing helix chain 'D' and resid 1226 through 1245 removed outlier: 3.727A pdb=" N VAL D1240 " --> pdb=" O GLU D1236 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLN D1244 " --> pdb=" O VAL D1240 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY D1245 " --> pdb=" O TYR D1241 " (cutoff:3.500A) Processing helix chain 'D' and resid 1249 through 1261 removed outlier: 4.344A pdb=" N ILE D1253 " --> pdb=" O ASN D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1291 Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1328 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1359 through 1361 No H-bonds generated for 'chain 'D' and resid 1359 through 1361' Processing helix chain 'D' and resid 1362 through 1376 removed outlier: 3.812A pdb=" N ALA D1374 " --> pdb=" O MET D1370 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA D1375 " --> pdb=" O ARG D1371 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 14 Processing helix chain 'E' and resid 17 through 33 removed outlier: 3.691A pdb=" N LEU E 21 " --> pdb=" O PHE E 17 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 Processing helix chain 'E' and resid 62 through 74 Processing helix chain 'a' and resid 13 through 25 Processing helix chain 'a' and resid 41 through 49 Processing helix chain 'a' and resid 94 through 99 Processing helix chain 'a' and resid 113 through 125 removed outlier: 3.587A pdb=" N GLU a 118 " --> pdb=" O MET a 114 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU a 120 " --> pdb=" O VAL a 116 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU a 121 " --> pdb=" O GLN a 117 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ARG a 122 " --> pdb=" O GLU a 118 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL a 123 " --> pdb=" O LYS a 119 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ILE a 124 " --> pdb=" O LEU a 120 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLU a 125 " --> pdb=" O LEU a 121 " (cutoff:3.500A) Processing helix chain 'a' and resid 151 through 158 removed outlier: 4.214A pdb=" N MET a 155 " --> pdb=" O ASP a 151 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ASN a 157 " --> pdb=" O PRO a 153 " (cutoff:3.500A) Processing helix chain 'a' and resid 178 through 183 removed outlier: 3.789A pdb=" N ARG a 182 " --> pdb=" O PRO a 178 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU a 183 " --> pdb=" O LEU a 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 178 through 183' Processing helix chain 'a' and resid 184 through 201 removed outlier: 3.881A pdb=" N LEU a 188 " --> pdb=" O SER a 184 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU a 200 " --> pdb=" O GLN a 196 " (cutoff:3.500A) Processing helix chain 'a' and resid 210 through 220 Processing helix chain 'a' and resid 225 through 241 removed outlier: 4.078A pdb=" N LEU a 229 " --> pdb=" O ASN a 225 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR a 238 " --> pdb=" O GLU a 234 " (cutoff:3.500A) Processing helix chain 'b' and resid 14 through 26 removed outlier: 3.591A pdb=" N LEU b 25 " --> pdb=" O GLN b 21 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 51 removed outlier: 3.581A pdb=" N SER b 47 " --> pdb=" O GLU b 43 " (cutoff:3.500A) Processing helix chain 'b' and resid 53 through 58 removed outlier: 3.782A pdb=" N GLN b 57 " --> pdb=" O SER b 54 " (cutoff:3.500A) Processing helix chain 'b' and resid 72 through 78 Processing helix chain 'b' and resid 96 through 100 removed outlier: 3.812A pdb=" N ALA b 99 " --> pdb=" O PHE b 96 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ASP b 100 " --> pdb=" O GLU b 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 96 through 100' Processing helix chain 'b' and resid 113 through 121 Processing helix chain 'b' and resid 151 through 159 Processing helix chain 'b' and resid 162 through 169 removed outlier: 3.824A pdb=" N LEU b 166 " --> pdb=" O ARG b 162 " (cutoff:3.500A) Processing helix chain 'b' and resid 178 through 183 Processing helix chain 'b' and resid 185 through 201 removed outlier: 3.934A pdb=" N ARG b 199 " --> pdb=" O ILE b 195 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU b 200 " --> pdb=" O GLN b 196 " (cutoff:3.500A) Processing helix chain 'b' and resid 210 through 219 Processing helix chain 'b' and resid 226 through 241 removed outlier: 3.532A pdb=" N SER b 236 " --> pdb=" O VAL b 232 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY b 241 " --> pdb=" O VAL b 237 " (cutoff:3.500A) Processing helix chain 'c' and resid 13 through 26 removed outlier: 3.816A pdb=" N HIS c 24 " --> pdb=" O GLU c 20 " (cutoff:3.500A) Processing helix chain 'c' and resid 41 through 52 removed outlier: 3.624A pdb=" N SER c 47 " --> pdb=" O GLU c 43 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ARG c 48 " --> pdb=" O LEU c 44 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N HIS c 50 " --> pdb=" O ALA c 46 " (cutoff:3.500A) Processing helix chain 'c' and resid 69 through 79 removed outlier: 3.662A pdb=" N ASP c 74 " --> pdb=" O GLU c 70 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU c 77 " --> pdb=" O LEU c 73 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N PHE c 78 " --> pdb=" O ASP c 74 " (cutoff:3.500A) Processing helix chain 'c' and resid 94 through 100 Processing helix chain 'c' and resid 113 through 125 Processing helix chain 'c' and resid 126 through 128 No H-bonds generated for 'chain 'c' and resid 126 through 128' Processing helix chain 'c' and resid 151 through 158 removed outlier: 3.695A pdb=" N MET c 155 " --> pdb=" O ASP c 151 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU c 158 " --> pdb=" O ALA c 154 " (cutoff:3.500A) Processing helix chain 'c' and resid 162 through 169 removed outlier: 3.933A pdb=" N LEU c 166 " --> pdb=" O ARG c 162 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU c 169 " --> pdb=" O LEU c 165 " (cutoff:3.500A) Processing helix chain 'c' and resid 184 through 202 removed outlier: 4.161A pdb=" N LEU c 188 " --> pdb=" O SER c 184 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 220 Processing helix chain 'c' and resid 225 through 241 removed outlier: 3.660A pdb=" N ASN c 231 " --> pdb=" O ARG c 227 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS c 240 " --> pdb=" O SER c 236 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY c 241 " --> pdb=" O VAL c 237 " (cutoff:3.500A) Processing helix chain 'd' and resid 3 through 7 removed outlier: 3.881A pdb=" N ASN d 7 " --> pdb=" O TYR d 4 " (cutoff:3.500A) Processing helix chain 'd' and resid 12 through 26 removed outlier: 3.739A pdb=" N HIS d 24 " --> pdb=" O GLU d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 43 through 52 Processing helix chain 'd' and resid 70 through 78 removed outlier: 3.845A pdb=" N ASP d 74 " --> pdb=" O GLU d 70 " (cutoff:3.500A) Processing helix chain 'd' and resid 109 through 112 Processing helix chain 'd' and resid 113 through 127 removed outlier: 3.643A pdb=" N ARG d 122 " --> pdb=" O GLU d 118 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLU d 125 " --> pdb=" O LEU d 121 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR d 126 " --> pdb=" O ARG d 122 " (cutoff:3.500A) Processing helix chain 'd' and resid 151 through 158 removed outlier: 3.907A pdb=" N MET d 155 " --> pdb=" O ASP d 151 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL d 156 " --> pdb=" O LEU d 152 " (cutoff:3.500A) Processing helix chain 'd' and resid 162 through 170 Processing helix chain 'd' and resid 184 through 201 removed outlier: 3.926A pdb=" N LEU d 188 " --> pdb=" O SER d 184 " (cutoff:3.500A) Processing helix chain 'd' and resid 210 through 220 removed outlier: 3.599A pdb=" N ARG d 214 " --> pdb=" O THR d 210 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR d 220 " --> pdb=" O THR d 216 " (cutoff:3.500A) Processing helix chain 'd' and resid 226 through 241 removed outlier: 3.754A pdb=" N ASN d 231 " --> pdb=" O ARG d 227 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL d 232 " --> pdb=" O GLU d 228 " (cutoff:3.500A) Processing helix chain 'f' and resid 12 through 26 removed outlier: 3.516A pdb=" N SER f 23 " --> pdb=" O LEU f 19 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N HIS f 24 " --> pdb=" O GLU f 20 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 53 removed outlier: 3.559A pdb=" N ILE f 45 " --> pdb=" O GLY f 41 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER f 47 " --> pdb=" O GLU f 43 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N TYR f 51 " --> pdb=" O SER f 47 " (cutoff:3.500A) Processing helix chain 'f' and resid 72 through 78 Processing helix chain 'f' and resid 94 through 99 Processing helix chain 'f' and resid 109 through 112 Processing helix chain 'f' and resid 113 through 126 removed outlier: 3.719A pdb=" N LEU f 121 " --> pdb=" O GLN f 117 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ARG f 122 " --> pdb=" O GLU f 118 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N VAL f 123 " --> pdb=" O LYS f 119 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR f 126 " --> pdb=" O ARG f 122 " (cutoff:3.500A) Processing helix chain 'f' and resid 151 through 159 removed outlier: 3.843A pdb=" N ASN f 157 " --> pdb=" O PRO f 153 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU f 158 " --> pdb=" O ALA f 154 " (cutoff:3.500A) Processing helix chain 'f' and resid 162 through 168 removed outlier: 3.581A pdb=" N LEU f 166 " --> pdb=" O ARG f 162 " (cutoff:3.500A) Processing helix chain 'f' and resid 178 through 183 removed outlier: 3.569A pdb=" N ARG f 182 " --> pdb=" O PRO f 178 " (cutoff:3.500A) Processing helix chain 'f' and resid 185 through 201 Processing helix chain 'f' and resid 210 through 219 Processing helix chain 'f' and resid 225 through 241 removed outlier: 3.667A pdb=" N LEU f 229 " --> pdb=" O ASN f 225 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N TYR f 238 " --> pdb=" O GLU f 234 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY f 241 " --> pdb=" O VAL f 237 " (cutoff:3.500A) Processing helix chain 'e' and resid 14 through 23 Processing helix chain 'e' and resid 43 through 53 removed outlier: 3.717A pdb=" N HIS e 50 " --> pdb=" O ALA e 46 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR e 51 " --> pdb=" O SER e 47 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N SER e 53 " --> pdb=" O LEU e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 72 through 79 removed outlier: 3.634A pdb=" N PHE e 78 " --> pdb=" O ASP e 74 " (cutoff:3.500A) Processing helix chain 'e' and resid 94 through 99 removed outlier: 3.716A pdb=" N ALA e 99 " --> pdb=" O ARG e 95 " (cutoff:3.500A) Processing helix chain 'e' and resid 113 through 120 removed outlier: 3.535A pdb=" N GLU e 118 " --> pdb=" O MET e 114 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS e 119 " --> pdb=" O MET e 115 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU e 120 " --> pdb=" O VAL e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 151 through 159 removed outlier: 3.697A pdb=" N ASN e 157 " --> pdb=" O PRO e 153 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU e 158 " --> pdb=" O ALA e 154 " (cutoff:3.500A) Processing helix chain 'e' and resid 162 through 169 Processing helix chain 'e' and resid 178 through 183 Processing helix chain 'e' and resid 184 through 201 removed outlier: 4.108A pdb=" N LEU e 188 " --> pdb=" O SER e 184 " (cutoff:3.500A) Processing helix chain 'e' and resid 211 through 220 removed outlier: 3.575A pdb=" N LEU e 218 " --> pdb=" O ARG e 214 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN e 219 " --> pdb=" O GLU e 215 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR e 220 " --> pdb=" O THR e 216 " (cutoff:3.500A) Processing helix chain 'e' and resid 228 through 241 Processing helix chain 'M' and resid 16 through 25 Processing helix chain 'M' and resid 29 through 44 removed outlier: 3.572A pdb=" N GLN M 35 " --> pdb=" O LEU M 31 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU M 36 " --> pdb=" O GLU M 32 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA M 40 " --> pdb=" O GLU M 36 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER M 43 " --> pdb=" O GLN M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 120 through 130 removed outlier: 3.656A pdb=" N GLN M 127 " --> pdb=" O TYR M 123 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 147 Processing helix chain 'M' and resid 157 through 166 Processing helix chain 'M' and resid 171 through 182 Processing helix chain 'M' and resid 196 through 206 removed outlier: 4.115A pdb=" N PHE M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 223 removed outlier: 3.922A pdb=" N ASP M 222 " --> pdb=" O LEU M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 229 Processing helix chain 'M' and resid 231 through 240 Processing helix chain 'M' and resid 245 through 255 removed outlier: 3.858A pdb=" N ALA M 249 " --> pdb=" O VAL M 245 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 265 removed outlier: 3.858A pdb=" N GLN M 262 " --> pdb=" O ARG M 259 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE M 264 " --> pdb=" O GLY M 261 " (cutoff:3.500A) Processing helix chain 'M' and resid 300 through 305 Processing helix chain 'M' and resid 312 through 351 removed outlier: 3.829A pdb=" N GLN M 350 " --> pdb=" O CYS M 346 " (cutoff:3.500A) Processing helix chain 'M' and resid 353 through 358 Processing helix chain 'M' and resid 366 through 374 removed outlier: 3.538A pdb=" N ILE M 370 " --> pdb=" O VAL M 366 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA M 373 " --> pdb=" O ASP M 369 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL M 374 " --> pdb=" O ILE M 370 " (cutoff:3.500A) Processing helix chain 'M' and resid 377 through 386 removed outlier: 3.573A pdb=" N THR M 386 " --> pdb=" O SER M 382 " (cutoff:3.500A) Processing helix chain 'M' and resid 400 through 403 Processing helix chain 'M' and resid 410 through 412 No H-bonds generated for 'chain 'M' and resid 410 through 412' Processing helix chain 'M' and resid 417 through 430 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 454 through 465 Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 18 removed outlier: 4.992A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU A 28 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 98 through 105 removed outlier: 8.157A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LYS A 145 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 90 through 92 Processing sheet with id=AA4, first strand: chain 'B' and resid 16 through 18 removed outlier: 3.808A pdb=" N ALA B 24 " --> pdb=" O MET B 205 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET B 205 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.840A pdb=" N GLY B 149 " --> pdb=" O GLY B 53 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N LYS B 145 " --> pdb=" O THR B 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 90 through 92 Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 7.584A pdb=" N VAL B 110 " --> pdb=" O ILE B 130 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 13 through 14 removed outlier: 6.379A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.997A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 59 through 60 removed outlier: 6.997A pdb=" N LYS C 99 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N TYR C 73 " --> pdb=" O ARG C 97 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ARG C 97 " --> pdb=" O TYR C 73 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N LEU C 75 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 143 through 145 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 removed outlier: 6.507A pdb=" N SER C 147 " --> pdb=" O SER C 531 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 156 removed outlier: 3.713A pdb=" N LEU C 184 " --> pdb=" O ILE C 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 240 Processing sheet with id=AB6, first strand: chain 'C' and resid 580 through 581 removed outlier: 3.734A pdb=" N LYS C 593 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLU C 602 " --> pdb=" O LYS C 593 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N THR C 595 " --> pdb=" O THR C 600 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N THR C 600 " --> pdb=" O THR C 595 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 580 through 581 Processing sheet with id=AB8, first strand: chain 'C' and resid 616 through 617 Processing sheet with id=AB9, first strand: chain 'C' and resid 717 through 718 removed outlier: 4.024A pdb=" N ASP C 781 " --> pdb=" O ALA C 718 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 723 through 727 removed outlier: 3.634A pdb=" N GLN C 725 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 757 through 758 removed outlier: 3.776A pdb=" N THR C 757 " --> pdb=" O ILE C 765 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE C 765 " --> pdb=" O THR C 757 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'C' and resid 768 through 769 Processing sheet with id=AC4, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC5, first strand: chain 'C' and resid 1209 through 1210 removed outlier: 7.215A pdb=" N ILE C 816 " --> pdb=" O LYS C1078 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ASN C1080 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL C 818 " --> pdb=" O ASN C1080 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N ILE C1096 " --> pdb=" O ASN C 799 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG C 801 " --> pdb=" O ILE C1096 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N LEU C1098 " --> pdb=" O ARG C 801 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N ALA C 803 " --> pdb=" O LEU C1098 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE C 804 " --> pdb=" O THR C1226 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N THR C1226 " --> pdb=" O PHE C 804 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 839 removed outlier: 6.688A pdb=" N ILE C1049 " --> pdb=" O VAL C 933 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N VAL C 933 " --> pdb=" O ILE C1049 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N LYS C1051 " --> pdb=" O VAL C 931 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N VAL C 931 " --> pdb=" O LYS C1051 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TYR C1053 " --> pdb=" O ILE C 929 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N LYS C1057 " --> pdb=" O SER C 925 " (cutoff:3.500A) removed outlier: 9.005A pdb=" N SER C 925 " --> pdb=" O LYS C1057 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 882 through 884 removed outlier: 6.551A pdb=" N LEU C 918 " --> pdb=" O LEU C 883 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 887 through 889 Processing sheet with id=AC9, first strand: chain 'C' and resid 1335 through 1339 removed outlier: 3.641A pdb=" N GLU C1338 " --> pdb=" O LYS D 21 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 103 through 105 Processing sheet with id=AD2, first strand: chain 'D' and resid 145 through 146 Processing sheet with id=AD3, first strand: chain 'D' and resid 316 through 317 removed outlier: 3.536A pdb=" N THR D 317 " --> pdb=" O ASN D 320 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN D 320 " --> pdb=" O THR D 317 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'D' and resid 354 through 357 removed outlier: 5.631A pdb=" N VAL D 354 " --> pdb=" O ILE D 447 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N LEU D 449 " --> pdb=" O VAL D 354 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N THR D 356 " --> pdb=" O LEU D 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'D' and resid 366 through 369 removed outlier: 6.192A pdb=" N CYS D 366 " --> pdb=" O VAL D 440 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE D 442 " --> pdb=" O CYS D 366 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU D 368 " --> pdb=" O ILE D 442 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'D' and resid 434 through 437 Processing sheet with id=AD7, first strand: chain 'D' and resid 548 through 549 Processing sheet with id=AD8, first strand: chain 'D' and resid 552 through 559 removed outlier: 4.157A pdb=" N ASP D 558 " --> pdb=" O GLU D 562 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU D 562 " --> pdb=" O ASP D 558 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 820 through 822 removed outlier: 4.893A pdb=" N VAL D 843 " --> pdb=" O ARG D 883 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR D 844 " --> pdb=" O THR D 862 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR D 862 " --> pdb=" O THR D 844 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 965 through 967 Processing sheet with id=AE2, first strand: chain 'D' and resid 1265 through 1266 Processing sheet with id=AE3, first strand: chain 'a' and resid 103 through 104 removed outlier: 6.046A pdb=" N VAL a 32 " --> pdb=" O CYS a 146 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N THR a 148 " --> pdb=" O VAL a 32 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE a 34 " --> pdb=" O THR a 148 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'a' and resid 79 through 80 Processing sheet with id=AE5, first strand: chain 'b' and resid 62 through 63 removed outlier: 3.809A pdb=" N ASP b 107 " --> pdb=" O LEU b 63 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU b 33 " --> pdb=" O VAL b 174 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'b' and resid 128 through 129 removed outlier: 3.700A pdb=" N LEU b 129 " --> pdb=" O LEU b 138 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 147 through 148 removed outlier: 5.178A pdb=" N ILE c 34 " --> pdb=" O THR c 148 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'c' and resid 61 through 64 removed outlier: 6.907A pdb=" N ILE c 61 " --> pdb=" O PHE c 105 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASP c 107 " --> pdb=" O ILE c 61 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU c 63 " --> pdb=" O ASP c 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'd' and resid 103 through 107 removed outlier: 3.506A pdb=" N THR d 148 " --> pdb=" O ILE d 34 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N LEU d 33 " --> pdb=" O VAL d 174 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'd' and resid 128 through 129 removed outlier: 3.995A pdb=" N LEU d 138 " --> pdb=" O LEU d 129 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'f' and resid 60 through 64 removed outlier: 3.620A pdb=" N PHE f 105 " --> pdb=" O ILE f 61 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU f 63 " --> pdb=" O PHE f 105 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N VAL f 32 " --> pdb=" O CYS f 146 " (cutoff:3.500A) removed outlier: 8.093A pdb=" N THR f 148 " --> pdb=" O VAL f 32 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ILE f 34 " --> pdb=" O THR f 148 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU f 33 " --> pdb=" O VAL f 174 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'f' and resid 128 through 129 Processing sheet with id=AF4, first strand: chain 'e' and resid 32 through 35 removed outlier: 3.709A pdb=" N VAL e 32 " --> pdb=" O LEU e 144 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE e 105 " --> pdb=" O ILE e 61 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASP e 107 " --> pdb=" O LEU e 63 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'e' and resid 128 through 129 Processing sheet with id=AF6, first strand: chain 'M' and resid 47 through 48 Processing sheet with id=AF7, first strand: chain 'M' and resid 287 through 289 removed outlier: 6.198A pdb=" N VAL M 276 " --> pdb=" O HIS M 391 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE M 397 " --> pdb=" O LEU M 390 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'M' and resid 406 through 408 1436 hydrogen bonds defined for protein. 4101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 89 hydrogen bonds 178 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 59 stacking parallelities Total time for adding SS restraints: 10.21 Time building geometry restraints manager: 4.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.29: 6940 1.29 - 1.50: 17573 1.50 - 1.70: 17495 1.70 - 1.91: 292 1.91 - 2.11: 6 Bond restraints: 42306 Sorted by residual: bond pdb=" CZ ARG a 98 " pdb=" NH2 ARG a 98 " ideal model delta sigma weight residual 1.330 1.694 -0.364 1.30e-02 5.92e+03 7.83e+02 bond pdb=" C ASP a 185 " pdb=" O ASP a 185 " ideal model delta sigma weight residual 1.235 1.560 -0.325 1.25e-02 6.40e+03 6.77e+02 bond pdb=" C SER e 62 " pdb=" O SER e 62 " ideal model delta sigma weight residual 1.234 1.504 -0.270 1.18e-02 7.18e+03 5.22e+02 bond pdb=" CZ ARG b 143 " pdb=" NH1 ARG b 143 " ideal model delta sigma weight residual 1.323 1.640 -0.317 1.40e-02 5.10e+03 5.14e+02 bond pdb=" CZ ARG a 48 " pdb=" NH1 ARG a 48 " ideal model delta sigma weight residual 1.323 1.599 -0.276 1.40e-02 5.10e+03 3.88e+02 ... (remaining 42301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.12: 56477 7.12 - 14.24: 1029 14.24 - 21.36: 158 21.36 - 28.48: 27 28.48 - 35.60: 10 Bond angle restraints: 57701 Sorted by residual: angle pdb=" C PRO M 258 " pdb=" CA PRO M 258 " pdb=" CB PRO M 258 " ideal model delta sigma weight residual 111.46 82.32 29.14 1.29e+00 6.01e-01 5.10e+02 angle pdb=" NE ARG b 143 " pdb=" CZ ARG b 143 " pdb=" NH2 ARG b 143 " ideal model delta sigma weight residual 119.20 101.29 17.91 9.00e-01 1.23e+00 3.96e+02 angle pdb=" NE ARG a 98 " pdb=" CZ ARG a 98 " pdb=" NH1 ARG a 98 " ideal model delta sigma weight residual 121.50 103.00 18.50 1.00e+00 1.00e+00 3.42e+02 angle pdb=" NE ARG a 48 " pdb=" CZ ARG a 48 " pdb=" NH1 ARG a 48 " ideal model delta sigma weight residual 121.50 139.49 -17.99 1.00e+00 1.00e+00 3.24e+02 angle pdb=" C ILE e 45 " pdb=" CA ILE e 45 " pdb=" CB ILE e 45 " ideal model delta sigma weight residual 112.04 88.60 23.44 1.31e+00 5.83e-01 3.20e+02 ... (remaining 57696 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.84: 24346 27.84 - 55.68: 1152 55.68 - 83.52: 101 83.52 - 111.36: 6 111.36 - 139.20: 7 Dihedral angle restraints: 25612 sinusoidal: 10510 harmonic: 15102 Sorted by residual: dihedral pdb=" C PRO M 258 " pdb=" N PRO M 258 " pdb=" CA PRO M 258 " pdb=" CB PRO M 258 " ideal model delta harmonic sigma weight residual -120.70 -84.40 -36.30 0 2.50e+00 1.60e-01 2.11e+02 dihedral pdb=" N LEU b 49 " pdb=" C LEU b 49 " pdb=" CA LEU b 49 " pdb=" CB LEU b 49 " ideal model delta harmonic sigma weight residual 122.80 151.44 -28.64 0 2.50e+00 1.60e-01 1.31e+02 dihedral pdb=" N THR M 119 " pdb=" C THR M 119 " pdb=" CA THR M 119 " pdb=" CB THR M 119 " ideal model delta harmonic sigma weight residual 123.40 151.29 -27.89 0 2.50e+00 1.60e-01 1.24e+02 ... (remaining 25609 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 6376 0.287 - 0.573: 240 0.573 - 0.860: 44 0.860 - 1.146: 8 1.146 - 1.433: 4 Chirality restraints: 6672 Sorted by residual: chirality pdb=" C1' ADP f 601 " pdb=" C2' ADP f 601 " pdb=" N9 ADP f 601 " pdb=" O4' ADP f 601 " both_signs ideal model delta sigma weight residual False 2.48 1.05 1.43 2.00e-01 2.50e+01 5.13e+01 chirality pdb=" CA THR M 119 " pdb=" N THR M 119 " pdb=" C THR M 119 " pdb=" CB THR M 119 " both_signs ideal model delta sigma weight residual False 2.53 1.24 1.29 2.00e-01 2.50e+01 4.16e+01 chirality pdb=" CA GLU f 234 " pdb=" N GLU f 234 " pdb=" C GLU f 234 " pdb=" CB GLU f 234 " both_signs ideal model delta sigma weight residual False 2.51 1.32 1.20 2.00e-01 2.50e+01 3.57e+01 ... (remaining 6669 not shown) Planarity restraints: 7320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 285 " -0.070 2.00e-02 2.50e+03 1.00e-01 2.52e+02 pdb=" CG TRP M 285 " 0.124 2.00e-02 2.50e+03 pdb=" CD1 TRP M 285 " -0.103 2.00e-02 2.50e+03 pdb=" CD2 TRP M 285 " 0.089 2.00e-02 2.50e+03 pdb=" NE1 TRP M 285 " -0.112 2.00e-02 2.50e+03 pdb=" CE2 TRP M 285 " 0.187 2.00e-02 2.50e+03 pdb=" CE3 TRP M 285 " -0.018 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 285 " 0.036 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 285 " -0.023 2.00e-02 2.50e+03 pdb=" CH2 TRP M 285 " -0.110 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 126 " 0.012 2.00e-02 2.50e+03 6.33e-02 1.00e+02 pdb=" CG TRP M 126 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP M 126 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TRP M 126 " -0.065 2.00e-02 2.50e+03 pdb=" NE1 TRP M 126 " -0.062 2.00e-02 2.50e+03 pdb=" CE2 TRP M 126 " -0.095 2.00e-02 2.50e+03 pdb=" CE3 TRP M 126 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 126 " 0.095 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 126 " -0.060 2.00e-02 2.50e+03 pdb=" CH2 TRP M 126 " 0.053 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 222 " 0.081 2.00e-02 2.50e+03 5.97e-02 8.92e+01 pdb=" CG TRP a 222 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP a 222 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP a 222 " 0.045 2.00e-02 2.50e+03 pdb=" NE1 TRP a 222 " -0.037 2.00e-02 2.50e+03 pdb=" CE2 TRP a 222 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP a 222 " -0.134 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 222 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 222 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP a 222 " 0.080 2.00e-02 2.50e+03 ... (remaining 7317 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 399 2.50 - 3.10: 30769 3.10 - 3.70: 62288 3.70 - 4.30: 86593 4.30 - 4.90: 139358 Nonbonded interactions: 319407 Sorted by model distance: nonbonded pdb=" O2A ADP f 601 " pdb=" O2B ADP f 601 " model vdw 1.898 3.040 nonbonded pdb=" N ASP a 185 " pdb=" N ILE a 186 " model vdw 1.973 2.560 nonbonded pdb=" O PRO M 258 " pdb=" CG PRO M 258 " model vdw 2.046 3.440 nonbonded pdb=" O LYS f 5 " pdb=" NZ LYS f 5 " model vdw 2.079 3.120 nonbonded pdb=" N GLU a 130 " pdb=" OE1 GLU a 130 " model vdw 2.081 3.120 ... (remaining 319402 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 'a' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 54 or (resid 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 79 or (resid 80 through 82 and (name N or name \ CA or name C or name O or name CB )) or (resid 83 through 86 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 87 through 92 and (name N or na \ me CA or name C or name O or name CB )) or resid 93 through 102 or (resid 103 an \ d (name N or name CA or name C or name O or name CB )) or resid 104 through 134 \ or (resid 135 and (name N or name CA or name C or name O or name CB )) or resid \ 136 through 220 or (resid 221 and (name N or name CA or name C or name O or name \ CB )) or resid 222 through 258)) selection = (chain 'b' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 54 or (resid 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 79 or (resid 80 through 82 and (name N or name \ CA or name C or name O or name CB )) or (resid 83 through 86 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 87 through 92 and (name N or na \ me CA or name C or name O or name CB )) or resid 93 through 102 or (resid 103 an \ d (name N or name CA or name C or name O or name CB )) or resid 104 through 134 \ or (resid 135 and (name N or name CA or name C or name O or name CB )) or resid \ 136 through 237 or (resid 238 and (name N or name CA or name C or name O or name \ CB )) or resid 239 through 257 or (resid 258 and (name N or name CA or name C o \ r name O or name CB )))) selection = (chain 'c' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 220 or (resid 221 and (name N or name CA or name C or name \ O or name CB )) or resid 222 through 237 or (resid 238 and (name N or name CA or \ name C or name O or name CB )) or resid 239 through 257 or (resid 258 and (name \ N or name CA or name C or name O or name CB )))) selection = (chain 'd' and (resid 3 through 54 or (resid 55 and (name N or name CA or name C \ or name O or name CB )) or resid 56 through 79 or (resid 80 through 82 and (nam \ e N or name CA or name C or name O or name CB )) or (resid 83 through 86 and (na \ me N or name CA or name C or name O or name CB )) or (resid 87 through 92 and (n \ ame N or name CA or name C or name O or name CB )) or resid 93 through 102 or (r \ esid 103 and (name N or name CA or name C or name O or name CB )) or resid 104 t \ hrough 134 or (resid 135 and (name N or name CA or name C or name O or name CB ) \ ) or resid 136 through 220 or (resid 221 and (name N or name CA or name C or nam \ e O or name CB )) or resid 222 through 237 or (resid 238 and (name N or name CA \ or name C or name O or name CB )) or resid 239 through 257 or (resid 258 and (na \ me N or name CA or name C or name O or name CB )))) selection = (chain 'e' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 54 or (resid 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 79 or (resid 80 through 82 and (name N or name \ CA or name C or name O or name CB )) or (resid 83 through 86 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 87 through 92 and (name N or na \ me CA or name C or name O or name CB )) or resid 93 through 102 or (resid 103 an \ d (name N or name CA or name C or name O or name CB )) or resid 104 through 134 \ or (resid 135 and (name N or name CA or name C or name O or name CB )) or resid \ 136 through 220 or (resid 221 and (name N or name CA or name C or name O or name \ CB )) or resid 222 through 237 or (resid 238 and (name N or name CA or name C o \ r name O or name CB )) or resid 239 through 257 or (resid 258 and (name N or nam \ e CA or name C or name O or name CB )))) selection = (chain 'f' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 54 or (resid 55 and (name N or name CA or name C or name O \ or name CB )) or resid 56 through 79 or (resid 80 through 82 and (name N or name \ CA or name C or name O or name CB )) or (resid 83 through 86 and (name N or nam \ e CA or name C or name O or name CB )) or (resid 87 through 92 and (name N or na \ me CA or name C or name O or name CB )) or resid 93 through 102 or (resid 103 an \ d (name N or name CA or name C or name O or name CB )) or resid 104 through 134 \ or (resid 135 and (name N or name CA or name C or name O or name CB )) or resid \ 136 through 237 or (resid 238 and (name N or name CA or name C or name O or name \ CB )) or resid 239 through 258)) } 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=0.20 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: 1.240 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: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 40.430 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6844 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 : 0.021 0.364 42308 Z= 1.327 Angle : 2.212 35.602 57701 Z= 1.353 Chirality : 0.126 1.433 6672 Planarity : 0.009 0.113 7320 Dihedral : 14.787 139.204 15864 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 37.17 Ramachandran Plot: Outliers : 1.33 % Allowed : 8.18 % Favored : 90.49 % Rotamer: Outliers : 10.34 % Allowed : 10.80 % Favored : 78.87 % Cbeta Deviations : 3.75 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.11), residues: 5205 helix: -0.85 (0.12), residues: 1796 sheet: -1.71 (0.24), residues: 438 loop : -2.87 (0.10), residues: 2971 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.063 0.001 ARG b 143 TYR 0.117 0.004 TYR M 153 PHE 0.119 0.007 PHE f 15 TRP 0.187 0.014 TRP M 285 HIS 0.042 0.002 HIS d 50 Details of bonding type rmsd covalent geometry : bond 0.02067 (42306) covalent geometry : angle 2.21203 (57701) hydrogen bonds : bond 0.20307 ( 1516) hydrogen bonds : angle 7.17930 ( 4279) Misc. bond : bond 0.24661 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 425 poor density : 841 time to evaluate : 1.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 131 CYS cc_start: 0.7606 (t) cc_final: 0.7292 (t) REVERT: C 160 ASP cc_start: 0.6747 (m-30) cc_final: 0.5526 (m-30) REVERT: C 208 ILE cc_start: 0.8248 (OUTLIER) cc_final: 0.7278 (mt) REVERT: C 437 ASN cc_start: 0.8003 (m-40) cc_final: 0.7625 (m-40) REVERT: C 696 ASP cc_start: 0.8019 (t70) cc_final: 0.7576 (t0) REVERT: C 843 THR cc_start: 0.7159 (p) cc_final: 0.6921 (p) REVERT: C 917 SER cc_start: 0.7854 (p) cc_final: 0.7545 (t) REVERT: C 955 GLN cc_start: 0.8473 (tp40) cc_final: 0.8118 (tm-30) REVERT: C 1026 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7728 (pt0) REVERT: C 1030 GLU cc_start: 0.8292 (tp30) cc_final: 0.8058 (tp30) REVERT: C 1304 MET cc_start: 0.8140 (tpp) cc_final: 0.7790 (tpt) REVERT: D 48 THR cc_start: 0.8142 (p) cc_final: 0.7711 (p) REVERT: D 265 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6445 (mp) REVERT: D 340 GLN cc_start: 0.1882 (OUTLIER) cc_final: 0.0638 (pp30) REVERT: D 505 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6701 (m-30) REVERT: D 517 CYS cc_start: 0.2835 (OUTLIER) cc_final: 0.2452 (p) REVERT: D 781 LYS cc_start: 0.7049 (OUTLIER) cc_final: 0.6843 (mtmt) REVERT: D 826 ILE cc_start: 0.6497 (OUTLIER) cc_final: 0.6063 (pt) REVERT: D 901 ARG cc_start: 0.5917 (OUTLIER) cc_final: 0.4554 (ppt-90) REVERT: D 1040 MET cc_start: 0.3980 (mtp) cc_final: 0.2567 (mmt) REVERT: a 118 GLU cc_start: 0.6020 (OUTLIER) cc_final: 0.4886 (pt0) REVERT: a 143 ARG cc_start: 0.5092 (OUTLIER) cc_final: 0.4552 (ttp-170) REVERT: a 250 ILE cc_start: 0.0307 (OUTLIER) cc_final: -0.0218 (tt) REVERT: b 57 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8805 (pp30) REVERT: b 139 GLN cc_start: 0.9318 (OUTLIER) cc_final: 0.9080 (tm-30) REVERT: c 136 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7657 (tm-30) REVERT: c 138 LEU cc_start: 0.5385 (OUTLIER) cc_final: 0.5151 (tt) REVERT: c 187 MET cc_start: 0.5721 (mmm) cc_final: 0.5508 (mmm) REVERT: d 42 LYS cc_start: 0.6906 (mmmt) cc_final: 0.6523 (mtmm) REVERT: d 55 ARG cc_start: 0.3239 (OUTLIER) cc_final: 0.2816 (pmt-80) REVERT: d 69 ASN cc_start: 0.8081 (OUTLIER) cc_final: 0.7459 (p0) REVERT: d 222 TRP cc_start: 0.6086 (m-10) cc_final: 0.3531 (m-10) REVERT: e 42 LYS cc_start: 0.4467 (OUTLIER) cc_final: 0.4183 (mtmm) REVERT: e 49 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8730 (tt) REVERT: e 255 PHE cc_start: 0.3298 (OUTLIER) cc_final: 0.2584 (m-80) REVERT: M 11 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6676 (pm20) REVERT: M 31 LEU cc_start: 0.8229 (OUTLIER) cc_final: 0.7999 (mm) REVERT: M 127 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8316 (pt0) REVERT: M 185 PHE cc_start: 0.8741 (OUTLIER) cc_final: 0.8470 (m-10) REVERT: M 259 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8227 (ttm170) REVERT: M 416 SER cc_start: 0.9489 (OUTLIER) cc_final: 0.9199 (m) REVERT: M 441 LYS cc_start: 0.9636 (OUTLIER) cc_final: 0.9323 (mmmm) outliers start: 425 outliers final: 113 residues processed: 1197 average time/residue: 0.2699 time to fit residues: 507.3408 Evaluate side-chains 594 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 141 poor density : 453 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 1026 GLU Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 340 GLN Chi-restraints excluded: chain D residue 347 VAL Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 781 LYS Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 56 TRP Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 118 GLU Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain a residue 143 ARG Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 171 PHE Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 196 GLN Chi-restraints excluded: chain a residue 225 ASN Chi-restraints excluded: chain a residue 226 ILE Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain b residue 32 VAL Chi-restraints excluded: chain b residue 48 ARG Chi-restraints excluded: chain b residue 57 GLN Chi-restraints excluded: chain b residue 62 SER Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 139 GLN Chi-restraints excluded: chain b residue 143 ARG Chi-restraints excluded: chain b residue 204 PRO Chi-restraints excluded: chain b residue 235 ARG Chi-restraints excluded: chain b residue 239 ARG Chi-restraints excluded: chain b residue 256 LYS Chi-restraints excluded: chain c residue 5 LYS Chi-restraints excluded: chain c residue 29 ASP Chi-restraints excluded: chain c residue 56 TRP Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 136 GLN Chi-restraints excluded: chain c residue 138 LEU Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 229 LEU Chi-restraints excluded: chain c residue 233 VAL Chi-restraints excluded: chain c residue 236 SER Chi-restraints excluded: chain d residue 55 ARG Chi-restraints excluded: chain d residue 56 TRP Chi-restraints excluded: chain d residue 69 ASN Chi-restraints excluded: chain d residue 70 GLU Chi-restraints excluded: chain d residue 95 ARG Chi-restraints excluded: chain d residue 96 PHE Chi-restraints excluded: chain d residue 98 ARG Chi-restraints excluded: chain d residue 139 GLN Chi-restraints excluded: chain d residue 235 ARG Chi-restraints excluded: chain f residue 5 LYS Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 15 PHE Chi-restraints excluded: chain f residue 34 ILE Chi-restraints excluded: chain f residue 50 HIS Chi-restraints excluded: chain f residue 51 TYR Chi-restraints excluded: chain f residue 55 ARG Chi-restraints excluded: chain f residue 63 LEU Chi-restraints excluded: chain f residue 129 LEU Chi-restraints excluded: chain f residue 136 GLN Chi-restraints excluded: chain f residue 214 ARG Chi-restraints excluded: chain f residue 237 VAL Chi-restraints excluded: chain e residue 22 VAL Chi-restraints excluded: chain e residue 42 LYS Chi-restraints excluded: chain e residue 49 LEU Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 91 ARG Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 158 GLU Chi-restraints excluded: chain e residue 174 VAL Chi-restraints excluded: chain e residue 199 ARG Chi-restraints excluded: chain e residue 255 PHE Chi-restraints excluded: chain M residue 7 LEU Chi-restraints excluded: chain M residue 8 ARG Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 11 GLN Chi-restraints excluded: chain M residue 15 MET Chi-restraints excluded: chain M residue 16 THR Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 118 GLN Chi-restraints excluded: chain M residue 127 GLN Chi-restraints excluded: chain M residue 131 THR Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 154 LEU Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 196 ARG Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 217 ARG Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 240 ARG Chi-restraints excluded: chain M residue 246 LEU Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 259 ARG Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 292 ASP Chi-restraints excluded: chain M residue 306 MET Chi-restraints excluded: chain M residue 340 LEU Chi-restraints excluded: chain M residue 355 PHE Chi-restraints excluded: chain M residue 370 ILE Chi-restraints excluded: chain M residue 372 GLN Chi-restraints excluded: chain M residue 381 ILE Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 416 SER Chi-restraints excluded: chain M residue 441 LYS Chi-restraints excluded: chain M residue 455 ARG Chi-restraints excluded: chain M residue 460 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 394 optimal weight: 50.0000 chunk 430 optimal weight: 20.0000 chunk 41 optimal weight: 20.0000 chunk 265 optimal weight: 2.9990 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 20.0000 chunk 310 optimal weight: 8.9990 chunk 488 optimal weight: 0.8980 chunk 366 optimal weight: 20.0000 chunk 223 optimal weight: 1.9990 chunk 516 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS B 147 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 526 HIS C 580 GLN C 649 GLN C 686 GLN C 761 GLN C1268 GLN D 94 GLN D 232 ASN D 340 GLN D 341 ASN D 430 HIS D 450 HIS D 465 GLN D 700 ASN E 29 GLN a 21 GLN a 50 HIS a 225 ASN a 231 ASN b 92 HIS b 139 GLN b 157 ASN c 64 ASN ** c 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 157 ASN ** c 225 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 92 HIS f 7 ASN f 13 ASN f 24 HIS f 50 HIS f 136 GLN f 157 ASN f 175 GLN e 24 HIS e 89 GLN ** e 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 225 ASN M 20 GLN M 35 GLN M 118 GLN M 127 GLN M 205 GLN M 229 ASN M 322 ASN M 324 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.184875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.155686 restraints weight = 78094.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.151598 restraints weight = 141453.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.149483 restraints weight = 124040.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.148930 restraints weight = 118626.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.147315 restraints weight = 99578.869| |-----------------------------------------------------------------------------| r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3990 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3990 r_free = 0.3990 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3989 r_free = 0.3989 target_work(ls_wunit_k1) = 0.145 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3989 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6945 moved from start: 0.3719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 42308 Z= 0.280 Angle : 0.899 15.460 57701 Z= 0.447 Chirality : 0.050 0.242 6672 Planarity : 0.006 0.073 7320 Dihedral : 14.161 143.709 6874 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.19 % Allowed : 7.72 % Favored : 92.08 % Rotamer: Outliers : 5.62 % Allowed : 15.83 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.29 (0.11), residues: 5205 helix: -0.14 (0.12), residues: 1875 sheet: -1.17 (0.25), residues: 439 loop : -2.65 (0.10), residues: 2891 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG a 98 TYR 0.030 0.003 TYR c 51 PHE 0.033 0.003 PHE c 15 TRP 0.016 0.003 TRP b 222 HIS 0.013 0.002 HIS f 24 Details of bonding type rmsd covalent geometry : bond 0.00660 (42306) covalent geometry : angle 0.89938 (57701) hydrogen bonds : bond 0.05318 ( 1516) hydrogen bonds : angle 5.02054 ( 4279) Misc. bond : bond 0.00110 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 231 poor density : 461 time to evaluate : 1.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 174 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6627 (m-30) REVERT: C 176 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8503 (mt) REVERT: C 211 ARG cc_start: 0.7820 (mtp85) cc_final: 0.7456 (mtt-85) REVERT: C 696 ASP cc_start: 0.8308 (t70) cc_final: 0.7889 (t0) REVERT: C 1166 ASP cc_start: 0.7360 (t0) cc_final: 0.7123 (t0) REVERT: D 281 ARG cc_start: 0.7244 (tpt90) cc_final: 0.6977 (tpp-160) REVERT: D 299 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8982 (tp) REVERT: D 428 THR cc_start: 0.8423 (OUTLIER) cc_final: 0.8163 (t) REVERT: D 479 GLU cc_start: 0.8460 (mt-10) cc_final: 0.8259 (mt-10) REVERT: D 901 ARG cc_start: 0.6028 (OUTLIER) cc_final: 0.4544 (ppt-90) REVERT: E 62 GLN cc_start: 0.7256 (tp40) cc_final: 0.6974 (tp-100) REVERT: a 229 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7685 (pp) REVERT: b 77 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7349 (mt) REVERT: c 115 MET cc_start: 0.7098 (mmm) cc_final: 0.6815 (mmm) REVERT: d 69 ASN cc_start: 0.4696 (OUTLIER) cc_final: 0.4452 (p0) REVERT: M 28 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8190 (pp) REVERT: M 185 PHE cc_start: 0.8698 (OUTLIER) cc_final: 0.8144 (m-10) REVERT: M 279 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6898 (ppt90) REVERT: M 474 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7923 (ttpp) outliers start: 231 outliers final: 110 residues processed: 661 average time/residue: 0.2671 time to fit residues: 284.9596 Evaluate side-chains 497 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 375 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 650 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1054 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 44 ILE Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 339 ARG Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 592 VAL Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 862 THR Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1321 SER Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 131 ARG Chi-restraints excluded: chain a residue 173 VAL Chi-restraints excluded: chain a residue 229 LEU Chi-restraints excluded: chain a residue 234 GLU Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 77 LEU Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 140 VAL Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 226 ILE Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 24 HIS Chi-restraints excluded: chain d residue 43 GLU Chi-restraints excluded: chain d residue 45 ILE Chi-restraints excluded: chain d residue 69 ASN Chi-restraints excluded: chain d residue 70 GLU Chi-restraints excluded: chain d residue 98 ARG Chi-restraints excluded: chain d residue 125 GLU Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 158 GLU Chi-restraints excluded: chain e residue 164 ASP Chi-restraints excluded: chain e residue 176 LEU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 196 ARG Chi-restraints excluded: chain M residue 227 LEU Chi-restraints excluded: chain M residue 233 ARG Chi-restraints excluded: chain M residue 240 ARG Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 381 ILE Chi-restraints excluded: chain M residue 472 GLN Chi-restraints excluded: chain M residue 474 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 389 optimal weight: 50.0000 chunk 191 optimal weight: 0.6980 chunk 217 optimal weight: 7.9990 chunk 344 optimal weight: 0.9980 chunk 144 optimal weight: 2.9990 chunk 359 optimal weight: 8.9990 chunk 441 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 333 optimal weight: 50.0000 chunk 180 optimal weight: 0.5980 chunk 337 optimal weight: 0.1980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 594 GLN D 736 GLN D 865 HIS a 196 GLN ** b 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 139 GLN d 64 ASN f 117 GLN e 7 ASN e 149 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.185635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.157979 restraints weight = 77919.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.154223 restraints weight = 126393.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.150748 restraints weight = 115063.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.149917 restraints weight = 102415.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.149249 restraints weight = 87311.909| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4019 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4019 r_free = 0.4019 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4019 r_free = 0.4019 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.4019 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6877 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 42308 Z= 0.144 Angle : 0.719 11.220 57701 Z= 0.353 Chirality : 0.044 0.251 6672 Planarity : 0.005 0.068 7320 Dihedral : 13.319 144.324 6640 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.05 % Favored : 92.80 % Rotamer: Outliers : 4.45 % Allowed : 17.75 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.11), residues: 5205 helix: 0.42 (0.12), residues: 1870 sheet: -0.71 (0.26), residues: 416 loop : -2.45 (0.10), residues: 2919 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 48 TYR 0.023 0.002 TYR c 51 PHE 0.020 0.002 PHE C 337 TRP 0.037 0.002 TRP c 222 HIS 0.009 0.001 HIS D 865 Details of bonding type rmsd covalent geometry : bond 0.00321 (42306) covalent geometry : angle 0.71868 (57701) hydrogen bonds : bond 0.04069 ( 1516) hydrogen bonds : angle 4.65242 ( 4279) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 183 poor density : 395 time to evaluate : 1.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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 27 THR cc_start: 0.8490 (OUTLIER) cc_final: 0.8250 (p) REVERT: B 174 ASP cc_start: 0.6801 (OUTLIER) cc_final: 0.6476 (m-30) REVERT: C 158 ASP cc_start: 0.7348 (p0) cc_final: 0.6410 (p0) REVERT: C 176 ILE cc_start: 0.8751 (OUTLIER) cc_final: 0.8442 (mt) REVERT: C 211 ARG cc_start: 0.7771 (mtp85) cc_final: 0.7429 (mtt-85) REVERT: C 696 ASP cc_start: 0.8267 (t70) cc_final: 0.7786 (t0) REVERT: C 796 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8120 (pp) REVERT: C 1107 MET cc_start: 0.8037 (mpp) cc_final: 0.7346 (mtm) REVERT: C 1166 ASP cc_start: 0.7291 (t0) cc_final: 0.7028 (t0) REVERT: D 281 ARG cc_start: 0.7288 (tpt90) cc_final: 0.6995 (tpp-160) REVERT: D 299 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8893 (tp) REVERT: D 826 ILE cc_start: 0.6087 (OUTLIER) cc_final: 0.5766 (pt) REVERT: D 901 ARG cc_start: 0.6171 (OUTLIER) cc_final: 0.4729 (ppt-90) REVERT: a 250 ILE cc_start: -0.2863 (OUTLIER) cc_final: -0.3913 (mp) REVERT: d 69 ASN cc_start: 0.5250 (OUTLIER) cc_final: 0.4923 (p0) REVERT: M 28 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8352 (pp) REVERT: M 185 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.8136 (m-10) REVERT: M 271 TYR cc_start: 0.6467 (OUTLIER) cc_final: 0.6119 (p90) REVERT: M 279 ARG cc_start: 0.7277 (OUTLIER) cc_final: 0.6844 (ptt-90) outliers start: 183 outliers final: 98 residues processed: 544 average time/residue: 0.2492 time to fit residues: 224.7941 Evaluate side-chains 455 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 344 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 204 GLU Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 339 ARG Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 526 VAL Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 826 ILE Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain D residue 1351 VAL Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 106 LEU Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain a residue 252 ILE Chi-restraints excluded: chain b residue 103 THR Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 69 ASN Chi-restraints excluded: chain d residue 98 ARG Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 148 THR Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 146 CYS Chi-restraints excluded: chain e residue 176 LEU Chi-restraints excluded: chain e residue 226 ILE Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 196 ARG Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 240 ARG Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 351 GLN Chi-restraints excluded: chain M residue 381 ILE Chi-restraints excluded: chain M residue 472 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 496 optimal weight: 9.9990 chunk 472 optimal weight: 0.8980 chunk 331 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 43 optimal weight: 0.3980 chunk 397 optimal weight: 8.9990 chunk 362 optimal weight: 0.0770 chunk 299 optimal weight: 50.0000 chunk 104 optimal weight: 2.9990 chunk 347 optimal weight: 8.9990 chunk 500 optimal weight: 20.0000 overall best weight: 2.0742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 465 GLN D 700 ASN D 712 GLN D1218 HIS ** a 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 117 GLN ** c 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 24 HIS ** e 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 GLN M 432 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.183447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.154751 restraints weight = 77091.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.150298 restraints weight = 121946.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.146966 restraints weight = 114407.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.145934 restraints weight = 102202.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.142908 restraints weight = 104380.987| |-----------------------------------------------------------------------------| r_work (final): 0.3936 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3935 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3935 r_free = 0.3935 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3935 r_free = 0.3935 target_work(ls_wunit_k1) = 0.141 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3935 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 42308 Z= 0.175 Angle : 0.713 15.686 57701 Z= 0.349 Chirality : 0.044 0.210 6672 Planarity : 0.005 0.060 7320 Dihedral : 13.188 137.283 6624 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 7.61 % Favored : 92.26 % Rotamer: Outliers : 4.69 % Allowed : 18.12 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.11), residues: 5205 helix: 0.51 (0.12), residues: 1897 sheet: -0.56 (0.26), residues: 418 loop : -2.34 (0.11), residues: 2890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 378 TYR 0.021 0.002 TYR b 51 PHE 0.024 0.002 PHE C 337 TRP 0.023 0.002 TRP c 222 HIS 0.022 0.001 HIS d 24 Details of bonding type rmsd covalent geometry : bond 0.00410 (42306) covalent geometry : angle 0.71315 (57701) hydrogen bonds : bond 0.04110 ( 1516) hydrogen bonds : angle 4.58450 ( 4279) Misc. bond : bond 0.00043 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 193 poor density : 371 time to evaluate : 1.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: C 37 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8215 (pttm) REVERT: C 176 ILE cc_start: 0.8806 (OUTLIER) cc_final: 0.8441 (mt) REVERT: C 211 ARG cc_start: 0.7794 (mtp85) cc_final: 0.7503 (mtt-85) REVERT: C 696 ASP cc_start: 0.8239 (t70) cc_final: 0.7586 (t0) REVERT: C 1107 MET cc_start: 0.8135 (mpp) cc_final: 0.7558 (mtm) REVERT: C 1166 ASP cc_start: 0.7515 (t0) cc_final: 0.7290 (t0) REVERT: D 281 ARG cc_start: 0.7360 (tpt90) cc_final: 0.7070 (tpp-160) REVERT: D 299 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8915 (tp) REVERT: D 535 ARG cc_start: 0.6782 (mtm110) cc_final: 0.6254 (mtm180) REVERT: D 901 ARG cc_start: 0.6223 (OUTLIER) cc_final: 0.4753 (ppt-90) REVERT: a 1 MET cc_start: 0.4116 (tpt) cc_final: 0.2667 (tpt) REVERT: e 197 MET cc_start: 0.2055 (ptp) cc_final: 0.1661 (ptm) REVERT: M 28 LEU cc_start: 0.8960 (OUTLIER) cc_final: 0.8513 (pp) REVERT: M 125 MET cc_start: 0.8617 (mmm) cc_final: 0.8326 (mmm) REVERT: M 185 PHE cc_start: 0.8839 (OUTLIER) cc_final: 0.8234 (m-10) REVERT: M 271 TYR cc_start: 0.6603 (OUTLIER) cc_final: 0.6239 (p90) REVERT: M 279 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6728 (ptt-90) REVERT: M 456 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.8102 (tpp80) outliers start: 193 outliers final: 123 residues processed: 534 average time/residue: 0.2500 time to fit residues: 220.9590 Evaluate side-chains 474 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 342 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 29 GLU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 188 PHE Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 515 MET Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 339 ARG Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 89 GLN Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 73 LEU Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 196 GLN Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 43 GLU Chi-restraints excluded: chain d residue 51 TYR Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 176 LEU Chi-restraints excluded: chain f residue 8 LEU Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 148 THR Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 146 CYS Chi-restraints excluded: chain e residue 176 LEU Chi-restraints excluded: chain e residue 226 ILE Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 196 ARG Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 381 ILE Chi-restraints excluded: chain M residue 441 LYS Chi-restraints excluded: chain M residue 456 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 254 optimal weight: 10.0000 chunk 171 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 308 optimal weight: 10.0000 chunk 502 optimal weight: 0.1980 chunk 35 optimal weight: 6.9990 chunk 315 optimal weight: 0.8980 chunk 279 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 865 HIS ** a 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 HIS d 24 HIS ** d 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 117 GLN M 351 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.181763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.151817 restraints weight = 76860.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.146056 restraints weight = 131005.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.144135 restraints weight = 127008.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.143362 restraints weight = 119340.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.141772 restraints weight = 98400.813| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3922 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3922 r_free = 0.3922 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3922 r_free = 0.3922 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3922 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.5070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 42308 Z= 0.204 Angle : 0.725 14.536 57701 Z= 0.358 Chirality : 0.045 0.233 6672 Planarity : 0.005 0.067 7320 Dihedral : 13.150 137.816 6611 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.74 % Favored : 92.14 % Rotamer: Outliers : 4.94 % Allowed : 18.65 % Favored : 76.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.53 (0.11), residues: 5205 helix: 0.52 (0.12), residues: 1898 sheet: -0.56 (0.26), residues: 425 loop : -2.28 (0.11), residues: 2882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG c 182 TYR 0.023 0.002 TYR M 401 PHE 0.023 0.002 PHE C 57 TRP 0.026 0.001 TRP c 222 HIS 0.010 0.001 HIS D 865 Details of bonding type rmsd covalent geometry : bond 0.00486 (42306) covalent geometry : angle 0.72522 (57701) hydrogen bonds : bond 0.04294 ( 1516) hydrogen bonds : angle 4.61853 ( 4279) Misc. bond : bond 0.00026 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 203 poor density : 350 time to evaluate : 1.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 HIS cc_start: 0.6333 (t-90) cc_final: 0.6091 (t-90) REVERT: C 176 ILE cc_start: 0.8905 (OUTLIER) cc_final: 0.8534 (mt) REVERT: C 696 ASP cc_start: 0.8427 (t70) cc_final: 0.7809 (t0) REVERT: C 1107 MET cc_start: 0.8221 (mpp) cc_final: 0.7683 (mtm) REVERT: D 281 ARG cc_start: 0.7328 (tpt90) cc_final: 0.7086 (tpp-160) REVERT: D 298 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7259 (mpp) REVERT: D 299 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.8984 (tp) REVERT: D 447 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8104 (mt) REVERT: D 465 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7866 (mp10) REVERT: D 901 ARG cc_start: 0.6128 (OUTLIER) cc_final: 0.4771 (ppt-90) REVERT: a 1 MET cc_start: 0.3725 (tpt) cc_final: 0.2299 (mmp) REVERT: c 115 MET cc_start: 0.6753 (mmm) cc_final: 0.6495 (mmm) REVERT: e 197 MET cc_start: 0.1343 (ptp) cc_final: 0.1105 (ptm) REVERT: M 28 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8613 (pp) REVERT: M 125 MET cc_start: 0.8545 (mmm) cc_final: 0.8321 (mmm) REVERT: M 185 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8094 (m-10) REVERT: M 271 TYR cc_start: 0.6677 (OUTLIER) cc_final: 0.6350 (p90) REVERT: M 279 ARG cc_start: 0.7332 (OUTLIER) cc_final: 0.6765 (ptt-90) REVERT: M 456 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.8049 (tpp80) outliers start: 203 outliers final: 132 residues processed: 523 average time/residue: 0.2501 time to fit residues: 216.6058 Evaluate side-chains 472 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 329 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 203 ILE Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1270 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 416 ILE Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 736 GLN Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 865 HIS Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 189 MET Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 80 HIS Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 196 GLN Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 104 LEU Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 164 ASP Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 95 ARG Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 176 LEU Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 148 THR Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 146 CYS Chi-restraints excluded: chain e residue 226 ILE Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 127 GLN Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 381 ILE Chi-restraints excluded: chain M residue 456 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 498 optimal weight: 9.9990 chunk 438 optimal weight: 5.9990 chunk 505 optimal weight: 0.0270 chunk 297 optimal weight: 20.0000 chunk 305 optimal weight: 3.9990 chunk 201 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 312 optimal weight: 2.9990 chunk 286 optimal weight: 30.0000 chunk 84 optimal weight: 6.9990 overall best weight: 2.4046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 490 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 419 HIS D 465 GLN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 24 HIS c 196 GLN d 24 HIS ** d 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.181824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.151415 restraints weight = 76848.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.147152 restraints weight = 134993.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.144530 restraints weight = 126021.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.143673 restraints weight = 127264.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.141867 restraints weight = 103950.857| |-----------------------------------------------------------------------------| r_work (final): 0.3921 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3920 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3920 r_free = 0.3920 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3920 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 42308 Z= 0.182 Angle : 0.708 13.868 57701 Z= 0.348 Chirality : 0.044 0.202 6672 Planarity : 0.005 0.082 7320 Dihedral : 13.059 137.600 6601 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.82 % Favored : 92.08 % Rotamer: Outliers : 4.77 % Allowed : 19.38 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.45 (0.11), residues: 5205 helix: 0.58 (0.12), residues: 1897 sheet: -0.40 (0.26), residues: 434 loop : -2.25 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 211 TYR 0.020 0.002 TYR M 361 PHE 0.022 0.001 PHE C 57 TRP 0.035 0.002 TRP c 222 HIS 0.025 0.001 HIS b 80 Details of bonding type rmsd covalent geometry : bond 0.00431 (42306) covalent geometry : angle 0.70826 (57701) hydrogen bonds : bond 0.04105 ( 1516) hydrogen bonds : angle 4.57204 ( 4279) Misc. bond : bond 0.00021 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 342 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 LYS cc_start: 0.7449 (ttpt) cc_final: 0.7187 (tmmt) REVERT: C 176 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8543 (mt) REVERT: C 563 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8694 (t) REVERT: C 696 ASP cc_start: 0.8335 (t70) cc_final: 0.7805 (t0) REVERT: C 1107 MET cc_start: 0.8069 (mpp) cc_final: 0.7512 (mtm) REVERT: D 281 ARG cc_start: 0.7393 (tpt90) cc_final: 0.7139 (tpp-160) REVERT: D 299 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8950 (tp) REVERT: D 901 ARG cc_start: 0.6224 (OUTLIER) cc_final: 0.4830 (ppt-90) REVERT: D 1040 MET cc_start: 0.2547 (OUTLIER) cc_final: 0.1763 (mtt) REVERT: a 1 MET cc_start: 0.4335 (tpt) cc_final: 0.3529 (mmm) REVERT: a 119 LYS cc_start: 0.7111 (OUTLIER) cc_final: 0.5984 (tttp) REVERT: f 1 MET cc_start: -0.0157 (mmt) cc_final: -0.0503 (mmp) REVERT: e 197 MET cc_start: 0.1658 (ptp) cc_final: 0.0948 (ptm) REVERT: M 28 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8634 (pp) REVERT: M 185 PHE cc_start: 0.8922 (OUTLIER) cc_final: 0.8230 (m-10) REVERT: M 271 TYR cc_start: 0.6786 (OUTLIER) cc_final: 0.6406 (p90) REVERT: M 279 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.6788 (ptt-90) REVERT: M 456 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.7971 (tpp80) outliers start: 196 outliers final: 139 residues processed: 507 average time/residue: 0.2476 time to fit residues: 208.7888 Evaluate side-chains 475 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 325 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 117 HIS Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1270 PHE Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 776 THR Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1178 THR Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 4 VAL Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 119 LYS Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 144 LEU Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain a residue 252 ILE Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 63 LEU Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 196 GLN Chi-restraints excluded: chain c residue 63 LEU Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 51 TYR Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 176 LEU Chi-restraints excluded: chain d residue 229 LEU Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 148 THR Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 146 CYS Chi-restraints excluded: chain e residue 176 LEU Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 127 GLN Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 381 ILE Chi-restraints excluded: chain M residue 441 LYS Chi-restraints excluded: chain M residue 446 LEU Chi-restraints excluded: chain M residue 456 ARG Chi-restraints excluded: chain M residue 472 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 424 optimal weight: 0.6980 chunk 410 optimal weight: 10.0000 chunk 508 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 381 optimal weight: 30.0000 chunk 228 optimal weight: 0.5980 chunk 395 optimal weight: 9.9990 chunk 253 optimal weight: 3.9990 chunk 174 optimal weight: 2.9990 chunk 273 optimal weight: 6.9990 chunk 451 optimal weight: 30.0000 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 462 ASN C1111 GLN ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 196 GLN ** b 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 80 HIS c 196 GLN ** d 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.181571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.151052 restraints weight = 76414.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.146430 restraints weight = 136609.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.144053 restraints weight = 130437.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.143103 restraints weight = 123917.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.141379 restraints weight = 100960.425| |-----------------------------------------------------------------------------| r_work (final): 0.3914 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3916 r_free = 0.3916 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3916 r_free = 0.3916 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 42308 Z= 0.185 Angle : 0.714 12.946 57701 Z= 0.353 Chirality : 0.044 0.360 6672 Planarity : 0.005 0.058 7320 Dihedral : 13.035 137.309 6597 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.26 % Favored : 91.64 % Rotamer: Outliers : 4.55 % Allowed : 19.60 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.11), residues: 5205 helix: 0.62 (0.12), residues: 1896 sheet: -0.37 (0.26), residues: 421 loop : -2.22 (0.11), residues: 2888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 240 TYR 0.055 0.002 TYR b 51 PHE 0.023 0.001 PHE C 57 TRP 0.034 0.002 TRP c 222 HIS 0.009 0.001 HIS b 24 Details of bonding type rmsd covalent geometry : bond 0.00438 (42306) covalent geometry : angle 0.71375 (57701) hydrogen bonds : bond 0.04114 ( 1516) hydrogen bonds : angle 4.59951 ( 4279) Misc. bond : bond 0.00016 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 528 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 187 poor density : 341 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 176 ILE cc_start: 0.8903 (OUTLIER) cc_final: 0.8571 (mt) REVERT: C 563 THR cc_start: 0.8993 (OUTLIER) cc_final: 0.8714 (t) REVERT: C 696 ASP cc_start: 0.8387 (t70) cc_final: 0.7814 (t0) REVERT: C 1038 GLN cc_start: 0.8114 (pm20) cc_final: 0.7862 (pm20) REVERT: C 1107 MET cc_start: 0.8106 (mpp) cc_final: 0.7579 (mtm) REVERT: D 281 ARG cc_start: 0.7394 (tpt90) cc_final: 0.7046 (tpp-160) REVERT: D 299 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.8967 (tp) REVERT: D 447 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8209 (mt) REVERT: D 535 ARG cc_start: 0.6851 (mtm110) cc_final: 0.6495 (mtm180) REVERT: D 901 ARG cc_start: 0.6399 (OUTLIER) cc_final: 0.4927 (ppt-90) REVERT: D 1040 MET cc_start: 0.2746 (OUTLIER) cc_final: 0.1894 (mtt) REVERT: a 1 MET cc_start: 0.4475 (tpt) cc_final: 0.3520 (mmm) REVERT: c 115 MET cc_start: 0.7080 (mmm) cc_final: 0.6497 (mmm) REVERT: f 1 MET cc_start: -0.0342 (mmt) cc_final: -0.0611 (mmp) REVERT: e 197 MET cc_start: 0.1625 (ptp) cc_final: 0.0881 (ptm) REVERT: M 28 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8672 (pp) REVERT: M 185 PHE cc_start: 0.8973 (OUTLIER) cc_final: 0.8242 (m-10) REVERT: M 271 TYR cc_start: 0.6743 (OUTLIER) cc_final: 0.6350 (p90) REVERT: M 279 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.6718 (ptt-90) REVERT: M 456 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.7984 (tpp80) outliers start: 187 outliers final: 142 residues processed: 499 average time/residue: 0.2398 time to fit residues: 197.6407 Evaluate side-chains 475 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 322 time to evaluate : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 400 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 646 SER Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1138 VAL Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1270 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1295 SER Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 505 ASP Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 816 THR Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1040 MET Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1292 LEU Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain a residue 252 ILE Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 80 HIS Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 122 ARG Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 196 GLN Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain d residue 176 LEU Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 148 THR Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 176 LEU Chi-restraints excluded: chain e residue 188 LEU Chi-restraints excluded: chain e residue 226 ILE Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 127 GLN Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 271 TYR Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 441 LYS Chi-restraints excluded: chain M residue 446 LEU Chi-restraints excluded: chain M residue 456 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 45 optimal weight: 10.0000 chunk 146 optimal weight: 0.0670 chunk 382 optimal weight: 8.9990 chunk 305 optimal weight: 0.8980 chunk 414 optimal weight: 8.9990 chunk 473 optimal weight: 40.0000 chunk 466 optimal weight: 50.0000 chunk 26 optimal weight: 9.9990 chunk 216 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 362 optimal weight: 2.9990 overall best weight: 1.5924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 132 HIS ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1244 GLN ** a 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.182277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.151839 restraints weight = 76605.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.146326 restraints weight = 127687.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.144226 restraints weight = 127618.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.142958 restraints weight = 117185.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.140192 restraints weight = 108818.883| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3901 r_free = 0.3901 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.5528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 42308 Z= 0.146 Angle : 0.695 17.005 57701 Z= 0.339 Chirality : 0.043 0.266 6672 Planarity : 0.004 0.081 7320 Dihedral : 12.999 138.055 6595 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.80 % Favored : 92.08 % Rotamer: Outliers : 4.09 % Allowed : 20.60 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.12), residues: 5205 helix: 0.72 (0.12), residues: 1895 sheet: -0.20 (0.26), residues: 432 loop : -2.19 (0.11), residues: 2878 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 240 TYR 0.026 0.001 TYR d 126 PHE 0.018 0.001 PHE C 57 TRP 0.037 0.002 TRP c 222 HIS 0.008 0.001 HIS b 80 Details of bonding type rmsd covalent geometry : bond 0.00338 (42306) covalent geometry : angle 0.69453 (57701) hydrogen bonds : bond 0.03809 ( 1516) hydrogen bonds : angle 4.55125 ( 4279) Misc. bond : bond 0.00011 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 509 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 168 poor density : 341 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: A 117 HIS cc_start: 0.6329 (t-90) cc_final: 0.6063 (t-90) REVERT: B 95 LYS cc_start: 0.7670 (ttpt) cc_final: 0.7366 (tmmt) REVERT: C 176 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8574 (mt) REVERT: C 563 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8726 (t) REVERT: C 696 ASP cc_start: 0.8242 (t70) cc_final: 0.7800 (t0) REVERT: C 1038 GLN cc_start: 0.8077 (pm20) cc_final: 0.7823 (pm20) REVERT: C 1107 MET cc_start: 0.8167 (mpp) cc_final: 0.7628 (mtm) REVERT: D 137 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7144 (mtp180) REVERT: D 281 ARG cc_start: 0.7464 (tpt90) cc_final: 0.7121 (tpp-160) REVERT: D 299 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8887 (tp) REVERT: D 447 ILE cc_start: 0.8829 (OUTLIER) cc_final: 0.8490 (mt) REVERT: D 535 ARG cc_start: 0.6843 (mtm110) cc_final: 0.6601 (mtm180) REVERT: D 901 ARG cc_start: 0.6401 (OUTLIER) cc_final: 0.5014 (ppt-90) REVERT: D 1040 MET cc_start: 0.2989 (mtt) cc_final: 0.2101 (mtt) REVERT: a 1 MET cc_start: 0.4441 (tpt) cc_final: 0.3098 (mmm) REVERT: f 119 LYS cc_start: 0.6270 (tptt) cc_final: 0.6012 (tptt) REVERT: M 28 LEU cc_start: 0.9111 (OUTLIER) cc_final: 0.8764 (pp) REVERT: M 185 PHE cc_start: 0.8944 (OUTLIER) cc_final: 0.8271 (m-10) REVERT: M 279 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6675 (ptt-90) REVERT: M 456 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.8038 (tpp80) outliers start: 168 outliers final: 138 residues processed: 483 average time/residue: 0.2449 time to fit residues: 196.0682 Evaluate side-chains 477 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 329 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 172 LEU Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 577 VAL Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1270 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 447 ILE Chi-restraints excluded: chain D residue 485 MET Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 641 ILE Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1237 VAL Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1287 ILE Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 43 GLU Chi-restraints excluded: chain a residue 90 LYS Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain a residue 252 ILE Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 122 ARG Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 196 GLN Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 148 THR Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 176 LEU Chi-restraints excluded: chain e residue 188 LEU Chi-restraints excluded: chain e residue 226 ILE Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 127 GLN Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 200 LEU Chi-restraints excluded: chain M residue 225 ASP Chi-restraints excluded: chain M residue 241 LEU Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 278 VAL Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 381 ILE Chi-restraints excluded: chain M residue 441 LYS Chi-restraints excluded: chain M residue 446 LEU Chi-restraints excluded: chain M residue 456 ARG Chi-restraints excluded: chain M residue 472 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 370 optimal weight: 40.0000 chunk 506 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 462 optimal weight: 0.0870 chunk 494 optimal weight: 8.9990 chunk 119 optimal weight: 0.9980 chunk 225 optimal weight: 5.9990 chunk 81 optimal weight: 30.0000 chunk 362 optimal weight: 30.0000 chunk 135 optimal weight: 0.6980 chunk 230 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN C 150 HIS ** D 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 465 GLN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 50 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 = 0.4447 r_free = 0.4447 target = 0.183654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.153381 restraints weight = 76959.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.149171 restraints weight = 134975.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.147305 restraints weight = 115318.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.145682 restraints weight = 112827.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.144013 restraints weight = 102874.003| |-----------------------------------------------------------------------------| r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3951 r_free = 0.3951 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3951 r_free = 0.3951 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3951 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7009 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 42308 Z= 0.121 Angle : 0.684 16.743 57701 Z= 0.331 Chirality : 0.042 0.220 6672 Planarity : 0.004 0.050 7320 Dihedral : 12.929 139.306 6593 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.63 % Favored : 92.26 % Rotamer: Outliers : 3.55 % Allowed : 21.13 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.12), residues: 5205 helix: 0.79 (0.12), residues: 1905 sheet: -0.14 (0.26), residues: 426 loop : -2.12 (0.11), residues: 2874 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 473 TYR 0.025 0.001 TYR d 126 PHE 0.016 0.001 PHE C 225 TRP 0.025 0.001 TRP c 222 HIS 0.010 0.001 HIS f 50 Details of bonding type rmsd covalent geometry : bond 0.00270 (42306) covalent geometry : angle 0.68404 (57701) hydrogen bonds : bond 0.03467 ( 1516) hydrogen bonds : angle 4.49132 ( 4279) Misc. bond : bond 0.00013 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 337 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 117 HIS cc_start: 0.6217 (t-90) cc_final: 0.5951 (t-90) REVERT: B 95 LYS cc_start: 0.7504 (ttpt) cc_final: 0.7253 (tmmt) REVERT: C 176 ILE cc_start: 0.8787 (OUTLIER) cc_final: 0.8521 (mt) REVERT: C 563 THR cc_start: 0.8953 (OUTLIER) cc_final: 0.8675 (t) REVERT: C 696 ASP cc_start: 0.8304 (t70) cc_final: 0.7888 (t0) REVERT: C 1038 GLN cc_start: 0.7980 (pm20) cc_final: 0.7771 (pm20) REVERT: C 1107 MET cc_start: 0.8159 (mpp) cc_final: 0.7637 (mtm) REVERT: D 137 ARG cc_start: 0.7631 (OUTLIER) cc_final: 0.7399 (mtp180) REVERT: D 281 ARG cc_start: 0.7381 (tpt90) cc_final: 0.7044 (tpp-160) REVERT: D 299 LEU cc_start: 0.9162 (OUTLIER) cc_final: 0.8836 (tp) REVERT: D 901 ARG cc_start: 0.6281 (OUTLIER) cc_final: 0.4891 (ppt-90) REVERT: D 1040 MET cc_start: 0.2796 (mtt) cc_final: 0.1931 (mtt) REVERT: a 1 MET cc_start: 0.4562 (tpt) cc_final: 0.3281 (mmm) REVERT: c 115 MET cc_start: 0.6880 (mmm) cc_final: 0.6603 (mmm) REVERT: f 119 LYS cc_start: 0.5935 (tptt) cc_final: 0.5734 (tptt) REVERT: e 197 MET cc_start: 0.1039 (ptp) cc_final: 0.0452 (ptm) REVERT: e 211 GLU cc_start: 0.6363 (tp30) cc_final: 0.6067 (tp30) REVERT: M 28 LEU cc_start: 0.9150 (OUTLIER) cc_final: 0.8787 (pp) REVERT: M 185 PHE cc_start: 0.8811 (OUTLIER) cc_final: 0.8122 (m-10) REVERT: M 279 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6634 (ptt-90) outliers start: 146 outliers final: 115 residues processed: 460 average time/residue: 0.2329 time to fit residues: 177.7348 Evaluate side-chains 451 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 328 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 95 LYS Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 155 VAL Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 487 LEU Chi-restraints excluded: chain C residue 511 LEU Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1270 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 137 ARG Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 422 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 651 HIS Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 43 GLU Chi-restraints excluded: chain a residue 90 LYS Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain a residue 252 ILE Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 111 THR Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 196 GLN Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 148 THR Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 176 LEU Chi-restraints excluded: chain e residue 226 ILE Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 27 GLN Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 127 GLN Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 241 LEU Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 446 LEU Chi-restraints excluded: chain M residue 472 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 116 optimal weight: 0.0020 chunk 341 optimal weight: 50.0000 chunk 434 optimal weight: 0.3980 chunk 153 optimal weight: 20.0000 chunk 80 optimal weight: 30.0000 chunk 139 optimal weight: 0.8980 chunk 274 optimal weight: 4.9990 chunk 519 optimal weight: 20.0000 chunk 288 optimal weight: 8.9990 chunk 81 optimal weight: 10.0000 chunk 387 optimal weight: 50.0000 overall best weight: 3.0592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 465 GLN ** D 716 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 141 ASN e 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.180810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.149600 restraints weight = 76075.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.145256 restraints weight = 132699.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.141789 restraints weight = 121831.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.141296 restraints weight = 107802.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.138656 restraints weight = 98687.300| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3880 r_free = 0.3880 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 42308 Z= 0.218 Angle : 0.750 17.150 57701 Z= 0.368 Chirality : 0.045 0.244 6672 Planarity : 0.005 0.058 7320 Dihedral : 13.025 139.108 6593 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.40 % Favored : 91.49 % Rotamer: Outliers : 3.45 % Allowed : 21.13 % Favored : 75.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.12), residues: 5205 helix: 0.71 (0.12), residues: 1901 sheet: -0.17 (0.26), residues: 428 loop : -2.12 (0.11), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 535 TYR 0.027 0.002 TYR M 361 PHE 0.025 0.001 PHE C 57 TRP 0.023 0.002 TRP b 222 HIS 0.013 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00525 (42306) covalent geometry : angle 0.75034 (57701) hydrogen bonds : bond 0.04376 ( 1516) hydrogen bonds : angle 4.60906 ( 4279) Misc. bond : bond 0.00011 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10410 Ramachandran restraints generated. 5205 Oldfield, 0 Emsley, 5205 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 331 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 LYS cc_start: 0.7618 (ttpt) cc_final: 0.7336 (tmmt) REVERT: C 176 ILE cc_start: 0.8879 (OUTLIER) cc_final: 0.8613 (mt) REVERT: C 563 THR cc_start: 0.9022 (OUTLIER) cc_final: 0.8758 (t) REVERT: C 696 ASP cc_start: 0.8330 (t70) cc_final: 0.7886 (t0) REVERT: C 1038 GLN cc_start: 0.8110 (pm20) cc_final: 0.7870 (pm20) REVERT: C 1107 MET cc_start: 0.8150 (mpp) cc_final: 0.7620 (mtm) REVERT: D 281 ARG cc_start: 0.7615 (tpt90) cc_final: 0.7264 (tpp-160) REVERT: D 299 LEU cc_start: 0.9247 (OUTLIER) cc_final: 0.8907 (tp) REVERT: D 901 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.5448 (ppt-90) REVERT: D 1040 MET cc_start: 0.2921 (mtt) cc_final: 0.2611 (mtt) REVERT: E 30 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7641 (mtt) REVERT: a 1 MET cc_start: 0.4430 (tpt) cc_final: 0.3026 (mmm) REVERT: e 197 MET cc_start: 0.0811 (ptp) cc_final: 0.0294 (ptm) REVERT: M 28 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8804 (pp) REVERT: M 185 PHE cc_start: 0.9020 (OUTLIER) cc_final: 0.8326 (m-10) REVERT: M 279 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6538 (ppt90) outliers start: 142 outliers final: 119 residues processed: 454 average time/residue: 0.2364 time to fit residues: 178.5080 Evaluate side-chains 444 residues out of total 4492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 317 time to evaluate : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 38 THR Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 133 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 124 VAL Chi-restraints excluded: chain B residue 228 LEU Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain C residue 32 LEU Chi-restraints excluded: chain C residue 47 TYR Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 182 SER Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain C residue 289 VAL Chi-restraints excluded: chain C residue 458 GLU Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 471 VAL Chi-restraints excluded: chain C residue 563 THR Chi-restraints excluded: chain C residue 697 LYS Chi-restraints excluded: chain C residue 714 VAL Chi-restraints excluded: chain C residue 736 VAL Chi-restraints excluded: chain C residue 796 LEU Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 937 ASP Chi-restraints excluded: chain C residue 960 LEU Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1056 VAL Chi-restraints excluded: chain C residue 1119 MET Chi-restraints excluded: chain C residue 1143 GLU Chi-restraints excluded: chain C residue 1225 VAL Chi-restraints excluded: chain C residue 1233 LEU Chi-restraints excluded: chain C residue 1238 LEU Chi-restraints excluded: chain C residue 1239 VAL Chi-restraints excluded: chain C residue 1270 PHE Chi-restraints excluded: chain C residue 1273 MET Chi-restraints excluded: chain C residue 1293 VAL Chi-restraints excluded: chain C residue 1309 VAL Chi-restraints excluded: chain D residue 66 LYS Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 117 LEU Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 241 VAL Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 265 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain D residue 301 GLU Chi-restraints excluded: chain D residue 316 ILE Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 361 LEU Chi-restraints excluded: chain D residue 418 GLU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 517 CYS Chi-restraints excluded: chain D residue 527 LEU Chi-restraints excluded: chain D residue 563 LEU Chi-restraints excluded: chain D residue 570 LYS Chi-restraints excluded: chain D residue 582 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 644 MET Chi-restraints excluded: chain D residue 717 VAL Chi-restraints excluded: chain D residue 806 ASP Chi-restraints excluded: chain D residue 820 ILE Chi-restraints excluded: chain D residue 882 VAL Chi-restraints excluded: chain D residue 901 ARG Chi-restraints excluded: chain D residue 915 ILE Chi-restraints excluded: chain D residue 1266 ILE Chi-restraints excluded: chain D residue 1268 ASN Chi-restraints excluded: chain D residue 1313 SER Chi-restraints excluded: chain E residue 30 MET Chi-restraints excluded: chain a residue 38 ARG Chi-restraints excluded: chain a residue 43 GLU Chi-restraints excluded: chain a residue 90 LYS Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain a residue 132 VAL Chi-restraints excluded: chain a residue 250 ILE Chi-restraints excluded: chain a residue 252 ILE Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 122 ARG Chi-restraints excluded: chain b residue 124 ILE Chi-restraints excluded: chain b residue 129 LEU Chi-restraints excluded: chain b residue 196 GLN Chi-restraints excluded: chain c residue 144 LEU Chi-restraints excluded: chain c residue 251 ILE Chi-restraints excluded: chain d residue 111 THR Chi-restraints excluded: chain d residue 165 LEU Chi-restraints excluded: chain d residue 174 VAL Chi-restraints excluded: chain f residue 56 TRP Chi-restraints excluded: chain f residue 148 THR Chi-restraints excluded: chain e residue 90 LYS Chi-restraints excluded: chain e residue 126 TYR Chi-restraints excluded: chain e residue 129 LEU Chi-restraints excluded: chain e residue 175 GLN Chi-restraints excluded: chain e residue 176 LEU Chi-restraints excluded: chain e residue 226 ILE Chi-restraints excluded: chain M residue 9 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 41 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 127 GLN Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 182 ILE Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 190 VAL Chi-restraints excluded: chain M residue 195 LEU Chi-restraints excluded: chain M residue 256 LEU Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 381 ILE Chi-restraints excluded: chain M residue 472 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 523 random chunks: chunk 154 optimal weight: 4.9990 chunk 168 optimal weight: 3.9990 chunk 24 optimal weight: 0.0770 chunk 361 optimal weight: 30.0000 chunk 470 optimal weight: 20.0000 chunk 145 optimal weight: 3.9990 chunk 250 optimal weight: 1.9990 chunk 173 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 357 optimal weight: 0.0470 chunk 67 optimal weight: 0.6980 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.181128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.150967 restraints weight = 76880.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.146428 restraints weight = 130798.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.144099 restraints weight = 125618.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.142691 restraints weight = 127583.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.140807 restraints weight = 110643.910| |-----------------------------------------------------------------------------| r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3906 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3906 r_free = 0.3906 target_work(ls_wunit_k1) = 0.139 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3906 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.5819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.375 42308 Z= 0.243 Angle : 0.829 59.197 57701 Z= 0.425 Chirality : 0.045 0.468 6672 Planarity : 0.005 0.102 7320 Dihedral : 13.026 139.147 6593 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.45 % Favored : 91.43 % Rotamer: Outliers : 3.28 % Allowed : 21.57 % Favored : 75.15 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.42 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.25 (0.12), residues: 5205 helix: 0.71 (0.12), residues: 1901 sheet: -0.19 (0.26), residues: 428 loop : -2.12 (0.11), residues: 2876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG D 535 TYR 0.024 0.002 TYR M 361 PHE 0.023 0.001 PHE C 57 TRP 0.020 0.002 TRP b 222 HIS 0.018 0.001 HIS d 24 Details of bonding type rmsd covalent geometry : bond 0.00578 (42306) covalent geometry : angle 0.82924 (57701) hydrogen bonds : bond 0.04269 ( 1516) hydrogen bonds : angle 4.61270 ( 4279) Misc. bond : bond 0.00010 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7783.65 seconds wall clock time: 134 minutes 51.58 seconds (8091.58 seconds total)