Starting phenix.real_space_refine on Fri Feb 6 22:43:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qxi_14200/02_2026/7qxi_14200.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qxi_14200/02_2026/7qxi_14200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7qxi_14200/02_2026/7qxi_14200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qxi_14200/02_2026/7qxi_14200.map" model { file = "/net/cci-nas-00/data/ceres_data/7qxi_14200/02_2026/7qxi_14200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qxi_14200/02_2026/7qxi_14200.cif" } resolution = 3.4 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: 5 Type Number sf(0) Gaussians P 72 5.49 5 S 103 5.16 5 C 17908 2.51 5 N 5122 2.21 5 O 5723 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.05s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28928 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 309, 2316 Classifications: {'peptide': 309} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 14, 'TRANS': 294} Chain breaks: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 6, 'PHE:plan': 1, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 58 Chain: "B" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1671 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 56 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 30 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: 9632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1334, 9632 Classifications: {'peptide': 1334} Incomplete info: {'truncation_to_alanine': 207} Link IDs: {'PTRANS': 53, 'TRANS': 1280} Chain breaks: 5 Unresolved non-hydrogen bonds: 784 Unresolved non-hydrogen angles: 966 Unresolved non-hydrogen dihedrals: 649 Unresolved non-hydrogen chiralities: 46 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: "M" Number of atoms: 3162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3162 Classifications: {'peptide': 403} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 17, 'TRANS': 385} Chain breaks: 1 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 3, 'HIS:plan': 1, 'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 37 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} 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: 7.25, per 1000 atoms: 0.25 Number of scatterers: 28928 At special positions: 0 Unit cell: (171.6, 176, 161.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 103 16.00 P 72 15.00 O 5723 8.00 N 5122 7.00 C 17908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.4 seconds 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6842 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 38 sheets defined 37.8% alpha, 9.4% beta 33 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'A' and resid 35 through 50 removed outlier: 3.839A pdb=" N ALA A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG A 45 " --> pdb=" O ASN A 41 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 87 removed outlier: 3.890A pdb=" N LEU A 83 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY A 87 " --> pdb=" O LEU A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 162 removed outlier: 3.995A pdb=" N ARG A 158 " --> pdb=" O PRO A 154 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS A 160 " --> pdb=" O SER A 156 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 233 removed outlier: 4.100A pdb=" N ALA A 230 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N PHE A 231 " --> pdb=" O GLN A 227 " (cutoff:3.500A) removed outlier: 4.192A 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 removed outlier: 3.832A pdb=" N VAL A 282 " --> pdb=" O ILE A 278 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLN A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 283' Processing helix chain 'A' and resid 285 through 290 Processing helix chain 'A' and resid 296 through 308 Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.503A pdb=" N LEU B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B 50 " --> pdb=" O ILE B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 85 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 228 removed outlier: 3.979A pdb=" N LEU B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 6 through 10 removed outlier: 3.643A pdb=" N LYS C 9 " --> pdb=" O THR C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 40 removed outlier: 4.532A pdb=" N LYS C 37 " --> pdb=" O ASP C 33 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N PHE C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ILE C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 57 removed outlier: 3.725A pdb=" N SER C 55 " --> pdb=" O ALA C 51 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N VAL C 56 " --> pdb=" O ALA C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 89 removed outlier: 3.641A pdb=" N GLN C 86 " --> pdb=" O VAL C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 214 removed outlier: 3.643A pdb=" N ASN C 214 " --> pdb=" O ARG C 211 " (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: 4.005A pdb=" N ALA C 293 " --> pdb=" O VAL C 289 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY C 294 " --> pdb=" O GLU C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 318 through 327 removed outlier: 4.039A pdb=" N ALA C 323 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYS C 324 " --> pdb=" O ASP C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 352 removed outlier: 3.577A pdb=" N ARG C 352 " --> pdb=" O SER C 348 " (cutoff:3.500A) Processing helix chain 'C' and resid 358 through 364 removed outlier: 3.873A pdb=" N VAL C 364 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 366 through 371 Processing helix chain 'C' and resid 380 through 390 removed outlier: 3.801A pdb=" N PHE C 385 " --> pdb=" O ALA C 381 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N PHE C 389 " --> pdb=" O PHE C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 399 through 409 Processing helix chain 'C' and resid 421 through 438 removed outlier: 3.563A pdb=" N ILE C 425 " --> pdb=" O SER C 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 449 No H-bonds generated for 'chain 'C' and resid 447 through 449' Processing helix chain 'C' and resid 455 through 458 removed outlier: 3.599A pdb=" N GLU C 458 " --> pdb=" O SER C 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 455 through 458' Processing helix chain 'C' and resid 459 through 481 removed outlier: 3.658A pdb=" N ARG C 470 " --> pdb=" O VAL C 466 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL C 471 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA C 474 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU C 481 " --> pdb=" O GLU C 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 495 through 507 removed outlier: 3.622A pdb=" N SER C 499 " --> pdb=" O ALA C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 527 Processing helix chain 'C' and resid 551 through 555 removed outlier: 3.846A pdb=" N TYR C 555 " --> pdb=" O PRO C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 609 through 613 Processing helix chain 'C' and resid 664 through 668 removed outlier: 3.716A pdb=" N ILE C 668 " --> pdb=" O ALA C 665 " (cutoff:3.500A) Processing helix chain 'C' and resid 670 through 674 Processing helix chain 'C' and resid 675 through 687 removed outlier: 3.730A pdb=" N ARG C 687 " --> pdb=" O ALA C 683 " (cutoff:3.500A) Processing helix chain 'C' and resid 704 through 712 Processing helix chain 'C' and resid 820 through 825 Processing helix chain 'C' and resid 860 through 864 removed outlier: 4.201A pdb=" N LYS C 864 " --> pdb=" O ALA C 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 896 through 906 removed outlier: 3.880A pdb=" N LYS C 900 " --> pdb=" O THR C 896 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 979 removed outlier: 3.548A pdb=" N ILE C 948 " --> pdb=" O ARG C 944 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 961 " --> pdb=" O LYS C 957 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU C 963 " --> pdb=" O ASP C 959 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 964 " --> pdb=" O LEU C 960 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA C 969 " --> pdb=" O GLN C 965 " (cutoff:3.500A) Processing helix chain 'C' and resid 986 through 992 removed outlier: 3.703A pdb=" N LEU C 992 " --> pdb=" O LYS C 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 993 through 1000 removed outlier: 3.583A pdb=" N TRP C 997 " --> pdb=" O PRO C 993 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 998 " --> pdb=" O ARG C 994 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLU C 999 " --> pdb=" O ASP C 995 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU C1000 " --> pdb=" O ARG C 996 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 993 through 1000' Processing helix chain 'C' and resid 1005 through 1037 removed outlier: 3.854A pdb=" N ASN C1009 " --> pdb=" O GLU C1005 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS C1032 " --> pdb=" O LYS C1028 " (cutoff:3.500A) Processing helix chain 'C' and resid 1101 through 1106 removed outlier: 4.023A pdb=" N SER C1105 " --> pdb=" O LEU C1101 " (cutoff:3.500A) Processing helix chain 'C' and resid 1108 through 1134 removed outlier: 3.846A pdb=" N ILE C1112 " --> pdb=" O ASN C1108 " (cutoff:3.500A) Processing helix chain 'C' and resid 1137 through 1150 Processing helix chain 'C' and resid 1167 through 1176 Processing helix chain 'C' and resid 1191 through 1202 Processing helix chain 'C' and resid 1271 through 1280 removed outlier: 3.511A pdb=" N VAL C1275 " --> pdb=" O GLY C1271 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA C1277 " --> pdb=" O MET C1273 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA C1280 " --> pdb=" O TRP C1276 " (cutoff:3.500A) Processing helix chain 'C' and resid 1283 through 1292 removed outlier: 3.842A pdb=" N THR C1292 " --> pdb=" O GLN C1288 " (cutoff:3.500A) Processing helix chain 'C' and resid 1297 through 1311 removed outlier: 3.685A pdb=" N THR C1302 " --> pdb=" O VAL C1298 " (cutoff:3.500A) Processing helix chain 'C' and resid 1320 through 1332 removed outlier: 4.189A pdb=" N ASN C1324 " --> pdb=" O PRO C1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 5 through 10 Processing helix chain 'D' and resid 29 through 34 removed outlier: 3.703A pdb=" N TRP D 33 " --> pdb=" O MET D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 101 removed outlier: 3.788A pdb=" N ARG D 101 " --> pdb=" O ARG D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.558A pdb=" N LEU D 127 " --> pdb=" O ARG D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 140 Processing helix chain 'D' and resid 161 through 173 removed outlier: 4.110A pdb=" N GLU D 170 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N GLU D 171 " --> pdb=" O ASP D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 176 No H-bonds generated for 'chain 'D' and resid 174 through 176' Processing helix chain 'D' and resid 181 through 191 removed outlier: 4.342A pdb=" N ILE D 185 " --> pdb=" O GLY D 181 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLN D 186 " --> pdb=" O ALA D 182 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 208 removed outlier: 3.968A pdb=" N GLU D 199 " --> pdb=" O GLU D 195 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLN D 200 " --> pdb=" O GLN D 196 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 230 Processing helix chain 'D' and resid 233 through 237 Processing helix chain 'D' and resid 265 through 284 removed outlier: 3.982A pdb=" N TYR D 269 " --> pdb=" O LEU D 265 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASP D 284 " --> pdb=" O LYS D 280 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 308 removed outlier: 3.567A pdb=" N LEU D 307 " --> pdb=" O VAL D 303 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASP D 308 " --> pdb=" O ASP D 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 328 through 332 removed outlier: 3.861A pdb=" N ILE D 331 " --> pdb=" O ALA D 328 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS D 332 " --> pdb=" O ASP D 329 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 328 through 332' Processing helix chain 'D' and resid 336 through 340 Processing helix chain 'D' and resid 377 through 388 Processing helix chain 'D' and resid 393 through 404 Processing helix chain 'D' and resid 405 through 416 removed outlier: 4.139A pdb=" N TRP D 409 " --> pdb=" O GLU D 405 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ASP D 410 " --> pdb=" O ALA D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' 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: 4.373A pdb=" N ALA D 455 " --> pdb=" O PRO D 451 " (cutoff:3.500A) removed outlier: 4.433A 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 503 through 513 Processing helix chain 'D' and resid 531 through 537 removed outlier: 3.591A pdb=" N ARG D 535 " --> pdb=" O LYS D 531 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR D 537 " --> pdb=" O ALA D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 583 removed outlier: 3.993A pdb=" N MET D 581 " --> pdb=" O ALA D 577 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE D 582 " --> pdb=" O ILE D 578 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 612 removed outlier: 3.864A pdb=" N ILE D 601 " --> pdb=" O GLY D 597 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 636 removed outlier: 3.616A pdb=" N GLY D 636 " --> pdb=" O ALA D 632 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 670 Processing helix chain 'D' and resid 674 through 702 removed outlier: 3.624A pdb=" N ASN D 700 " --> pdb=" O ALA D 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 720 through 728 removed outlier: 3.612A pdb=" N SER D 728 " --> pdb=" O MET D 724 " (cutoff:3.500A) Processing helix chain 'D' and resid 733 through 742 removed outlier: 3.639A pdb=" N GLN D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU D 740 " --> pdb=" O GLN D 736 " (cutoff:3.500A) Processing helix chain 'D' and resid 749 through 753 removed outlier: 3.690A pdb=" N GLY D 752 " --> pdb=" O LYS D 749 " (cutoff:3.500A) Processing helix chain 'D' and resid 768 through 804 removed outlier: 3.939A pdb=" N HIS D 777 " --> pdb=" O PHE D 773 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N GLY D 778 " --> pdb=" O ILE D 774 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ALA D 779 " --> pdb=" O SER D 775 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N THR D 790 " --> pdb=" O THR D 786 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ALA D 791 " --> pdb=" O ALA D 787 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN D 792 " --> pdb=" O LEU D 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 867 through 875 removed outlier: 4.101A pdb=" N LEU D 871 " --> pdb=" O GLN D 867 " (cutoff:3.500A) Processing helix chain 'D' and resid 895 through 900 removed outlier: 4.321A pdb=" N TYR D 899 " --> pdb=" O CYS D 895 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLY D 900 " --> pdb=" O ALA D 896 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 895 through 900' Processing helix chain 'D' and resid 914 through 919 Processing helix chain 'D' and resid 1139 through 1146 Processing helix chain 'D' and resid 1216 through 1224 removed outlier: 3.945A pdb=" N LEU D1221 " --> pdb=" O PRO D1217 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ARG D1222 " --> pdb=" O HIS D1218 " (cutoff:3.500A) Processing helix chain 'D' and resid 1224 through 1243 removed outlier: 4.043A pdb=" N ALA D1228 " --> pdb=" O ARG D1224 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N VAL D1229 " --> pdb=" O GLY D1225 " (cutoff:3.500A) Processing helix chain 'D' and resid 1250 through 1259 removed outlier: 4.054A pdb=" N ILE D1256 " --> pdb=" O HIS D1252 " (cutoff:3.500A) Processing helix chain 'D' and resid 1279 through 1294 removed outlier: 4.319A pdb=" N LEU D1292 " --> pdb=" O ALA D1288 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA D1294 " --> pdb=" O ARG D1290 " (cutoff:3.500A) Processing helix chain 'D' and resid 1308 through 1313 Processing helix chain 'D' and resid 1318 through 1323 removed outlier: 4.043A pdb=" N ALA D1323 " --> pdb=" O ILE D1320 " (cutoff:3.500A) Processing helix chain 'D' and resid 1327 through 1339 Processing helix chain 'D' and resid 1346 through 1354 Processing helix chain 'D' and resid 1362 through 1372 Processing helix chain 'E' and resid 6 through 14 removed outlier: 3.778A pdb=" N GLU E 11 " --> pdb=" O GLN E 7 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N LYS E 12 " --> pdb=" O ASP E 8 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ILE E 13 " --> pdb=" O ALA E 9 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 33 removed outlier: 3.532A pdb=" N ARG E 26 " --> pdb=" O VAL E 22 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN E 29 " --> pdb=" O ARG E 25 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N MET E 30 " --> pdb=" O ARG E 26 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 4.033A pdb=" N LEU E 51 " --> pdb=" O THR E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 74 removed outlier: 3.705A pdb=" N ASP E 65 " --> pdb=" O ASN E 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 16 through 21 removed outlier: 3.766A pdb=" N GLN M 21 " --> pdb=" O PRO M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 40 Processing helix chain 'M' and resid 121 through 131 removed outlier: 3.515A pdb=" N GLU M 129 " --> pdb=" O MET M 125 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU M 130 " --> pdb=" O TRP M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 134 through 146 removed outlier: 3.593A pdb=" N SER M 143 " --> pdb=" O ALA M 139 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 164 removed outlier: 3.814A pdb=" N ILE M 161 " --> pdb=" O GLN M 157 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 182 removed outlier: 3.608A pdb=" N VAL M 175 " --> pdb=" O GLY M 171 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL M 178 " --> pdb=" O GLU M 174 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE M 182 " --> pdb=" O VAL M 178 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 203 Processing helix chain 'M' and resid 212 through 222 removed outlier: 3.834A pdb=" N ASP M 222 " --> pdb=" O LEU M 218 " (cutoff:3.500A) Processing helix chain 'M' and resid 223 through 229 removed outlier: 4.116A pdb=" N LEU M 227 " --> pdb=" O HIS M 223 " (cutoff:3.500A) Processing helix chain 'M' and resid 232 through 239 removed outlier: 3.570A pdb=" N VAL M 238 " --> pdb=" O THR M 234 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 255 removed outlier: 3.581A pdb=" N LEU M 246 " --> pdb=" O LYS M 242 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS M 247 " --> pdb=" O GLU M 243 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU M 248 " --> pdb=" O GLU M 244 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 263 Processing helix chain 'M' and resid 302 through 307 removed outlier: 3.658A pdb=" N ALA M 305 " --> pdb=" O GLN M 302 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET M 306 " --> pdb=" O TYR M 303 " (cutoff:3.500A) Processing helix chain 'M' and resid 312 through 342 removed outlier: 3.575A pdb=" N GLY M 316 " --> pdb=" O ASN M 312 " (cutoff:3.500A) Processing helix chain 'M' and resid 346 through 351 Processing helix chain 'M' and resid 366 through 374 Processing helix chain 'M' and resid 377 through 386 Processing helix chain 'M' and resid 398 through 403 Processing helix chain 'M' and resid 416 through 430 Processing helix chain 'M' and resid 438 through 450 Processing helix chain 'M' and resid 454 through 465 removed outlier: 3.939A pdb=" N VAL M 458 " --> pdb=" O ALA M 454 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU M 465 " --> pdb=" O TYR M 461 " (cutoff:3.500A) Processing helix chain 'M' and resid 469 through 474 removed outlier: 3.574A pdb=" N LYS M 474 " --> pdb=" O SER M 470 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 18 removed outlier: 5.020A pdb=" N ASP A 15 " --> pdb=" O THR A 27 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N THR A 27 " --> pdb=" O ASP A 15 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 201 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 105 removed outlier: 7.963A pdb=" N SER A 141 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N ILE A 61 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ARG A 143 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL A 59 " --> pdb=" O ARG A 143 " (cutoff:3.500A) removed outlier: 6.872A 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 91 Processing sheet with id=AA4, first strand: chain 'B' and resid 23 through 27 removed outlier: 7.181A pdb=" N LEU B 198 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ALA B 189 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N VAL B 187 " --> pdb=" O LYS B 200 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL B 202 " --> pdb=" O TYR B 185 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N TYR B 185 " --> pdb=" O VAL B 202 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N GLU B 204 " --> pdb=" O ILE B 183 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ILE B 183 " --> pdb=" O GLU B 204 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLU B 206 " --> pdb=" O GLU B 181 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 52 through 59 removed outlier: 3.686A pdb=" N ALA B 55 " --> pdb=" O GLN B 147 " (cutoff:3.500A) removed outlier: 7.714A 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 91 Processing sheet with id=AA7, first strand: chain 'B' and resid 110 through 111 removed outlier: 6.334A 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: 6.192A pdb=" N LYS C 13 " --> pdb=" O ALA C1183 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 66 through 75 removed outlier: 6.011A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU C 102 " --> pdb=" O ASP C 116 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N ASP C 116 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ILE C 104 " --> pdb=" O VAL C 114 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL C 114 " --> pdb=" O ILE C 104 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 66 through 75 removed outlier: 6.011A pdb=" N SER C 66 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N TYR C 105 " --> pdb=" O SER C 66 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N LEU C 68 " --> pdb=" O VAL C 103 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N VAL C 103 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N TYR C 70 " --> pdb=" O ARG C 101 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ARG C 101 " --> pdb=" O TYR C 70 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N SER C 72 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLY C 125 " --> pdb=" O LEU C 96 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL C 98 " --> pdb=" O TYR C 123 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N TYR C 123 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU C 100 " --> pdb=" O GLU C 121 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N GLU C 121 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 136 through 138 Processing sheet with id=AB3, first strand: chain 'C' and resid 451 through 454 removed outlier: 4.458A pdb=" N SER C 147 " --> pdb=" O ARG C 529 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N SER C 574 " --> pdb=" O CYS C 559 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 154 through 156 Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 239 Processing sheet with id=AB6, first strand: chain 'C' and resid 580 through 581 removed outlier: 7.051A pdb=" N LEU C 587 " --> pdb=" O LEU C 606 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU C 606 " --> pdb=" O LEU C 587 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N THR C 589 " --> pdb=" O HIS C 604 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N HIS C 604 " --> pdb=" O THR C 589 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR C 591 " --> pdb=" O GLU C 602 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLU C 602 " --> pdb=" O TYR C 591 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LYS C 593 " --> pdb=" O THR C 600 " (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 634 through 637 Processing sheet with id=AB9, first strand: chain 'C' and resid 716 through 717 removed outlier: 6.895A pdb=" N ALA C 716 " --> pdb=" O LEU C 783 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 723 through 727 removed outlier: 3.567A pdb=" N GLN C 725 " --> pdb=" O VAL C 733 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL C 733 " --> pdb=" O GLN C 725 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N VAL C 727 " --> pdb=" O ARG C 731 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARG C 731 " --> pdb=" O VAL C 727 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 789 through 790 Processing sheet with id=AC3, first strand: chain 'C' and resid 798 through 803 removed outlier: 3.610A pdb=" N GLY C1228 " --> pdb=" O VAL C 802 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER C1077 " --> pdb=" O ILE C 816 " (cutoff:3.500A) removed outlier: 7.777A pdb=" N VAL C 818 " --> pdb=" O SER C1077 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ILE C1079 " --> pdb=" O VAL C 818 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 798 through 803 removed outlier: 3.610A pdb=" N GLY C1228 " --> pdb=" O VAL C 802 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 830 through 832 removed outlier: 3.627A pdb=" N HIS C 832 " --> pdb=" O VAL C1056 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N CYS C 838 " --> pdb=" O VAL C1050 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 830 through 832 removed outlier: 3.627A pdb=" N HIS C 832 " --> pdb=" O VAL C1056 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP C 930 " --> pdb=" O TYR C1053 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ALA C1055 " --> pdb=" O VAL C 928 " (cutoff:3.500A) removed outlier: 5.767A pdb=" N VAL C 928 " --> pdb=" O ALA C1055 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 887 through 888 Processing sheet with id=AC8, first strand: chain 'C' and resid 1268 through 1269 Processing sheet with id=AC9, first strand: chain 'C' and resid 1335 through 1336 Processing sheet with id=AD1, first strand: chain 'D' and resid 44 through 45 removed outlier: 3.919A pdb=" N LYS D 50 " --> pdb=" O ASN D 45 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'D' and resid 104 through 105 Processing sheet with id=AD3, first strand: chain 'D' and resid 365 through 369 Processing sheet with id=AD4, first strand: chain 'D' and resid 526 through 527 Processing sheet with id=AD5, first strand: chain 'D' and resid 553 through 556 Processing sheet with id=AD6, first strand: chain 'D' and resid 820 through 822 removed outlier: 3.676A pdb=" N VAL D 880 " --> pdb=" O MET D 822 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 825 through 827 removed outlier: 7.229A pdb=" N VAL D 825 " --> pdb=" O LYS D 832 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ASP D 830 " --> pdb=" O GLU D 827 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 843 through 844 removed outlier: 4.428A pdb=" N THR D 862 " --> pdb=" O THR D 844 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 1002 through 1003 removed outlier: 3.749A pdb=" N ASN D1019 " --> pdb=" O VAL D1002 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 1265 through 1266 Processing sheet with id=AE2, first strand: chain 'M' and resid 47 through 48 removed outlier: 3.752A pdb=" N GLU M 48 " --> pdb=" O LYS M 298 " (cutoff:3.500A) 935 hydrogen bonds defined for protein. 2613 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 86 hydrogen bonds 172 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 8.30 Time building geometry restraints manager: 3.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 4910 1.29 - 1.43: 6911 1.43 - 1.57: 17304 1.57 - 1.71: 182 1.71 - 1.85: 180 Bond restraints: 29487 Sorted by residual: bond pdb=" CA PRO M 258 " pdb=" C PRO M 258 " ideal model delta sigma weight residual 1.522 1.407 0.115 1.18e-02 7.18e+03 9.43e+01 bond pdb=" C4' DG N -10 " pdb=" O4' DG N -10 " ideal model delta sigma weight residual 1.450 1.605 -0.155 2.00e-02 2.50e+03 6.00e+01 bond pdb=" CA LEU M 203 " pdb=" C LEU M 203 " ideal model delta sigma weight residual 1.522 1.420 0.102 1.37e-02 5.33e+03 5.59e+01 bond pdb=" C GLU M 48 " pdb=" O GLU M 48 " ideal model delta sigma weight residual 1.234 1.148 0.086 1.28e-02 6.10e+03 4.55e+01 bond pdb=" CA ASN M 44 " pdb=" C ASN M 44 " ideal model delta sigma weight residual 1.523 1.427 0.096 1.55e-02 4.16e+03 3.85e+01 ... (remaining 29482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 40035 4.26 - 8.51: 258 8.51 - 12.77: 28 12.77 - 17.03: 2 17.03 - 21.28: 1 Bond angle restraints: 40324 Sorted by residual: angle pdb=" O3' DG N -10 " pdb=" P DA N -9 " pdb=" O5' DA N -9 " ideal model delta sigma weight residual 104.00 82.72 21.28 1.50e+00 4.44e-01 2.01e+02 angle pdb=" C ASN M 44 " pdb=" CA ASN M 44 " pdb=" CB ASN M 44 " ideal model delta sigma weight residual 110.44 101.89 8.55 9.00e-01 1.23e+00 9.02e+01 angle pdb=" C THR C 896 " pdb=" N PRO C 897 " pdb=" CA PRO C 897 " ideal model delta sigma weight residual 119.84 130.82 -10.98 1.25e+00 6.40e-01 7.72e+01 angle pdb=" C5' DG N -10 " pdb=" C4' DG N -10 " pdb=" O4' DG N -10 " ideal model delta sigma weight residual 109.40 96.49 12.91 1.50e+00 4.44e-01 7.40e+01 angle pdb=" N ARG M 24 " pdb=" CA ARG M 24 " pdb=" C ARG M 24 " ideal model delta sigma weight residual 114.16 103.25 10.91 1.48e+00 4.57e-01 5.44e+01 ... (remaining 40319 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.54: 17165 34.54 - 69.07: 654 69.07 - 103.61: 18 103.61 - 138.14: 0 138.14 - 172.68: 1 Dihedral angle restraints: 17838 sinusoidal: 7242 harmonic: 10596 Sorted by residual: dihedral pdb=" C CYS M 346 " pdb=" N CYS M 346 " pdb=" CA CYS M 346 " pdb=" CB CYS M 346 " ideal model delta harmonic sigma weight residual -122.60 -138.03 15.43 0 2.50e+00 1.60e-01 3.81e+01 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 -106.06 -14.64 0 2.50e+00 1.60e-01 3.43e+01 dihedral pdb=" CA ASP D 462 " pdb=" C ASP D 462 " pdb=" N GLY D 463 " pdb=" CA GLY D 463 " ideal model delta harmonic sigma weight residual -180.00 -151.25 -28.75 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 17835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.130: 4631 0.130 - 0.260: 104 0.260 - 0.390: 18 0.390 - 0.520: 5 0.520 - 0.649: 4 Chirality restraints: 4762 Sorted by residual: chirality pdb=" CA CYS M 346 " pdb=" N CYS M 346 " pdb=" C CYS M 346 " pdb=" CB CYS M 346 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" C4' DC N -13 " pdb=" C5' DC N -13 " pdb=" O4' DC N -13 " pdb=" C3' DC N -13 " both_signs ideal model delta sigma weight residual False -2.53 -1.90 -0.63 2.00e-01 2.50e+01 9.88e+00 chirality pdb=" C4' DG N -10 " pdb=" C5' DG N -10 " pdb=" O4' DG N -10 " pdb=" C3' DG N -10 " both_signs ideal model delta sigma weight residual False -2.53 -3.12 0.60 2.00e-01 2.50e+01 8.88e+00 ... (remaining 4759 not shown) Planarity restraints: 5045 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP M 285 " 0.107 2.00e-02 2.50e+03 5.73e-02 8.22e+01 pdb=" CG TRP M 285 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP M 285 " -0.087 2.00e-02 2.50e+03 pdb=" CD2 TRP M 285 " 0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP M 285 " -0.010 2.00e-02 2.50e+03 pdb=" CE2 TRP M 285 " 0.014 2.00e-02 2.50e+03 pdb=" CE3 TRP M 285 " -0.063 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 285 " 0.065 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 285 " -0.054 2.00e-02 2.50e+03 pdb=" CH2 TRP M 285 " 0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA T 17 " -0.053 2.00e-02 2.50e+03 2.36e-02 1.53e+01 pdb=" N9 DA T 17 " 0.045 2.00e-02 2.50e+03 pdb=" C8 DA T 17 " 0.008 2.00e-02 2.50e+03 pdb=" N7 DA T 17 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA T 17 " -0.007 2.00e-02 2.50e+03 pdb=" C6 DA T 17 " -0.008 2.00e-02 2.50e+03 pdb=" N6 DA T 17 " -0.004 2.00e-02 2.50e+03 pdb=" N1 DA T 17 " -0.021 2.00e-02 2.50e+03 pdb=" C2 DA T 17 " 0.011 2.00e-02 2.50e+03 pdb=" N3 DA T 17 " 0.012 2.00e-02 2.50e+03 pdb=" C4 DA T 17 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN M 44 " -0.020 2.00e-02 2.50e+03 3.91e-02 1.53e+01 pdb=" C ASN M 44 " 0.068 2.00e-02 2.50e+03 pdb=" O ASN M 44 " -0.025 2.00e-02 2.50e+03 pdb=" N PRO M 45 " -0.023 2.00e-02 2.50e+03 ... (remaining 5042 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 474 2.64 - 3.21: 26267 3.21 - 3.77: 43606 3.77 - 4.34: 56337 4.34 - 4.90: 91509 Nonbonded interactions: 218193 Sorted by model distance: nonbonded pdb=" O GLN M 39 " pdb=" NE2 GLN M 39 " model vdw 2.078 3.120 nonbonded pdb=" O ARG M 279 " pdb=" NH1 ARG M 279 " model vdw 2.094 3.120 nonbonded pdb=" N ASP M 197 " pdb=" OD1 ASP M 197 " model vdw 2.135 3.120 nonbonded pdb=" N ASP M 225 " pdb=" OD1 ASP M 225 " model vdw 2.174 3.120 nonbonded pdb=" N GLU C 987 " pdb=" OE1 GLU C 987 " model vdw 2.186 3.120 ... (remaining 218188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.20 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.490 Check model and map are aligned: 0.110 Set scattering table: 0.060 Process input model: 34.120 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 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 : 0.006 0.155 29487 Z= 0.370 Angle : 0.955 21.284 40324 Z= 0.620 Chirality : 0.058 0.649 4762 Planarity : 0.004 0.088 5045 Dihedral : 15.020 172.679 10996 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.36 % Favored : 91.87 % Rotamer: Outliers : 11.21 % Allowed : 8.63 % Favored : 80.15 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.87 (0.12), residues: 3655 helix: -1.56 (0.13), residues: 1241 sheet: -2.39 (0.26), residues: 323 loop : -3.40 (0.11), residues: 2091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG M 233 TYR 0.008 0.001 TYR D 679 PHE 0.039 0.001 PHE M 318 TRP 0.107 0.005 TRP M 285 HIS 0.007 0.000 HIS M 377 Details of bonding type rmsd covalent geometry : bond 0.00582 (29487) covalent geometry : angle 0.95509 (40324) hydrogen bonds : bond 0.20643 ( 1008) hydrogen bonds : angle 7.13935 ( 2785) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1108 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 313 poor density : 795 time to evaluate : 1.071 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: A 115 ILE cc_start: 0.7636 (OUTLIER) cc_final: 0.7393 (tt) REVERT: A 127 GLN cc_start: 0.8725 (mp10) cc_final: 0.8440 (mp10) REVERT: A 262 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6930 (mm) REVERT: A 312 LEU cc_start: 0.6953 (mt) cc_final: 0.6627 (mt) REVERT: A 313 SER cc_start: 0.7984 (t) cc_final: 0.7732 (p) REVERT: B 96 ASP cc_start: 0.6933 (m-30) cc_final: 0.6665 (t70) REVERT: B 130 ILE cc_start: 0.8975 (mm) cc_final: 0.8743 (mp) REVERT: B 147 GLN cc_start: 0.8206 (tt0) cc_final: 0.7892 (tm-30) REVERT: B 186 ASN cc_start: 0.7947 (t0) cc_final: 0.7727 (t0) REVERT: C 183 TRP cc_start: 0.8249 (m-10) cc_final: 0.7920 (m-10) REVERT: C 203 LYS cc_start: 0.8262 (mtmt) cc_final: 0.7535 (mtmm) REVERT: C 218 GLU cc_start: 0.8796 (pt0) cc_final: 0.8424 (tm-30) REVERT: C 503 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7696 (mttp) REVERT: C 524 ILE cc_start: 0.8851 (tt) cc_final: 0.8513 (tt) REVERT: C 542 ARG cc_start: 0.6234 (OUTLIER) cc_final: 0.5992 (ttm170) REVERT: C 589 THR cc_start: 0.7914 (OUTLIER) cc_final: 0.7683 (t) REVERT: C 835 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.6968 (pm20) REVERT: C 838 CYS cc_start: 0.9299 (OUTLIER) cc_final: 0.8980 (p) REVERT: C 840 SER cc_start: 0.8249 (OUTLIER) cc_final: 0.7691 (t) REVERT: C 868 SER cc_start: 0.7102 (OUTLIER) cc_final: 0.6843 (t) REVERT: C 903 ARG cc_start: 0.9190 (OUTLIER) cc_final: 0.8975 (mtp85) REVERT: C 925 SER cc_start: 0.9148 (OUTLIER) cc_final: 0.8841 (p) REVERT: C 962 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7519 (tp30) REVERT: C 1021 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.8907 (tp) REVERT: C 1024 GLU cc_start: 0.9231 (OUTLIER) cc_final: 0.8918 (mm-30) REVERT: C 1029 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8601 (tp) REVERT: C 1038 GLN cc_start: 0.8557 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: C 1057 LYS cc_start: 0.8949 (OUTLIER) cc_final: 0.8458 (tttt) REVERT: C 1058 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7811 (mtt-85) REVERT: C 1161 LEU cc_start: 0.8407 (OUTLIER) cc_final: 0.8086 (tt) REVERT: D 76 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7906 (ptmt) REVERT: D 165 TYR cc_start: 0.8273 (t80) cc_final: 0.8043 (t80) REVERT: D 227 PHE cc_start: 0.8809 (t80) cc_final: 0.8157 (t80) REVERT: D 321 LYS cc_start: 0.8725 (OUTLIER) cc_final: 0.8313 (tppt) REVERT: D 330 MET cc_start: 0.6597 (ptp) cc_final: 0.6252 (ptp) REVERT: D 453 VAL cc_start: 0.8877 (p) cc_final: 0.8658 (t) REVERT: D 518 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.8017 (m) REVERT: D 695 LYS cc_start: 0.8691 (OUTLIER) cc_final: 0.8337 (tptm) REVERT: D 788 LEU cc_start: 0.7844 (tt) cc_final: 0.7511 (mp) REVERT: D 1040 MET cc_start: 0.3379 (mtp) cc_final: 0.2563 (mmm) REVERT: E 7 GLN cc_start: 0.7729 (tp40) cc_final: 0.7512 (tp40) REVERT: E 60 ASN cc_start: 0.7984 (p0) cc_final: 0.7595 (p0) REVERT: E 63 ILE cc_start: 0.9198 (mm) cc_final: 0.8960 (mt) REVERT: M 42 GLU cc_start: 0.8614 (OUTLIER) cc_final: 0.8358 (pm20) REVERT: M 115 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7994 (mp0) REVERT: M 117 THR cc_start: 0.7427 (OUTLIER) cc_final: 0.7052 (t) REVERT: M 173 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8815 (pm20) REVERT: M 185 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.8503 (m-10) REVERT: M 196 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8404 (tmm-80) REVERT: M 203 LEU cc_start: 0.9007 (mt) cc_final: 0.8799 (mp) REVERT: M 223 HIS cc_start: 0.9364 (m-70) cc_final: 0.9128 (m90) REVERT: M 252 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8808 (tp) REVERT: M 265 GLN cc_start: 0.7907 (OUTLIER) cc_final: 0.7547 (tt0) REVERT: M 276 VAL cc_start: 0.7274 (OUTLIER) cc_final: 0.6968 (p) REVERT: M 280 LYS cc_start: 0.7550 (OUTLIER) cc_final: 0.7008 (mmmt) REVERT: M 306 MET cc_start: 0.8485 (mtt) cc_final: 0.7281 (mtm) REVERT: M 365 MET cc_start: 0.8352 (ptm) cc_final: 0.7634 (ptp) REVERT: M 378 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.7026 (pp20) REVERT: M 400 LYS cc_start: 0.5693 (OUTLIER) cc_final: 0.4836 (mmtt) REVERT: M 441 LYS cc_start: 0.9723 (mtpm) cc_final: 0.8307 (tmtt) REVERT: M 455 ARG cc_start: 0.6766 (OUTLIER) cc_final: 0.6285 (ptm-80) REVERT: M 456 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.7972 (mmm160) outliers start: 313 outliers final: 109 residues processed: 1051 average time/residue: 0.2091 time to fit residues: 330.8536 Evaluate side-chains 521 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 375 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 150 ARG Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 353 VAL Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 503 LYS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 677 ASN Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 835 GLU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 840 SER Chi-restraints excluded: chain C residue 842 ASP Chi-restraints excluded: chain C residue 850 ILE Chi-restraints excluded: chain C residue 854 ILE Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 868 SER Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 886 LYS Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 901 LEU Chi-restraints excluded: chain C residue 903 ARG Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 915 ASP Chi-restraints excluded: chain C residue 917 SER Chi-restraints excluded: chain C residue 918 LEU Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 927 THR Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 929 ILE Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain C residue 939 VAL Chi-restraints excluded: chain C residue 940 GLU Chi-restraints excluded: chain C residue 953 LEU Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 966 ILE Chi-restraints excluded: chain C residue 1011 LEU Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1017 GLN Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1022 LYS Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1029 LEU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1040 ASP Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1047 LEU Chi-restraints excluded: chain C residue 1051 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1057 LYS Chi-restraints excluded: chain C residue 1058 ARG Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1237 HIS Chi-restraints excluded: chain C residue 1250 SER Chi-restraints excluded: chain C residue 1251 TYR Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 76 LYS Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 518 VAL Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain M residue 23 ILE Chi-restraints excluded: chain M residue 24 ARG Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 115 GLU Chi-restraints excluded: chain M residue 117 THR Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 121 GLN Chi-restraints excluded: chain M residue 124 LEU Chi-restraints excluded: chain M residue 138 ARG Chi-restraints excluded: chain M residue 143 SER Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 148 VAL Chi-restraints excluded: chain M residue 149 ASP Chi-restraints excluded: chain M residue 150 ASP Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 173 GLU Chi-restraints excluded: chain M residue 176 GLU Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 184 ARG Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 196 ARG Chi-restraints excluded: chain M residue 199 LEU Chi-restraints excluded: chain M residue 201 ILE Chi-restraints excluded: chain M residue 217 ARG Chi-restraints excluded: chain M residue 226 LEU Chi-restraints excluded: chain M residue 252 LEU Chi-restraints excluded: chain M residue 264 ILE Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 276 VAL Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain M residue 288 GLU Chi-restraints excluded: chain M residue 289 LEU Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 297 LEU Chi-restraints excluded: chain M residue 336 ARG Chi-restraints excluded: chain M residue 340 LEU Chi-restraints excluded: chain M residue 342 ARG Chi-restraints excluded: chain M residue 378 GLU Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 387 GLN Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 391 HIS Chi-restraints excluded: chain M residue 399 LEU Chi-restraints excluded: chain M residue 400 LYS Chi-restraints excluded: chain M residue 455 ARG Chi-restraints excluded: chain M residue 456 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 197 optimal weight: 0.0470 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 50.0000 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 132 HIS A 227 GLN B 37 HIS C 462 ASN C 618 GLN C 659 GLN C 965 GLN C1038 GLN C1256 GLN C1314 GLN D 196 GLN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS D 777 HIS M 34 GLN M 127 GLN M 229 ASN M 254 GLN M 322 ASN M 387 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.159742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.112297 restraints weight = 61373.628| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 3.58 r_work: 0.3511 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3476 r_free = 0.3476 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3476 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 29487 Z= 0.157 Angle : 0.734 28.370 40324 Z= 0.355 Chirality : 0.045 0.228 4762 Planarity : 0.005 0.067 5045 Dihedral : 15.554 173.049 5080 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.55 % Favored : 92.37 % Rotamer: Outliers : 6.99 % Allowed : 17.34 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -2.81 (0.13), residues: 3655 helix: -0.26 (0.15), residues: 1260 sheet: -2.07 (0.26), residues: 338 loop : -3.03 (0.11), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 731 TYR 0.021 0.002 TYR B 68 PHE 0.019 0.002 PHE C 545 TRP 0.038 0.002 TRP A 321 HIS 0.012 0.001 HIS B 132 Details of bonding type rmsd covalent geometry : bond 0.00353 (29487) covalent geometry : angle 0.73356 (40324) hydrogen bonds : bond 0.04235 ( 1008) hydrogen bonds : angle 4.58951 ( 2785) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 602 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 407 time to evaluate : 1.022 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: A 7 GLU cc_start: 0.6993 (OUTLIER) cc_final: 0.6767 (mp0) REVERT: A 93 GLN cc_start: 0.8352 (tp-100) cc_final: 0.7843 (mp10) REVERT: A 127 GLN cc_start: 0.8896 (mp10) cc_final: 0.8653 (mp10) REVERT: A 313 SER cc_start: 0.8363 (t) cc_final: 0.7797 (p) REVERT: B 43 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8741 (mp) REVERT: B 145 LYS cc_start: 0.8734 (ptpt) cc_final: 0.8283 (ptmm) REVERT: B 147 GLN cc_start: 0.8190 (tt0) cc_final: 0.7867 (tm-30) REVERT: B 186 ASN cc_start: 0.8417 (t0) cc_final: 0.8114 (t0) REVERT: C 156 PHE cc_start: 0.8481 (m-10) cc_final: 0.8241 (m-10) REVERT: C 183 TRP cc_start: 0.7966 (m-10) cc_final: 0.7680 (m100) REVERT: C 203 LYS cc_start: 0.8207 (mtmt) cc_final: 0.7818 (mtmt) REVERT: C 385 PHE cc_start: 0.8662 (t80) cc_final: 0.8339 (t80) REVERT: C 407 ARG cc_start: 0.8644 (mmm-85) cc_final: 0.8306 (ttm170) REVERT: C 503 LYS cc_start: 0.8119 (OUTLIER) cc_final: 0.7721 (mttp) REVERT: C 542 ARG cc_start: 0.6405 (OUTLIER) cc_final: 0.6196 (ttm170) REVERT: C 545 PHE cc_start: 0.7162 (t80) cc_final: 0.6856 (t80) REVERT: C 589 THR cc_start: 0.8808 (OUTLIER) cc_final: 0.8422 (t) REVERT: C 639 LYS cc_start: 0.8370 (mmtm) cc_final: 0.8092 (mmtm) REVERT: C 766 ASN cc_start: 0.8387 (t0) cc_final: 0.8115 (t0) REVERT: C 873 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8757 (mt) REVERT: C 903 ARG cc_start: 0.9384 (OUTLIER) cc_final: 0.9099 (ptp-170) REVERT: C 954 LYS cc_start: 0.9272 (OUTLIER) cc_final: 0.8892 (tptp) REVERT: C 962 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7794 (tp30) REVERT: C 1021 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8729 (tp) REVERT: C 1024 GLU cc_start: 0.9315 (OUTLIER) cc_final: 0.8975 (mm-30) REVERT: C 1032 LYS cc_start: 0.9378 (OUTLIER) cc_final: 0.8790 (ttpt) REVERT: C 1038 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7951 (tm-30) REVERT: C 1051 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8582 (mtpp) REVERT: C 1053 TYR cc_start: 0.8780 (m-80) cc_final: 0.8518 (m-80) REVERT: C 1161 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8209 (tt) REVERT: D 69 GLU cc_start: 0.7080 (pt0) cc_final: 0.6831 (pt0) REVERT: D 227 PHE cc_start: 0.8848 (t80) cc_final: 0.8119 (t80) REVERT: D 321 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8441 (tppt) REVERT: D 398 LYS cc_start: 0.9290 (tttt) cc_final: 0.9025 (ttpp) REVERT: D 695 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8412 (tptm) REVERT: D 697 MET cc_start: 0.7727 (tpp) cc_final: 0.7406 (tmm) REVERT: D 698 MET cc_start: 0.7939 (mmm) cc_final: 0.7682 (mmm) REVERT: D 788 LEU cc_start: 0.8134 (tt) cc_final: 0.7741 (mm) REVERT: D 802 ASP cc_start: 0.8330 (m-30) cc_final: 0.8081 (m-30) REVERT: D 842 ARG cc_start: 0.8560 (OUTLIER) cc_final: 0.7812 (mtp85) REVERT: D 1040 MET cc_start: 0.4697 (mtp) cc_final: 0.3576 (mmm) REVERT: D 1144 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8851 (mp) REVERT: E 10 VAL cc_start: 0.8052 (t) cc_final: 0.7678 (t) REVERT: E 43 ASN cc_start: 0.7952 (t0) cc_final: 0.7675 (t0) REVERT: E 64 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8353 (mm) REVERT: M 180 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8356 (tmtt) REVERT: M 280 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7624 (mmmt) REVERT: M 297 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7416 (mm) REVERT: M 306 MET cc_start: 0.8448 (mtt) cc_final: 0.8143 (mpp) outliers start: 195 outliers final: 86 residues processed: 568 average time/residue: 0.1949 time to fit residues: 172.6439 Evaluate side-chains 422 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 313 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 346 TYR Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 479 LEU Chi-restraints excluded: chain C residue 503 LYS Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 542 ARG Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 838 CYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 862 LEU Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 903 ARG Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 1014 LEU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1042 LEU Chi-restraints excluded: chain C residue 1051 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1191 LYS Chi-restraints excluded: chain C residue 1237 HIS Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 158 ILE Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 265 GLN Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain M residue 296 ARG Chi-restraints excluded: chain M residue 297 LEU Chi-restraints excluded: chain M residue 336 ARG Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 353 optimal weight: 30.0000 chunk 132 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 301 optimal weight: 0.8980 chunk 204 optimal weight: 0.7980 chunk 166 optimal weight: 3.9990 chunk 227 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 367 optimal weight: 20.0000 chunk 220 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 132 HIS C 214 ASN C 238 GLN C 513 GLN C1236 ASN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 504 GLN D 777 HIS M 229 ASN M 322 ASN M 337 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.152051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.104407 restraints weight = 60729.407| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 3.40 r_work: 0.3340 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3307 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3307 r_free = 0.3307 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3307 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.106 29487 Z= 0.195 Angle : 0.712 24.712 40324 Z= 0.346 Chirality : 0.045 0.234 4762 Planarity : 0.005 0.058 5045 Dihedral : 14.709 172.764 4879 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.69 % Favored : 92.23 % Rotamer: Outliers : 6.20 % Allowed : 19.03 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.39 (0.13), residues: 3655 helix: 0.19 (0.15), residues: 1258 sheet: -1.77 (0.28), residues: 327 loop : -2.86 (0.12), residues: 2070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D1222 TYR 0.016 0.002 TYR C1231 PHE 0.015 0.002 PHE D 437 TRP 0.036 0.002 TRP A 321 HIS 0.020 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00453 (29487) covalent geometry : angle 0.71173 (40324) hydrogen bonds : bond 0.04208 ( 1008) hydrogen bonds : angle 4.35692 ( 2785) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 324 time to evaluate : 1.001 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: A 7 GLU cc_start: 0.7222 (OUTLIER) cc_final: 0.6985 (mp0) REVERT: A 127 GLN cc_start: 0.9005 (mp10) cc_final: 0.8783 (mp10) REVERT: A 183 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8744 (mm) REVERT: A 313 SER cc_start: 0.8499 (t) cc_final: 0.8200 (p) REVERT: B 43 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8826 (mp) REVERT: B 145 LYS cc_start: 0.8743 (ptpt) cc_final: 0.8275 (ptpp) REVERT: B 147 GLN cc_start: 0.8136 (tt0) cc_final: 0.7814 (tm-30) REVERT: B 186 ASN cc_start: 0.8538 (t0) cc_final: 0.8220 (t0) REVERT: C 156 PHE cc_start: 0.8532 (m-10) cc_final: 0.8256 (m-10) REVERT: C 186 PHE cc_start: 0.7596 (m-80) cc_final: 0.7368 (m-80) REVERT: C 202 ARG cc_start: 0.8348 (mtm110) cc_final: 0.8146 (mtm110) REVERT: C 203 LYS cc_start: 0.8309 (mtmt) cc_final: 0.7568 (mtmm) REVERT: C 238 GLN cc_start: 0.9380 (OUTLIER) cc_final: 0.9179 (pm20) REVERT: C 239 MET cc_start: 0.8144 (mmm) cc_final: 0.7809 (tpp) REVERT: C 385 PHE cc_start: 0.8726 (t80) cc_final: 0.8488 (t80) REVERT: C 407 ARG cc_start: 0.8725 (mmm-85) cc_final: 0.8341 (ttm170) REVERT: C 542 ARG cc_start: 0.6670 (mmp-170) cc_final: 0.6349 (ttm170) REVERT: C 545 PHE cc_start: 0.7143 (t80) cc_final: 0.6848 (t80) REVERT: C 589 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8618 (t) REVERT: C 628 HIS cc_start: 0.8024 (m90) cc_final: 0.7713 (m90) REVERT: C 639 LYS cc_start: 0.8372 (mmtm) cc_final: 0.8050 (mmtm) REVERT: C 685 MET cc_start: 0.8046 (mtm) cc_final: 0.7836 (mtt) REVERT: C 694 ARG cc_start: 0.7812 (mpp80) cc_final: 0.6959 (mtp85) REVERT: C 766 ASN cc_start: 0.8525 (t0) cc_final: 0.8265 (t0) REVERT: C 954 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8915 (tptp) REVERT: C 962 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8193 (tp30) REVERT: C 1021 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8742 (tp) REVERT: C 1024 GLU cc_start: 0.9303 (OUTLIER) cc_final: 0.8912 (mm-30) REVERT: C 1032 LYS cc_start: 0.9361 (OUTLIER) cc_final: 0.8714 (ttpt) REVERT: C 1038 GLN cc_start: 0.8596 (OUTLIER) cc_final: 0.8275 (tm-30) REVERT: C 1064 ASP cc_start: 0.8089 (m-30) cc_final: 0.7771 (m-30) REVERT: C 1161 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8262 (tt) REVERT: D 321 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8502 (tppt) REVERT: D 398 LYS cc_start: 0.9304 (tttt) cc_final: 0.8849 (ttpp) REVERT: D 643 ASP cc_start: 0.7551 (m-30) cc_final: 0.7333 (m-30) REVERT: D 695 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8567 (tptm) REVERT: D 697 MET cc_start: 0.7705 (tpp) cc_final: 0.7405 (tmm) REVERT: D 802 ASP cc_start: 0.8541 (m-30) cc_final: 0.8267 (m-30) REVERT: D 833 GLU cc_start: 0.7802 (tp30) cc_final: 0.7541 (tp30) REVERT: D 1040 MET cc_start: 0.4758 (mtp) cc_final: 0.3537 (mmm) REVERT: E 43 ASN cc_start: 0.8122 (t0) cc_final: 0.7781 (t0) REVERT: M 125 MET cc_start: 0.8991 (mmm) cc_final: 0.8714 (mmm) REVERT: M 180 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8888 (tptp) REVERT: M 185 PHE cc_start: 0.8739 (OUTLIER) cc_final: 0.8515 (m-10) REVERT: M 236 MET cc_start: 0.7958 (mmt) cc_final: 0.7669 (mmt) REVERT: M 423 LEU cc_start: 0.8709 (tp) cc_final: 0.8147 (pp) outliers start: 173 outliers final: 113 residues processed: 477 average time/residue: 0.2021 time to fit residues: 149.2758 Evaluate side-chains 408 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 279 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 GLU 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 A residue 277 TYR Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 238 GLN Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 477 GLU Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 962 GLU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 97 VAL Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain D residue 1357 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 184 ARG Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 296 ARG Chi-restraints excluded: chain M residue 336 ARG Chi-restraints excluded: chain M residue 337 ASN Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 58 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 9 optimal weight: 2.9990 chunk 151 optimal weight: 6.9990 chunk 76 optimal weight: 0.3980 chunk 98 optimal weight: 3.9990 chunk 181 optimal weight: 4.9990 chunk 82 optimal weight: 0.0070 chunk 363 optimal weight: 10.0000 overall best weight: 2.0804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 132 HIS C 214 ASN C1061 GLN C1314 GLN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1238 GLN E 31 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.151135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.098337 restraints weight = 60157.808| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 3.06 r_work: 0.3306 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 29487 Z= 0.162 Angle : 0.676 22.324 40324 Z= 0.326 Chirality : 0.044 0.331 4762 Planarity : 0.004 0.058 5045 Dihedral : 14.530 172.512 4833 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.58 % Favored : 92.34 % Rotamer: Outliers : 5.59 % Allowed : 20.03 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.11 (0.13), residues: 3655 helix: 0.44 (0.15), residues: 1275 sheet: -1.64 (0.28), residues: 315 loop : -2.73 (0.12), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D1140 TYR 0.030 0.001 TYR D 144 PHE 0.019 0.001 PHE C 186 TRP 0.038 0.002 TRP A 321 HIS 0.007 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00379 (29487) covalent geometry : angle 0.67638 (40324) hydrogen bonds : bond 0.03790 ( 1008) hydrogen bonds : angle 4.15153 ( 2785) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 156 poor density : 306 time to evaluate : 1.292 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: A 7 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: A 93 GLN cc_start: 0.8455 (tp40) cc_final: 0.7901 (mp10) REVERT: A 127 GLN cc_start: 0.9015 (mp10) cc_final: 0.8772 (mp10) REVERT: A 183 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8760 (mm) REVERT: A 313 SER cc_start: 0.8509 (t) cc_final: 0.8158 (p) REVERT: B 43 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8839 (mp) REVERT: B 68 TYR cc_start: 0.7858 (m-80) cc_final: 0.7645 (m-80) REVERT: B 145 LYS cc_start: 0.8674 (ptpt) cc_final: 0.8250 (ptpp) REVERT: B 147 GLN cc_start: 0.8118 (tt0) cc_final: 0.7831 (mt0) REVERT: B 186 ASN cc_start: 0.8582 (t0) cc_final: 0.8271 (t0) REVERT: B 212 ASP cc_start: 0.7539 (t0) cc_final: 0.7323 (t0) REVERT: C 156 PHE cc_start: 0.8523 (m-10) cc_final: 0.8163 (m-10) REVERT: C 183 TRP cc_start: 0.8407 (m-10) cc_final: 0.8065 (m100) REVERT: C 203 LYS cc_start: 0.8296 (mtmt) cc_final: 0.7864 (mtmt) REVERT: C 352 ARG cc_start: 0.9019 (ptp-170) cc_final: 0.8517 (mtp85) REVERT: C 370 MET cc_start: 0.8302 (tmm) cc_final: 0.8086 (tmm) REVERT: C 385 PHE cc_start: 0.8733 (t80) cc_final: 0.8469 (t80) REVERT: C 542 ARG cc_start: 0.6662 (mmp-170) cc_final: 0.6376 (ttm170) REVERT: C 545 PHE cc_start: 0.7235 (t80) cc_final: 0.6990 (t80) REVERT: C 589 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8647 (t) REVERT: C 628 HIS cc_start: 0.8002 (m90) cc_final: 0.7652 (m90) REVERT: C 766 ASN cc_start: 0.8483 (t0) cc_final: 0.8259 (t0) REVERT: C 844 LYS cc_start: 0.8655 (ptpt) cc_final: 0.8332 (ptpt) REVERT: C 954 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8868 (tptp) REVERT: C 1021 LEU cc_start: 0.9139 (OUTLIER) cc_final: 0.8668 (tp) REVERT: C 1024 GLU cc_start: 0.9381 (OUTLIER) cc_final: 0.9003 (mm-30) REVERT: C 1032 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.8662 (ttpt) REVERT: C 1038 GLN cc_start: 0.8665 (OUTLIER) cc_final: 0.8269 (tm-30) REVERT: C 1161 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8279 (tt) REVERT: C 1200 LYS cc_start: 0.8652 (tptt) cc_final: 0.8300 (ttpt) REVERT: D 222 LYS cc_start: 0.9081 (mtpt) cc_final: 0.8718 (mmtm) REVERT: D 239 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8379 (pp) REVERT: D 321 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8463 (tppt) REVERT: D 643 ASP cc_start: 0.7726 (m-30) cc_final: 0.7500 (m-30) REVERT: D 695 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8616 (tptm) REVERT: D 697 MET cc_start: 0.7755 (tpp) cc_final: 0.7354 (tmm) REVERT: D 833 GLU cc_start: 0.7866 (tp30) cc_final: 0.7631 (tp30) REVERT: D 1040 MET cc_start: 0.4888 (mtp) cc_final: 0.3670 (mpp) REVERT: E 62 GLN cc_start: 0.8755 (tm-30) cc_final: 0.8460 (tm-30) REVERT: M 125 MET cc_start: 0.8970 (mmm) cc_final: 0.8703 (mmm) REVERT: M 180 LYS cc_start: 0.9054 (OUTLIER) cc_final: 0.8263 (tmtt) REVERT: M 185 PHE cc_start: 0.8676 (OUTLIER) cc_final: 0.8465 (m-10) REVERT: M 236 MET cc_start: 0.8008 (mmt) cc_final: 0.7756 (mmt) REVERT: M 297 LEU cc_start: 0.7616 (OUTLIER) cc_final: 0.7365 (mm) REVERT: M 362 MET cc_start: 0.8701 (ptm) cc_final: 0.8247 (ppp) REVERT: M 423 LEU cc_start: 0.8597 (tp) cc_final: 0.8169 (pp) outliers start: 156 outliers final: 105 residues processed: 440 average time/residue: 0.1964 time to fit residues: 136.7727 Evaluate side-chains 393 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 272 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 GLU 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 A residue 281 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 150 HIS Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 239 LEU Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 285 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 28 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 296 ARG Chi-restraints excluded: chain M residue 297 LEU Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 283 optimal weight: 40.0000 chunk 299 optimal weight: 30.0000 chunk 121 optimal weight: 4.9990 chunk 153 optimal weight: 20.0000 chunk 44 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 267 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 303 optimal weight: 8.9990 chunk 348 optimal weight: 0.9980 chunk 142 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS A 283 GLN C 214 ASN C 387 ASN C 526 HIS C 965 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 HIS D 430 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 337 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.139819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.090226 restraints weight = 59978.940| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 3.50 r_work: 0.3017 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3018 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3018 r_free = 0.3018 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3018 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.5410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.091 29487 Z= 0.369 Angle : 0.836 15.512 40324 Z= 0.424 Chirality : 0.051 0.314 4762 Planarity : 0.006 0.065 5045 Dihedral : 14.752 174.131 4826 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.71 % Favored : 90.18 % Rotamer: Outliers : 7.45 % Allowed : 19.35 % Favored : 73.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.36 (0.13), residues: 3655 helix: -0.03 (0.15), residues: 1285 sheet: -1.34 (0.30), residues: 286 loop : -2.76 (0.12), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 202 TYR 0.021 0.002 TYR C 47 PHE 0.026 0.002 PHE B 35 TRP 0.036 0.002 TRP A 321 HIS 0.012 0.002 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00871 (29487) covalent geometry : angle 0.83642 (40324) hydrogen bonds : bond 0.05441 ( 1008) hydrogen bonds : angle 4.61311 ( 2785) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 208 poor density : 288 time to evaluate : 1.132 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: A 7 GLU cc_start: 0.7365 (OUTLIER) cc_final: 0.7108 (mp0) REVERT: A 313 SER cc_start: 0.8561 (t) cc_final: 0.8113 (p) REVERT: B 43 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.9000 (mp) REVERT: B 145 LYS cc_start: 0.8651 (ptpt) cc_final: 0.8229 (ptpp) REVERT: B 186 ASN cc_start: 0.8698 (t0) cc_final: 0.8353 (t0) REVERT: B 212 ASP cc_start: 0.8037 (t0) cc_final: 0.7684 (t0) REVERT: C 133 ASN cc_start: 0.9204 (OUTLIER) cc_final: 0.8961 (p0) REVERT: C 183 TRP cc_start: 0.8672 (m-10) cc_final: 0.8216 (m100) REVERT: C 202 ARG cc_start: 0.8639 (mtm110) cc_final: 0.8411 (mtm110) REVERT: C 203 LYS cc_start: 0.8536 (mtmt) cc_final: 0.7693 (mtmm) REVERT: C 542 ARG cc_start: 0.7184 (mmp-170) cc_final: 0.6578 (mmt90) REVERT: C 589 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8739 (t) REVERT: C 628 HIS cc_start: 0.8051 (m90) cc_final: 0.7676 (m90) REVERT: C 699 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8934 (mp) REVERT: C 704 MET cc_start: 0.7590 (pmm) cc_final: 0.7126 (ptp) REVERT: C 826 ASP cc_start: 0.8667 (OUTLIER) cc_final: 0.8204 (t0) REVERT: C 835 GLU cc_start: 0.8482 (pp20) cc_final: 0.7968 (pp20) REVERT: C 844 LYS cc_start: 0.8742 (ptpt) cc_final: 0.8324 (ptpt) REVERT: C 954 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8825 (tptp) REVERT: C 965 GLN cc_start: 0.8901 (OUTLIER) cc_final: 0.8543 (pp30) REVERT: C 1021 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8676 (tp) REVERT: C 1024 GLU cc_start: 0.9431 (OUTLIER) cc_final: 0.9033 (mm-30) REVERT: C 1032 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8751 (ttpt) REVERT: C 1161 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8495 (tt) REVERT: D 298 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8771 (mtp) REVERT: D 321 LYS cc_start: 0.8754 (OUTLIER) cc_final: 0.8425 (tppt) REVERT: D 352 ARG cc_start: 0.8387 (mmp80) cc_final: 0.7977 (mmm160) REVERT: D 503 SER cc_start: 0.8404 (t) cc_final: 0.8102 (p) REVERT: D 643 ASP cc_start: 0.8202 (m-30) cc_final: 0.7914 (m-30) REVERT: D 695 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8691 (tptm) REVERT: D 788 LEU cc_start: 0.8895 (tp) cc_final: 0.8583 (tt) REVERT: D 842 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8644 (mtp180) REVERT: D 1040 MET cc_start: 0.5743 (mtp) cc_final: 0.3940 (mmm) REVERT: D 1143 ASP cc_start: 0.7844 (m-30) cc_final: 0.7142 (t0) REVERT: E 62 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8651 (tm-30) REVERT: M 180 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8690 (tptp) REVERT: M 185 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8492 (m-10) REVERT: M 297 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7399 (mm) REVERT: M 362 MET cc_start: 0.8712 (ptm) cc_final: 0.8254 (ppp) REVERT: M 423 LEU cc_start: 0.8891 (tp) cc_final: 0.8491 (pp) outliers start: 208 outliers final: 143 residues processed: 465 average time/residue: 0.1894 time to fit residues: 139.6948 Evaluate side-chains 427 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 265 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 16 ILE Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 170 ARG Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 277 TYR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 146 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 371 ARG Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 583 GLU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 660 VAL Chi-restraints excluded: chain C residue 699 LEU Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 830 THR Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 965 GLN Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1114 GLU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1191 LYS Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 326 SER Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 424 ASN Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 429 LEU Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 624 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 645 VAL Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 706 VAL Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 786 THR Chi-restraints excluded: chain D residue 801 VAL Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 884 SER Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain D residue 1328 THR Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 136 THR Chi-restraints excluded: chain M residue 145 VAL Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 160 ASP Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 179 LEU Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 184 ARG Chi-restraints excluded: chain M residue 185 PHE Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 213 LEU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 296 ARG Chi-restraints excluded: chain M residue 297 LEU Chi-restraints excluded: chain M residue 317 GLN Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 43 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 184 optimal weight: 0.6980 chunk 189 optimal weight: 0.8980 chunk 183 optimal weight: 4.9990 chunk 348 optimal weight: 0.0060 chunk 263 optimal weight: 0.8980 chunk 367 optimal weight: 20.0000 chunk 262 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN B 194 GLN ** C 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN C1146 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1252 HIS ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.144401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.092613 restraints weight = 59504.016| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.23 r_work: 0.3133 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3135 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3135 r_free = 0.3135 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3135 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.5330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29487 Z= 0.121 Angle : 0.665 16.494 40324 Z= 0.323 Chirality : 0.043 0.255 4762 Planarity : 0.004 0.063 5045 Dihedral : 14.385 173.991 4821 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.39 % Favored : 92.53 % Rotamer: Outliers : 5.16 % Allowed : 21.71 % Favored : 73.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.95 (0.13), residues: 3655 helix: 0.43 (0.15), residues: 1296 sheet: -1.34 (0.29), residues: 299 loop : -2.57 (0.12), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D1149 TYR 0.015 0.001 TYR C 367 PHE 0.020 0.001 PHE C 545 TRP 0.023 0.001 TRP A 321 HIS 0.028 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00269 (29487) covalent geometry : angle 0.66479 (40324) hydrogen bonds : bond 0.03551 ( 1008) hydrogen bonds : angle 4.12968 ( 2785) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 445 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 301 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.9137 (mp10) cc_final: 0.8831 (mp10) REVERT: A 255 ARG cc_start: 0.7454 (mtm-85) cc_final: 0.6974 (mpp-170) REVERT: A 313 SER cc_start: 0.8483 (t) cc_final: 0.7766 (p) REVERT: A 317 ARG cc_start: 0.7611 (mmt180) cc_final: 0.7249 (mmp80) REVERT: B 18 GLN cc_start: 0.8898 (pm20) cc_final: 0.8427 (pp30) REVERT: B 43 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8800 (mp) REVERT: B 145 LYS cc_start: 0.8498 (ptpt) cc_final: 0.8163 (ptpp) REVERT: B 186 ASN cc_start: 0.8712 (t0) cc_final: 0.8363 (t0) REVERT: C 120 GLN cc_start: 0.6704 (tt0) cc_final: 0.6360 (tt0) REVERT: C 132 ASP cc_start: 0.8892 (t0) cc_final: 0.8652 (t0) REVERT: C 151 ARG cc_start: 0.8245 (ptm160) cc_final: 0.7948 (ptp-170) REVERT: C 183 TRP cc_start: 0.8600 (m-10) cc_final: 0.8227 (m100) REVERT: C 203 LYS cc_start: 0.8399 (mtmt) cc_final: 0.7877 (mtmt) REVERT: C 542 ARG cc_start: 0.7001 (mmp-170) cc_final: 0.6456 (mmt90) REVERT: C 545 PHE cc_start: 0.7791 (t80) cc_final: 0.7533 (t80) REVERT: C 589 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8649 (t) REVERT: C 628 HIS cc_start: 0.7933 (m90) cc_final: 0.7618 (m-70) REVERT: C 704 MET cc_start: 0.7162 (pmm) cc_final: 0.6778 (ptp) REVERT: C 844 LYS cc_start: 0.8719 (ptpt) cc_final: 0.8375 (ptpt) REVERT: C 936 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.6369 (ttm170) REVERT: C 954 LYS cc_start: 0.9143 (OUTLIER) cc_final: 0.8834 (tptp) REVERT: C 1011 LEU cc_start: 0.9628 (mm) cc_final: 0.9154 (tp) REVERT: C 1021 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8648 (tp) REVERT: C 1024 GLU cc_start: 0.9466 (OUTLIER) cc_final: 0.9096 (mm-30) REVERT: C 1032 LYS cc_start: 0.9331 (OUTLIER) cc_final: 0.8722 (ttpt) REVERT: C 1158 LYS cc_start: 0.8043 (tptm) cc_final: 0.7358 (tptt) REVERT: C 1161 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8306 (tt) REVERT: C 1200 LYS cc_start: 0.8680 (tptt) cc_final: 0.8355 (ttmt) REVERT: C 1222 GLU cc_start: 0.7258 (pm20) cc_final: 0.6982 (pm20) REVERT: C 1231 TYR cc_start: 0.9191 (t80) cc_final: 0.8702 (t80) REVERT: D 298 MET cc_start: 0.9065 (tpp) cc_final: 0.8705 (mtp) REVERT: D 321 LYS cc_start: 0.8608 (OUTLIER) cc_final: 0.8356 (tppt) REVERT: D 342 LEU cc_start: 0.8297 (OUTLIER) cc_final: 0.8031 (tp) REVERT: D 485 MET cc_start: 0.8738 (ttm) cc_final: 0.8326 (ttm) REVERT: D 643 ASP cc_start: 0.8160 (m-30) cc_final: 0.7777 (m-30) REVERT: D 695 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8625 (tptm) REVERT: D 788 LEU cc_start: 0.8763 (tp) cc_final: 0.8477 (tt) REVERT: D 868 TRP cc_start: 0.8611 (m-90) cc_final: 0.8323 (m-90) REVERT: D 1040 MET cc_start: 0.5753 (mtp) cc_final: 0.3949 (mmm) REVERT: E 62 GLN cc_start: 0.8940 (tm-30) cc_final: 0.8516 (tm-30) REVERT: E 67 ARG cc_start: 0.8773 (mmm-85) cc_final: 0.8560 (mmm-85) REVERT: M 180 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8564 (ttpt) REVERT: M 362 MET cc_start: 0.8786 (ptm) cc_final: 0.8307 (ppp) REVERT: M 423 LEU cc_start: 0.8903 (tp) cc_final: 0.8469 (pp) outliers start: 144 outliers final: 103 residues processed: 422 average time/residue: 0.1916 time to fit residues: 127.5768 Evaluate side-chains 388 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 273 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 366 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 696 ASP Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 184 ARG Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 296 ARG Chi-restraints excluded: chain M residue 317 GLN Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 354 optimal weight: 20.0000 chunk 142 optimal weight: 3.9990 chunk 160 optimal weight: 0.0770 chunk 178 optimal weight: 0.9980 chunk 302 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 254 optimal weight: 8.9990 chunk 268 optimal weight: 6.9990 chunk 15 optimal weight: 0.6980 chunk 214 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS B 194 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1314 GLN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 430 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 337 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.143681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.091976 restraints weight = 59707.864| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 3.77 r_work: 0.3072 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.5425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29487 Z= 0.148 Angle : 0.651 16.845 40324 Z= 0.319 Chirality : 0.043 0.228 4762 Planarity : 0.004 0.056 5045 Dihedral : 14.295 174.228 4818 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.48 % Favored : 91.44 % Rotamer: Outliers : 4.69 % Allowed : 22.72 % Favored : 72.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.79 (0.14), residues: 3655 helix: 0.59 (0.15), residues: 1299 sheet: -1.24 (0.29), residues: 299 loop : -2.51 (0.12), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG C 378 TYR 0.014 0.001 TYR D 679 PHE 0.016 0.001 PHE C 545 TRP 0.026 0.001 TRP A 321 HIS 0.015 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00346 (29487) covalent geometry : angle 0.65143 (40324) hydrogen bonds : bond 0.03604 ( 1008) hydrogen bonds : angle 4.06142 ( 2785) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 274 time to evaluate : 0.960 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: A 313 SER cc_start: 0.8456 (t) cc_final: 0.7703 (m) REVERT: A 317 ARG cc_start: 0.7549 (mmt180) cc_final: 0.7192 (mmp80) REVERT: B 18 GLN cc_start: 0.8953 (pm20) cc_final: 0.8429 (pp30) REVERT: B 43 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8789 (mp) REVERT: B 125 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8214 (ptmm) REVERT: B 186 ASN cc_start: 0.8811 (t0) cc_final: 0.8474 (t0) REVERT: C 120 GLN cc_start: 0.6820 (tt0) cc_final: 0.6467 (tt0) REVERT: C 183 TRP cc_start: 0.8677 (m-10) cc_final: 0.8268 (m100) REVERT: C 203 LYS cc_start: 0.8501 (mtmt) cc_final: 0.7964 (mtmt) REVERT: C 542 ARG cc_start: 0.7217 (mmp-170) cc_final: 0.6659 (mmt90) REVERT: C 545 PHE cc_start: 0.7824 (t80) cc_final: 0.7580 (t80) REVERT: C 589 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8632 (t) REVERT: C 628 HIS cc_start: 0.7892 (m90) cc_final: 0.7573 (m-70) REVERT: C 704 MET cc_start: 0.7284 (pmm) cc_final: 0.7023 (ptp) REVERT: C 844 LYS cc_start: 0.8727 (ptpt) cc_final: 0.8371 (ptpt) REVERT: C 936 ARG cc_start: 0.7491 (OUTLIER) cc_final: 0.6365 (ttm170) REVERT: C 954 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8812 (tptp) REVERT: C 1021 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8678 (tp) REVERT: C 1024 GLU cc_start: 0.9475 (OUTLIER) cc_final: 0.9086 (mm-30) REVERT: C 1032 LYS cc_start: 0.9332 (OUTLIER) cc_final: 0.8726 (ttpt) REVERT: C 1158 LYS cc_start: 0.8095 (tptm) cc_final: 0.7846 (tppt) REVERT: C 1161 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8378 (tt) REVERT: C 1200 LYS cc_start: 0.8746 (tptt) cc_final: 0.8439 (ttpt) REVERT: C 1222 GLU cc_start: 0.7317 (pm20) cc_final: 0.7090 (pm20) REVERT: C 1231 TYR cc_start: 0.9189 (t80) cc_final: 0.8958 (t80) REVERT: D 196 GLN cc_start: 0.8957 (tp-100) cc_final: 0.8703 (tm-30) REVERT: D 298 MET cc_start: 0.9130 (OUTLIER) cc_final: 0.8770 (mtp) REVERT: D 321 LYS cc_start: 0.8625 (OUTLIER) cc_final: 0.8302 (tppt) REVERT: D 342 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7920 (tp) REVERT: D 643 ASP cc_start: 0.8177 (m-30) cc_final: 0.7883 (m-30) REVERT: D 695 LYS cc_start: 0.8890 (OUTLIER) cc_final: 0.8651 (tptm) REVERT: D 788 LEU cc_start: 0.8761 (tp) cc_final: 0.8511 (tt) REVERT: D 868 TRP cc_start: 0.8641 (m-90) cc_final: 0.8331 (m-90) REVERT: D 1040 MET cc_start: 0.6111 (mtp) cc_final: 0.4257 (mmm) REVERT: E 62 GLN cc_start: 0.8963 (tm-30) cc_final: 0.8493 (tm-30) REVERT: M 180 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8567 (ttpt) REVERT: M 362 MET cc_start: 0.8840 (ptm) cc_final: 0.8303 (ppp) REVERT: M 423 LEU cc_start: 0.8926 (tp) cc_final: 0.8491 (pp) outliers start: 131 outliers final: 105 residues processed: 383 average time/residue: 0.1816 time to fit residues: 111.4463 Evaluate side-chains 384 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 265 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 882 ILE Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 184 ARG Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 317 GLN Chi-restraints excluded: chain M residue 337 ASN Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 345 optimal weight: 20.0000 chunk 44 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 285 optimal weight: 9.9990 chunk 120 optimal weight: 0.0980 chunk 178 optimal weight: 0.5980 chunk 270 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 0.2980 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS B 194 GLN C 214 ASN C 952 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1314 GLN D 335 GLN D 430 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.142904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.091788 restraints weight = 59718.205| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 3.69 r_work: 0.3070 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.5527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 29487 Z= 0.175 Angle : 0.667 17.166 40324 Z= 0.327 Chirality : 0.044 0.270 4762 Planarity : 0.004 0.056 5045 Dihedral : 14.299 174.222 4817 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.43 % Favored : 91.49 % Rotamer: Outliers : 5.20 % Allowed : 22.36 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.79 (0.14), residues: 3655 helix: 0.58 (0.15), residues: 1302 sheet: -1.25 (0.29), residues: 297 loop : -2.50 (0.12), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 378 TYR 0.014 0.001 TYR D 679 PHE 0.015 0.001 PHE C 545 TRP 0.023 0.001 TRP A 321 HIS 0.009 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00415 (29487) covalent geometry : angle 0.66730 (40324) hydrogen bonds : bond 0.03731 ( 1008) hydrogen bonds : angle 4.09169 ( 2785) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 275 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 SER cc_start: 0.8419 (t) cc_final: 0.7618 (m) REVERT: A 317 ARG cc_start: 0.7547 (mmt180) cc_final: 0.7187 (mmp80) REVERT: B 18 GLN cc_start: 0.8948 (pm20) cc_final: 0.8431 (pp30) REVERT: B 43 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8809 (mp) REVERT: B 125 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8126 (ptmm) REVERT: B 186 ASN cc_start: 0.8780 (t0) cc_final: 0.8438 (t0) REVERT: C 120 GLN cc_start: 0.6905 (tt0) cc_final: 0.6556 (tt0) REVERT: C 151 ARG cc_start: 0.8113 (ptm160) cc_final: 0.7908 (ptp-170) REVERT: C 183 TRP cc_start: 0.8689 (m-10) cc_final: 0.8280 (m100) REVERT: C 203 LYS cc_start: 0.8471 (mtmt) cc_final: 0.7942 (mtmt) REVERT: C 542 ARG cc_start: 0.7143 (mmp-170) cc_final: 0.6632 (mmt90) REVERT: C 545 PHE cc_start: 0.7859 (t80) cc_final: 0.7606 (t80) REVERT: C 589 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8651 (t) REVERT: C 628 HIS cc_start: 0.7911 (m90) cc_final: 0.7589 (m-70) REVERT: C 704 MET cc_start: 0.7348 (pmm) cc_final: 0.7111 (ptp) REVERT: C 844 LYS cc_start: 0.8684 (ptpt) cc_final: 0.8365 (ptpt) REVERT: C 903 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.9062 (ptp-170) REVERT: C 936 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6283 (ttm170) REVERT: C 954 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8801 (tptp) REVERT: C 1021 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8686 (tp) REVERT: C 1024 GLU cc_start: 0.9514 (OUTLIER) cc_final: 0.9119 (mm-30) REVERT: C 1032 LYS cc_start: 0.9335 (OUTLIER) cc_final: 0.8729 (ttpt) REVERT: C 1158 LYS cc_start: 0.8178 (tptm) cc_final: 0.7916 (tppt) REVERT: C 1161 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8364 (tt) REVERT: C 1200 LYS cc_start: 0.8755 (tptt) cc_final: 0.8457 (ttpt) REVERT: D 130 MET cc_start: 0.8432 (tmm) cc_final: 0.8098 (tmm) REVERT: D 196 GLN cc_start: 0.8944 (tp-100) cc_final: 0.8714 (tm-30) REVERT: D 298 MET cc_start: 0.9141 (OUTLIER) cc_final: 0.8793 (mtp) REVERT: D 314 ARG cc_start: 0.5215 (mtm-85) cc_final: 0.4182 (ttp80) REVERT: D 321 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8318 (tppt) REVERT: D 504 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.7910 (pt0) REVERT: D 643 ASP cc_start: 0.8183 (m-30) cc_final: 0.7931 (m-30) REVERT: D 695 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8658 (tptm) REVERT: D 697 MET cc_start: 0.8050 (tmm) cc_final: 0.7257 (tmm) REVERT: D 788 LEU cc_start: 0.8769 (tp) cc_final: 0.8524 (tt) REVERT: D 868 TRP cc_start: 0.8662 (m-90) cc_final: 0.8321 (m-90) REVERT: D 1040 MET cc_start: 0.6118 (mtp) cc_final: 0.4465 (mpp) REVERT: E 62 GLN cc_start: 0.8954 (tm-30) cc_final: 0.8481 (tm-30) REVERT: M 180 LYS cc_start: 0.8965 (OUTLIER) cc_final: 0.8574 (ttpt) REVERT: M 362 MET cc_start: 0.8835 (ptm) cc_final: 0.8336 (ppp) REVERT: M 386 THR cc_start: 0.8686 (OUTLIER) cc_final: 0.8462 (p) REVERT: M 423 LEU cc_start: 0.8904 (tp) cc_final: 0.8482 (pp) outliers start: 145 outliers final: 115 residues processed: 394 average time/residue: 0.1755 time to fit residues: 110.6708 Evaluate side-chains 396 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 265 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 903 ARG Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 931 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 184 ARG Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 317 GLN Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 258 optimal weight: 0.8980 chunk 355 optimal weight: 30.0000 chunk 127 optimal weight: 3.9990 chunk 100 optimal weight: 20.0000 chunk 201 optimal weight: 4.9990 chunk 76 optimal weight: 20.0000 chunk 213 optimal weight: 0.9990 chunk 236 optimal weight: 0.9990 chunk 286 optimal weight: 50.0000 chunk 70 optimal weight: 6.9990 chunk 114 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS C 952 GLN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1314 GLN D 335 GLN D 430 HIS ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 337 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.140976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.087256 restraints weight = 58726.801| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 3.29 r_work: 0.3036 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29487 Z= 0.176 Angle : 0.678 17.593 40324 Z= 0.332 Chirality : 0.044 0.331 4762 Planarity : 0.004 0.056 5045 Dihedral : 14.293 174.438 4816 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.67 % Favored : 91.24 % Rotamer: Outliers : 5.12 % Allowed : 22.43 % Favored : 72.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.74 (0.14), residues: 3655 helix: 0.62 (0.15), residues: 1296 sheet: -1.19 (0.30), residues: 285 loop : -2.46 (0.12), residues: 2074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 378 TYR 0.021 0.001 TYR C1231 PHE 0.015 0.001 PHE C 186 TRP 0.023 0.001 TRP A 321 HIS 0.011 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00416 (29487) covalent geometry : angle 0.67847 (40324) hydrogen bonds : bond 0.03721 ( 1008) hydrogen bonds : angle 4.09537 ( 2785) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 267 time to evaluate : 1.146 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: A 313 SER cc_start: 0.8342 (t) cc_final: 0.7503 (m) REVERT: A 317 ARG cc_start: 0.7480 (mmt180) cc_final: 0.7137 (mmp80) REVERT: B 18 GLN cc_start: 0.8976 (pm20) cc_final: 0.8418 (pp30) REVERT: B 43 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8786 (mp) REVERT: B 125 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8081 (ptmm) REVERT: B 137 ASN cc_start: 0.8994 (t0) cc_final: 0.8673 (t0) REVERT: B 186 ASN cc_start: 0.8810 (t0) cc_final: 0.8467 (t0) REVERT: C 120 GLN cc_start: 0.7082 (tt0) cc_final: 0.6681 (tt0) REVERT: C 151 ARG cc_start: 0.7985 (ptm160) cc_final: 0.7570 (ttp-170) REVERT: C 156 PHE cc_start: 0.8363 (m-10) cc_final: 0.7928 (m-10) REVERT: C 183 TRP cc_start: 0.8660 (m-10) cc_final: 0.8267 (m100) REVERT: C 203 LYS cc_start: 0.8491 (mtmt) cc_final: 0.7639 (mtmm) REVERT: C 542 ARG cc_start: 0.7097 (mmp-170) cc_final: 0.6588 (mtt-85) REVERT: C 589 THR cc_start: 0.8824 (OUTLIER) cc_final: 0.8609 (t) REVERT: C 628 HIS cc_start: 0.7836 (m90) cc_final: 0.7520 (m-70) REVERT: C 844 LYS cc_start: 0.8682 (ptpt) cc_final: 0.8337 (ptpt) REVERT: C 903 ARG cc_start: 0.9356 (OUTLIER) cc_final: 0.9045 (ptp-170) REVERT: C 936 ARG cc_start: 0.7350 (OUTLIER) cc_final: 0.6232 (ttm170) REVERT: C 954 LYS cc_start: 0.9107 (OUTLIER) cc_final: 0.8778 (tptp) REVERT: C 1017 GLN cc_start: 0.9344 (mm-40) cc_final: 0.8846 (mm110) REVERT: C 1021 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8664 (tp) REVERT: C 1024 GLU cc_start: 0.9514 (OUTLIER) cc_final: 0.9108 (mm-30) REVERT: C 1032 LYS cc_start: 0.9319 (OUTLIER) cc_final: 0.8711 (ttpt) REVERT: C 1158 LYS cc_start: 0.8281 (tptm) cc_final: 0.7963 (tppt) REVERT: C 1161 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8421 (tt) REVERT: C 1222 GLU cc_start: 0.7334 (pm20) cc_final: 0.7051 (pm20) REVERT: C 1314 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8481 (tp40) REVERT: D 196 GLN cc_start: 0.9012 (tp-100) cc_final: 0.8783 (tm-30) REVERT: D 298 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8757 (mtp) REVERT: D 314 ARG cc_start: 0.5290 (mtm-85) cc_final: 0.4202 (ttp80) REVERT: D 321 LYS cc_start: 0.8653 (pmtt) cc_final: 0.8270 (tppt) REVERT: D 485 MET cc_start: 0.8970 (ttm) cc_final: 0.8662 (ttm) REVERT: D 504 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7862 (pt0) REVERT: D 643 ASP cc_start: 0.8216 (m-30) cc_final: 0.7898 (m-30) REVERT: D 695 LYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8611 (tptm) REVERT: D 697 MET cc_start: 0.8057 (tmm) cc_final: 0.7301 (tmm) REVERT: D 788 LEU cc_start: 0.8796 (tp) cc_final: 0.8484 (tt) REVERT: D 868 TRP cc_start: 0.8658 (m-90) cc_final: 0.8287 (m-90) REVERT: D 1040 MET cc_start: 0.6011 (mtp) cc_final: 0.4437 (mpp) REVERT: E 62 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8485 (tm-30) REVERT: E 64 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8425 (mm) REVERT: E 67 ARG cc_start: 0.8818 (mmm-85) cc_final: 0.8616 (mmm-85) REVERT: M 180 LYS cc_start: 0.8901 (OUTLIER) cc_final: 0.8144 (tmtt) REVERT: M 362 MET cc_start: 0.8948 (ptm) cc_final: 0.8339 (ppp) REVERT: M 423 LEU cc_start: 0.8911 (tp) cc_final: 0.8501 (pp) outliers start: 143 outliers final: 117 residues processed: 385 average time/residue: 0.1880 time to fit residues: 116.0990 Evaluate side-chains 394 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 261 time to evaluate : 1.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 277 TYR Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 312 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 508 SER Chi-restraints excluded: chain C residue 533 LEU Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 903 ARG Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1011 LEU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 217 LEU Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 353 SER Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 393 THR Chi-restraints excluded: chain D residue 415 VAL Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 430 HIS Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 695 LYS Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 760 THR Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 120 LEU Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 184 ARG Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 317 GLN Chi-restraints excluded: chain M residue 337 ASN Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 140 optimal weight: 5.9990 chunk 235 optimal weight: 0.0170 chunk 249 optimal weight: 4.9990 chunk 48 optimal weight: 0.6980 chunk 92 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 223 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 40 optimal weight: 20.0000 chunk 221 optimal weight: 0.1980 overall best weight: 1.3822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS B 147 GLN C 214 ASN ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1314 GLN D 164 GLN D 335 GLN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 337 ASN ** 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 = 0.4108 r_free = 0.4108 target = 0.141849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.089225 restraints weight = 57570.004| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 3.22 r_work: 0.3069 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3074 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3074 r_free = 0.3074 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3074 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.5641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 29487 Z= 0.134 Angle : 0.662 17.759 40324 Z= 0.322 Chirality : 0.043 0.333 4762 Planarity : 0.004 0.057 5045 Dihedral : 14.254 174.553 4810 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.10 % Favored : 91.85 % Rotamer: Outliers : 4.73 % Allowed : 22.93 % Favored : 72.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.67 (0.14), residues: 3655 helix: 0.69 (0.15), residues: 1297 sheet: -1.22 (0.29), residues: 297 loop : -2.42 (0.12), residues: 2061 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 378 TYR 0.018 0.001 TYR C1231 PHE 0.022 0.001 PHE C 186 TRP 0.022 0.001 TRP A 321 HIS 0.008 0.001 HIS C 150 Details of bonding type rmsd covalent geometry : bond 0.00311 (29487) covalent geometry : angle 0.66240 (40324) hydrogen bonds : bond 0.03473 ( 1008) hydrogen bonds : angle 4.03187 ( 2785) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7310 Ramachandran restraints generated. 3655 Oldfield, 0 Emsley, 3655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 265 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 ARG cc_start: 0.7475 (mtm-85) cc_final: 0.7044 (mpp-170) REVERT: A 313 SER cc_start: 0.8333 (t) cc_final: 0.7494 (m) REVERT: B 18 GLN cc_start: 0.8959 (pm20) cc_final: 0.8427 (pp30) REVERT: B 43 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8719 (mp) REVERT: B 125 LYS cc_start: 0.8665 (OUTLIER) cc_final: 0.8155 (ptmm) REVERT: B 137 ASN cc_start: 0.8987 (t0) cc_final: 0.8667 (t0) REVERT: B 186 ASN cc_start: 0.8787 (t0) cc_final: 0.8450 (t0) REVERT: C 120 GLN cc_start: 0.7020 (tt0) cc_final: 0.6393 (tt0) REVERT: C 156 PHE cc_start: 0.8381 (m-10) cc_final: 0.8057 (m-10) REVERT: C 183 TRP cc_start: 0.8624 (m-10) cc_final: 0.8241 (m100) REVERT: C 203 LYS cc_start: 0.8455 (mtmt) cc_final: 0.7578 (mtmm) REVERT: C 488 MET cc_start: 0.8268 (OUTLIER) cc_final: 0.7870 (ptp) REVERT: C 542 ARG cc_start: 0.7002 (mmp-170) cc_final: 0.6528 (mtt-85) REVERT: C 589 THR cc_start: 0.8792 (OUTLIER) cc_final: 0.8578 (t) REVERT: C 628 HIS cc_start: 0.7830 (m90) cc_final: 0.7511 (m-70) REVERT: C 704 MET cc_start: 0.7082 (ptp) cc_final: 0.6731 (ptp) REVERT: C 844 LYS cc_start: 0.8673 (ptpt) cc_final: 0.8371 (ptpt) REVERT: C 903 ARG cc_start: 0.9348 (OUTLIER) cc_final: 0.9027 (ptp-170) REVERT: C 936 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.6227 (ttm170) REVERT: C 954 LYS cc_start: 0.9100 (OUTLIER) cc_final: 0.8782 (tptp) REVERT: C 1021 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8667 (tp) REVERT: C 1024 GLU cc_start: 0.9489 (OUTLIER) cc_final: 0.9174 (mm-30) REVERT: C 1032 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8709 (ttpt) REVERT: C 1158 LYS cc_start: 0.8178 (tptm) cc_final: 0.7963 (tppt) REVERT: C 1161 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8368 (tt) REVERT: C 1200 LYS cc_start: 0.8684 (tptt) cc_final: 0.8336 (ttpt) REVERT: C 1222 GLU cc_start: 0.7192 (pm20) cc_final: 0.6837 (pm20) REVERT: D 130 MET cc_start: 0.8354 (tmm) cc_final: 0.7892 (tmm) REVERT: D 196 GLN cc_start: 0.8969 (tp-100) cc_final: 0.8745 (tm-30) REVERT: D 298 MET cc_start: 0.9136 (tpp) cc_final: 0.8766 (mtp) REVERT: D 321 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8234 (tppt) REVERT: D 485 MET cc_start: 0.8917 (ttm) cc_final: 0.8576 (ttm) REVERT: D 504 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7827 (pt0) REVERT: D 643 ASP cc_start: 0.8140 (m-30) cc_final: 0.7838 (m-30) REVERT: D 697 MET cc_start: 0.8035 (tmm) cc_final: 0.7299 (tmm) REVERT: D 788 LEU cc_start: 0.8802 (tp) cc_final: 0.8466 (tt) REVERT: D 868 TRP cc_start: 0.8655 (m-90) cc_final: 0.8288 (m-90) REVERT: D 1040 MET cc_start: 0.5906 (mtp) cc_final: 0.4340 (mpp) REVERT: E 62 GLN cc_start: 0.8917 (tm-30) cc_final: 0.8449 (tm-30) REVERT: E 64 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8433 (mm) REVERT: M 180 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8193 (tmtt) REVERT: M 362 MET cc_start: 0.8993 (ptm) cc_final: 0.8429 (ppp) REVERT: M 423 LEU cc_start: 0.8949 (tp) cc_final: 0.8549 (pp) outliers start: 132 outliers final: 103 residues processed: 373 average time/residue: 0.1777 time to fit residues: 106.5027 Evaluate side-chains 380 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 262 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 23 HIS Chi-restraints excluded: chain A residue 54 CYS Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 23 HIS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 121 VAL Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 144 ILE Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 210 LEU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ILE Chi-restraints excluded: chain C residue 310 ILE Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 488 MET Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 630 VAL Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 733 VAL Chi-restraints excluded: chain C residue 741 MET Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 764 CYS Chi-restraints excluded: chain C residue 817 LEU Chi-restraints excluded: chain C residue 826 ASP Chi-restraints excluded: chain C residue 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 903 ARG Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 925 SER Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 933 VAL Chi-restraints excluded: chain C residue 936 ARG Chi-restraints excluded: chain C residue 954 LYS Chi-restraints excluded: chain C residue 975 ILE Chi-restraints excluded: chain C residue 1011 LEU Chi-restraints excluded: chain C residue 1021 LEU Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1036 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1161 LEU Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 164 GLN Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 321 LYS Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 387 LEU Chi-restraints excluded: chain D residue 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 504 GLN Chi-restraints excluded: chain D residue 544 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 707 ILE Chi-restraints excluded: chain D residue 743 MET Chi-restraints excluded: chain D residue 803 VAL Chi-restraints excluded: chain D residue 831 VAL Chi-restraints excluded: chain D residue 839 VAL Chi-restraints excluded: chain D residue 842 ARG Chi-restraints excluded: chain D residue 894 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1011 VAL Chi-restraints excluded: chain D residue 1309 ILE Chi-restraints excluded: chain E residue 3 ARG Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain M residue 25 LEU Chi-restraints excluded: chain M residue 26 LEU Chi-restraints excluded: chain M residue 46 LEU Chi-restraints excluded: chain M residue 111 VAL Chi-restraints excluded: chain M residue 151 THR Chi-restraints excluded: chain M residue 153 TYR Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 172 LEU Chi-restraints excluded: chain M residue 174 GLU Chi-restraints excluded: chain M residue 180 LYS Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 253 ILE Chi-restraints excluded: chain M residue 266 THR Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 294 ILE Chi-restraints excluded: chain M residue 317 GLN Chi-restraints excluded: chain M residue 390 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 342 optimal weight: 7.9990 chunk 318 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 264 optimal weight: 0.5980 chunk 262 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 333 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 235 optimal weight: 2.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 HIS ** C1268 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 GLN ** D 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN ** D 865 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 337 ASN ** 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 = 0.4078 r_free = 0.4078 target = 0.139632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.085334 restraints weight = 59269.121| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 3.26 r_work: 0.3006 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3013 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 29487 Z= 0.237 Angle : 0.717 15.222 40324 Z= 0.356 Chirality : 0.046 0.339 4762 Planarity : 0.005 0.056 5045 Dihedral : 14.308 174.950 4804 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.36 % Favored : 90.59 % Rotamer: Outliers : 4.59 % Allowed : 22.68 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.79 (0.13), residues: 3655 helix: 0.54 (0.15), residues: 1302 sheet: -1.28 (0.30), residues: 275 loop : -2.46 (0.12), residues: 2078 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 378 TYR 0.024 0.002 TYR C1231 PHE 0.026 0.002 PHE C 186 TRP 0.025 0.002 TRP A 321 HIS 0.027 0.001 HIS A 23 Details of bonding type rmsd covalent geometry : bond 0.00564 (29487) covalent geometry : angle 0.71729 (40324) hydrogen bonds : bond 0.04157 ( 1008) hydrogen bonds : angle 4.19987 ( 2785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8998.37 seconds wall clock time: 154 minutes 8.89 seconds (9248.89 seconds total)