Starting phenix.real_space_refine on Mon Sep 14 06:45:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7qxi_14200/09_2026/7qxi_14200.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qxi_14200/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/7qxi_14200/09_2026/7qxi_14200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qxi_14200/09_2026/7qxi_14200.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qxi_14200/09_2026/7qxi_14200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qxi_14200/09_2026/7qxi_14200.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 6.08, per 1000 atoms: 0.21 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: 2.82 Conformation dependent library (CDL) restraints added in 1.5 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: 4.80 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: 8.63 Time building geometry restraints manager: 3.68 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=" C4' DG N -10 " pdb=" O4' DG N -10 " ideal model delta sigma weight residual 1.446 1.605 -0.159 1.00e-02 1.00e+04 2.53e+02 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' DC N -13 " pdb=" O4' DC N -13 " ideal model delta sigma weight residual 1.446 1.349 0.097 1.00e-02 1.00e+04 9.33e+01 bond pdb=" C4' DC T 10 " pdb=" O4' DC T 10 " ideal model delta sigma weight residual 1.446 1.541 -0.095 1.00e-02 1.00e+04 9.06e+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 ... (remaining 29482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.26: 40032 4.26 - 8.51: 261 8.51 - 12.77: 28 12.77 - 17.03: 2 17.03 - 21.28: 1 Bond angle restraints: 40324 Sorted by residual: angle pdb=" O4' DC T 10 " pdb=" C4' DC T 10 " pdb=" C3' DC T 10 " ideal model delta sigma weight residual 106.00 96.34 9.66 6.00e-01 2.78e+00 2.59e+02 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 1.90e+00 2.77e-01 1.25e+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=" C4' DG N -10 " pdb=" O4' DG N -10 " pdb=" C1' DG N -10 " ideal model delta sigma weight residual 110.10 101.73 8.37 1.00e+00 1.00e+00 7.00e+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: 4626 0.130 - 0.260: 108 0.260 - 0.390: 19 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 -0.64 2.00e-01 2.50e+01 1.01e+01 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 0.59 2.00e-01 2.50e+01 8.69e+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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 33.860 Find NCS groups from input model: 0.230 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 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 0.159 29487 Z= 0.392 Angle : 0.954 21.284 40324 Z= 0.627 Chirality : 0.059 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/Z covalent geometry : bond 0.00579 / 0.39 (29487) covalent geometry : angle 0.95399 / 0.63 (40324) hydrogen bonds : bond 0.20643 / 14.46 ( 1008) hydrogen bonds : angle 7.13935 / 4.94 ( 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 : 1.114 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: 0.7695 (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: 0.4205 (mmmt) 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: 0.2190 time to fit residues: 350.4492 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 : 1.051 ------------------------------------------------------------------------------- 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... A 132 HIS B 37 HIS C 150 HIS C 462 ASN C 526 HIS ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 659 GLN C1009 ASN C1038 GLN C1256 GLN C1314 GLN D 104 HIS ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 430 HIS D 777 HIS D1238 GLN M 34 GLN M 39 GLN M 127 GLN M 229 ASN M 254 GLN M 322 ASN M 387 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.160170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.111855 restraints weight = 61516.449| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.18 r_work: 0.3562 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3530 r_free = 0.3530 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3529 r_free = 0.3529 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29487 Z= 0.163 Angle : 0.754 25.377 40324 Z= 0.370 Chirality : 0.047 0.424 4762 Planarity : 0.006 0.093 5045 Dihedral : 15.817 175.998 5080 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.61 % Favored : 92.28 % Rotamer: Outliers : 7.24 % Allowed : 17.59 % Favored : 75.17 % 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: -2.86 (0.13), residues: 3655 helix: -0.32 (0.15), residues: 1252 sheet: -1.96 (0.27), residues: 327 loop : -3.06 (0.11), residues: 2076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 77 TYR 0.021 0.002 TYR B 68 PHE 0.021 0.002 PHE M 318 TRP 0.036 0.002 TRP A 321 HIS 0.012 0.001 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.16 (29487) covalent geometry : angle 0.75386 / 0.37 (40324) hydrogen bonds : bond 0.04812 / 3.37 ( 1008) hydrogen bonds : angle 4.75248 / 3.28 ( 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 603 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 202 poor density : 401 time to evaluate : 1.047 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 7 GLU cc_start: 0.6900 (OUTLIER) cc_final: 0.6684 (mp0) REVERT: A 93 GLN cc_start: 0.8330 (tp-100) cc_final: 0.7854 (mp10) REVERT: A 127 GLN cc_start: 0.8908 (mp10) cc_final: 0.8654 (mp10) REVERT: A 313 SER cc_start: 0.8329 (t) cc_final: 0.7775 (p) REVERT: B 145 LYS cc_start: 0.8644 (ptpt) cc_final: 0.8123 (ptmm) REVERT: B 147 GLN cc_start: 0.8110 (tt0) cc_final: 0.7701 (tm-30) REVERT: B 186 ASN cc_start: 0.8379 (t0) cc_final: 0.8068 (t0) REVERT: C 183 TRP cc_start: 0.8099 (m-10) cc_final: 0.7793 (m-10) REVERT: C 203 LYS cc_start: 0.8263 (mtmt) cc_final: 0.7609 (mtmm) REVERT: C 345 PRO cc_start: 0.9378 (Cg_endo) cc_final: 0.9126 (Cg_exo) REVERT: C 385 PHE cc_start: 0.8652 (t80) cc_final: 0.8358 (t80) REVERT: C 407 ARG cc_start: 0.8636 (mmm-85) cc_final: 0.8351 (mmm-85) REVERT: C 503 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7709 (mttp) REVERT: C 542 ARG cc_start: 0.6415 (OUTLIER) cc_final: 0.6192 (ttm170) REVERT: C 545 PHE cc_start: 0.7114 (t80) cc_final: 0.6781 (t80) REVERT: C 589 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8418 (t) REVERT: C 639 LYS cc_start: 0.8316 (mmtm) cc_final: 0.8081 (mmtm) REVERT: C 766 ASN cc_start: 0.8394 (t0) cc_final: 0.8163 (t0) REVERT: C 838 CYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8630 (p) REVERT: C 890 LYS cc_start: 0.8264 (OUTLIER) cc_final: 0.7893 (tmmt) REVERT: C 903 ARG cc_start: 0.9346 (OUTLIER) cc_final: 0.9139 (ptm160) REVERT: C 954 LYS cc_start: 0.9296 (OUTLIER) cc_final: 0.8994 (tmmm) REVERT: C 962 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8101 (tp30) REVERT: C 973 SER cc_start: 0.9536 (OUTLIER) cc_final: 0.9267 (m) REVERT: C 1018 TYR cc_start: 0.8979 (t80) cc_final: 0.8724 (t80) REVERT: C 1021 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8637 (tp) REVERT: C 1022 LYS cc_start: 0.9456 (OUTLIER) cc_final: 0.9085 (mmtm) REVERT: C 1024 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.8977 (mm-30) REVERT: C 1032 LYS cc_start: 0.9336 (OUTLIER) cc_final: 0.8724 (ttpt) REVERT: C 1038 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: C 1051 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8557 (mtpp) REVERT: C 1161 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8201 (tt) REVERT: C 1230 MET cc_start: 0.8642 (ptm) cc_final: 0.8342 (ttp) REVERT: C 1304 MET cc_start: 0.8889 (tpp) cc_final: 0.8608 (tpp) REVERT: C 1314 GLN cc_start: 0.8633 (OUTLIER) cc_final: 0.8416 (mt0) REVERT: D 4 LEU cc_start: 0.7958 (OUTLIER) cc_final: 0.7134 (tt) REVERT: D 227 PHE cc_start: 0.8800 (t80) cc_final: 0.8082 (t80) REVERT: D 321 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8410 (tppt) REVERT: D 536 LEU cc_start: 0.6730 (tt) cc_final: 0.6097 (tt) REVERT: D 695 LYS cc_start: 0.8697 (OUTLIER) cc_final: 0.8418 (tptm) REVERT: D 697 MET cc_start: 0.7651 (tpp) cc_final: 0.7407 (tpp) REVERT: D 788 LEU cc_start: 0.8095 (tt) cc_final: 0.7773 (mm) REVERT: D 1040 MET cc_start: 0.4607 (mtp) cc_final: 0.3530 (mmm) REVERT: E 10 VAL cc_start: 0.8121 (t) cc_final: 0.7868 (t) REVERT: E 43 ASN cc_start: 0.7838 (t0) cc_final: 0.7569 (t0) REVERT: M 127 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.8474 (mt0) REVERT: M 180 LYS cc_start: 0.9025 (OUTLIER) cc_final: 0.8255 (tmtt) REVERT: M 265 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.6580 (mt0) REVERT: M 280 LYS cc_start: 0.7905 (OUTLIER) cc_final: 0.7390 (mmmt) REVERT: M 297 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7463 (mm) REVERT: M 306 MET cc_start: 0.8333 (mtt) cc_final: 0.8017 (ptp) outliers start: 202 outliers final: 93 residues processed: 573 average time/residue: 0.1984 time to fit residues: 178.9545 Evaluate side-chains 426 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 307 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 GLU 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 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 27 LEU 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 177 ILE 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 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 603 ILE Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 748 ILE Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 834 GLN 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 864 LYS Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 887 VAL Chi-restraints excluded: chain C residue 890 LYS Chi-restraints excluded: chain C residue 903 ARG Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 922 ASN Chi-restraints excluded: chain C residue 927 THR 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 973 SER Chi-restraints excluded: chain C residue 1011 LEU 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 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 1237 HIS Chi-restraints excluded: chain C residue 1314 GLN Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 72 CYS Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 VAL 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 421 VAL Chi-restraints excluded: chain D residue 428 THR 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 672 LEU 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 839 VAL Chi-restraints excluded: chain D residue 930 LEU Chi-restraints excluded: chain D residue 1144 LEU Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 6 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain M residue 25 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 127 GLN Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain M residue 150 ASP 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 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 201 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 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 Chi-restraints excluded: chain M residue 391 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 353 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 301 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 166 optimal weight: 5.9990 chunk 227 optimal weight: 0.9980 chunk 233 optimal weight: 4.9990 chunk 367 optimal weight: 50.0000 chunk 220 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 227 GLN A 283 GLN ** C 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 513 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1236 ASN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 477 GLN D 504 GLN D 777 HIS M 127 GLN M 229 ASN M 265 GLN M 322 ASN M 337 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.151830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.103645 restraints weight = 60772.951| |-----------------------------------------------------------------------------| r_work (start): 0.3546 rms_B_bonded: 3.44 r_work: 0.3318 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3285 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3285 r_free = 0.3285 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3285 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.3995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 29487 Z= 0.220 Angle : 0.753 15.696 40324 Z= 0.374 Chirality : 0.047 0.404 4762 Planarity : 0.005 0.066 5045 Dihedral : 15.076 175.337 4904 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.07 % Favored : 91.85 % Rotamer: Outliers : 6.23 % Allowed : 18.67 % Favored : 75.10 % 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: -2.50 (0.13), residues: 3655 helix: 0.07 (0.15), residues: 1262 sheet: -1.69 (0.27), residues: 341 loop : -2.94 (0.12), residues: 2052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D1140 TYR 0.018 0.002 TYR C1231 PHE 0.028 0.002 PHE C 230 TRP 0.048 0.002 TRP A 321 HIS 0.019 0.002 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.22 (29487) covalent geometry : angle 0.75285 / 0.37 (40324) hydrogen bonds : bond 0.04783 / 3.31 ( 1008) hydrogen bonds : angle 4.47409 / 3.10 ( 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 502 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 174 poor density : 328 time to evaluate : 1.030 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 7 GLU cc_start: 0.7188 (OUTLIER) cc_final: 0.6929 (mp0) REVERT: A 127 GLN cc_start: 0.9021 (mp10) cc_final: 0.8805 (mp10) REVERT: A 183 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8749 (mm) REVERT: A 313 SER cc_start: 0.8571 (t) cc_final: 0.8298 (p) REVERT: B 43 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8851 (mp) REVERT: B 145 LYS cc_start: 0.8763 (ptpt) cc_final: 0.8337 (ptpp) REVERT: B 147 GLN cc_start: 0.8062 (tt0) cc_final: 0.7817 (tm-30) REVERT: B 186 ASN cc_start: 0.8502 (t0) cc_final: 0.8209 (t0) REVERT: C 186 PHE cc_start: 0.7514 (m-80) cc_final: 0.7144 (m-80) REVERT: C 203 LYS cc_start: 0.8328 (mtmt) cc_final: 0.7609 (mtmm) REVERT: C 239 MET cc_start: 0.8236 (mmm) cc_final: 0.8020 (mmt) REVERT: C 385 PHE cc_start: 0.8736 (t80) cc_final: 0.8474 (t80) REVERT: C 407 ARG cc_start: 0.8759 (mmm-85) cc_final: 0.8385 (ttm170) REVERT: C 542 ARG cc_start: 0.6672 (mmp-170) cc_final: 0.6392 (ttm170) REVERT: C 545 PHE cc_start: 0.7191 (t80) cc_final: 0.6900 (t80) REVERT: C 589 THR cc_start: 0.8986 (OUTLIER) cc_final: 0.8639 (t) REVERT: C 628 HIS cc_start: 0.8004 (m90) cc_final: 0.7669 (m90) REVERT: C 639 LYS cc_start: 0.8388 (mmtm) cc_final: 0.8055 (mmtm) REVERT: C 681 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8257 (mtm) REVERT: C 685 MET cc_start: 0.8137 (mtm) cc_final: 0.7925 (mtt) REVERT: C 694 ARG cc_start: 0.7642 (mpp80) cc_final: 0.7285 (mtp85) REVERT: C 760 ASN cc_start: 0.8948 (m-40) cc_final: 0.8724 (m-40) REVERT: C 844 LYS cc_start: 0.8671 (ptpt) cc_final: 0.8315 (ptpt) REVERT: C 954 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8936 (tptp) REVERT: C 1021 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8749 (tp) REVERT: C 1022 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.8969 (mmtm) REVERT: C 1024 GLU cc_start: 0.9309 (OUTLIER) cc_final: 0.8994 (mm-30) REVERT: C 1032 LYS cc_start: 0.9374 (OUTLIER) cc_final: 0.8814 (ttpt) REVERT: C 1038 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: C 1064 ASP cc_start: 0.8089 (m-30) cc_final: 0.7781 (m-30) REVERT: C 1200 LYS cc_start: 0.8474 (tptt) cc_final: 0.8138 (ttmt) REVERT: D 159 ILE cc_start: 0.8786 (OUTLIER) cc_final: 0.8490 (tp) REVERT: D 222 LYS cc_start: 0.9030 (mtpt) cc_final: 0.8701 (mmtm) REVERT: D 321 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8484 (tppt) REVERT: D 643 ASP cc_start: 0.7651 (m-30) cc_final: 0.7438 (m-30) REVERT: D 695 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8592 (tptm) REVERT: D 1040 MET cc_start: 0.4681 (mtp) cc_final: 0.3480 (mmm) REVERT: D 1143 ASP cc_start: 0.7555 (m-30) cc_final: 0.7086 (t0) REVERT: E 43 ASN cc_start: 0.8165 (t0) cc_final: 0.7863 (t0) REVERT: M 125 MET cc_start: 0.9041 (mmm) cc_final: 0.8799 (mmm) REVERT: M 180 LYS cc_start: 0.9097 (OUTLIER) cc_final: 0.8824 (tptp) REVERT: M 236 MET cc_start: 0.8041 (mmt) cc_final: 0.7824 (mmt) REVERT: M 280 LYS cc_start: 0.8022 (OUTLIER) cc_final: 0.7670 (mmmt) REVERT: M 362 MET cc_start: 0.8782 (ptm) cc_final: 0.8380 (ppp) outliers start: 174 outliers final: 103 residues processed: 479 average time/residue: 0.1901 time to fit residues: 144.0703 Evaluate side-chains 391 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 272 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 65 LEU 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 289 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 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 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 538 LEU Chi-restraints excluded: chain C residue 576 SER Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 603 ILE Chi-restraints excluded: chain C residue 635 THR Chi-restraints excluded: chain C residue 681 MET Chi-restraints excluded: chain C residue 712 SER Chi-restraints excluded: chain C residue 817 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 865 LEU Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 922 ASN 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 1009 ASN Chi-restraints excluded: chain C residue 1011 LEU 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 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 1191 LYS Chi-restraints excluded: chain C residue 1217 THR Chi-restraints excluded: chain C residue 1230 MET Chi-restraints excluded: chain C residue 1254 VAL Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain C residue 1332 SER Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 93 THR Chi-restraints excluded: chain D residue 97 VAL 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 285 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 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 622 ASP 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 743 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 801 VAL 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 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 6 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 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 180 LYS Chi-restraints excluded: chain M residue 184 ARG Chi-restraints excluded: chain M residue 188 VAL Chi-restraints excluded: chain M residue 203 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 279 ARG Chi-restraints excluded: chain M residue 280 LYS 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: 3.9990 chunk 122 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 151 optimal weight: 0.3980 chunk 76 optimal weight: 30.0000 chunk 98 optimal weight: 5.9990 chunk 181 optimal weight: 2.9990 chunk 82 optimal weight: 10.0000 chunk 363 optimal weight: 20.0000 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN C 214 ASN C 238 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1061 GLN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.151084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.098673 restraints weight = 60094.567| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 3.35 r_work: 0.3272 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3270 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3270 r_free = 0.3270 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3270 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 29487 Z= 0.195 Angle : 0.691 16.220 40324 Z= 0.341 Chirality : 0.046 0.402 4762 Planarity : 0.004 0.059 5045 Dihedral : 14.785 173.774 4851 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.74 % Favored : 92.18 % Rotamer: Outliers : 5.91 % Allowed : 19.81 % Favored : 74.27 % 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: -2.26 (0.13), residues: 3655 helix: 0.25 (0.15), residues: 1273 sheet: -1.55 (0.29), residues: 322 loop : -2.79 (0.12), residues: 2060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 255 TYR 0.016 0.001 TYR C1231 PHE 0.018 0.001 PHE M 318 TRP 0.036 0.002 TRP A 321 HIS 0.010 0.001 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.19 (29487) covalent geometry : angle 0.69134 / 0.34 (40324) hydrogen bonds : bond 0.04190 / 2.90 ( 1008) hydrogen bonds : angle 4.30818 / 2.99 ( 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 454 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 289 time to evaluate : 0.852 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 7 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6879 (mp0) REVERT: A 127 GLN cc_start: 0.9073 (mp10) cc_final: 0.8810 (mp10) REVERT: A 183 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8811 (mm) REVERT: A 195 ARG cc_start: 0.7475 (tmt170) cc_final: 0.7191 (tmt170) REVERT: A 313 SER cc_start: 0.8497 (t) cc_final: 0.8204 (p) REVERT: B 43 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8843 (mp) REVERT: B 145 LYS cc_start: 0.8690 (ptpt) cc_final: 0.8290 (ptpp) REVERT: B 147 GLN cc_start: 0.8090 (tt0) cc_final: 0.7772 (tm-30) REVERT: B 186 ASN cc_start: 0.8585 (t0) cc_final: 0.8270 (t0) REVERT: C 183 TRP cc_start: 0.8375 (m-10) cc_final: 0.7990 (m100) REVERT: C 186 PHE cc_start: 0.7380 (m-80) cc_final: 0.7080 (m-80) REVERT: C 203 LYS cc_start: 0.8332 (mtmt) cc_final: 0.7595 (mtmm) REVERT: C 352 ARG cc_start: 0.9048 (ptp-170) cc_final: 0.8560 (mtp85) REVERT: C 385 PHE cc_start: 0.8750 (t80) cc_final: 0.8482 (t80) REVERT: C 542 ARG cc_start: 0.6743 (mmp-170) cc_final: 0.6405 (ttm170) REVERT: C 545 PHE cc_start: 0.7221 (t80) cc_final: 0.6961 (t80) REVERT: C 589 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8673 (t) REVERT: C 639 LYS cc_start: 0.8455 (mmtm) cc_final: 0.8106 (mmtm) REVERT: C 844 LYS cc_start: 0.8652 (ptpt) cc_final: 0.8318 (ptpt) REVERT: C 954 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8893 (tptp) REVERT: C 1021 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8677 (tp) REVERT: C 1022 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9188 (pttp) REVERT: C 1024 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.9039 (mm-30) REVERT: C 1032 LYS cc_start: 0.9327 (OUTLIER) cc_final: 0.8692 (ttpt) REVERT: C 1038 GLN cc_start: 0.8673 (OUTLIER) cc_final: 0.8290 (tm-30) REVERT: D 222 LYS cc_start: 0.9081 (mtpt) cc_final: 0.8737 (mmtm) REVERT: D 239 LEU cc_start: 0.8727 (OUTLIER) cc_final: 0.8415 (pp) REVERT: D 321 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8480 (tppt) REVERT: D 643 ASP cc_start: 0.7777 (m-30) cc_final: 0.7536 (m-30) REVERT: D 695 LYS cc_start: 0.8815 (OUTLIER) cc_final: 0.8512 (tptm) REVERT: D 868 TRP cc_start: 0.8500 (m-90) cc_final: 0.8163 (m-90) REVERT: D 1040 MET cc_start: 0.4852 (mtp) cc_final: 0.3638 (mpp) REVERT: M 125 MET cc_start: 0.9016 (mmm) cc_final: 0.8785 (mmm) REVERT: M 180 LYS cc_start: 0.9055 (OUTLIER) cc_final: 0.8783 (tptp) REVERT: M 236 MET cc_start: 0.8093 (mmt) cc_final: 0.7758 (mmt) REVERT: M 362 MET cc_start: 0.8773 (ptm) cc_final: 0.8305 (ppp) REVERT: M 423 LEU cc_start: 0.8371 (tp) cc_final: 0.7849 (pp) outliers start: 165 outliers final: 112 residues processed: 432 average time/residue: 0.1874 time to fit residues: 128.9918 Evaluate side-chains 392 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 266 time to evaluate : 0.888 ------------------------------------------------------------------------------- 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 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 A residue 289 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 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 27 LEU 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 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 479 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 635 THR Chi-restraints excluded: chain C residue 696 ASP 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 838 CYS Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 864 LYS Chi-restraints excluded: chain C residue 865 LEU Chi-restraints excluded: chain C residue 873 ILE Chi-restraints excluded: chain C residue 913 VAL Chi-restraints excluded: chain C residue 922 ASN 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 1009 ASN 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 1032 LYS Chi-restraints excluded: chain C residue 1038 GLN Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1151 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 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 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 421 VAL 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 615 LYS Chi-restraints excluded: chain D residue 622 ASP 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 801 VAL 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 874 GLU 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 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 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 180 LYS Chi-restraints excluded: chain M residue 188 VAL 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 279 ARG 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: 30.0000 chunk 299 optimal weight: 20.0000 chunk 121 optimal weight: 2.9990 chunk 153 optimal weight: 10.0000 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 30.0000 chunk 267 optimal weight: 8.9990 chunk 69 optimal weight: 8.9990 chunk 303 optimal weight: 0.3980 chunk 348 optimal weight: 8.9990 chunk 142 optimal weight: 8.9990 overall best weight: 4.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN C 214 ASN C 238 GLN ** 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 = 0.4202 r_free = 0.4202 target = 0.146804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.092612 restraints weight = 60184.338| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 3.47 r_work: 0.3150 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 29487 Z= 0.287 Angle : 0.767 15.890 40324 Z= 0.386 Chirality : 0.049 0.394 4762 Planarity : 0.005 0.061 5045 Dihedral : 14.866 174.116 4837 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.89 % Favored : 91.03 % Rotamer: Outliers : 7.13 % Allowed : 19.31 % Favored : 73.56 % 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: -2.34 (0.13), residues: 3655 helix: 0.05 (0.15), residues: 1295 sheet: -1.39 (0.30), residues: 293 loop : -2.80 (0.12), residues: 2067 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 293 TYR 0.047 0.002 TYR D 144 PHE 0.021 0.002 PHE D 437 TRP 0.033 0.002 TRP A 321 HIS 0.018 0.002 HIS C 150 Details of bonding type rmsd/Z covalent geometry : bond 0.00672 / 0.29 (29487) covalent geometry : angle 0.76652 / 0.39 (40324) hydrogen bonds : bond 0.04889 / 3.37 ( 1008) hydrogen bonds : angle 4.47104 / 3.11 ( 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 478 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 279 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7304 (OUTLIER) cc_final: 0.7058 (mp0) REVERT: A 127 GLN cc_start: 0.9200 (mp10) cc_final: 0.8946 (mp10) REVERT: A 183 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9097 (mm) REVERT: A 313 SER cc_start: 0.8556 (t) cc_final: 0.8179 (p) REVERT: B 43 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8961 (mp) REVERT: B 145 LYS cc_start: 0.8707 (ptpt) cc_final: 0.8407 (ptpp) REVERT: B 186 ASN cc_start: 0.8653 (t0) cc_final: 0.8352 (t0) REVERT: C 183 TRP cc_start: 0.8557 (m-10) cc_final: 0.8189 (m100) REVERT: C 203 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8030 (mtmt) REVERT: C 488 MET cc_start: 0.7127 (ppp) cc_final: 0.6336 (ppp) REVERT: C 542 ARG cc_start: 0.7063 (mmp-170) cc_final: 0.6550 (mmt90) REVERT: C 545 PHE cc_start: 0.7478 (t80) cc_final: 0.7239 (t80) REVERT: C 589 THR cc_start: 0.9045 (OUTLIER) cc_final: 0.8807 (t) REVERT: C 628 HIS cc_start: 0.8097 (m90) cc_final: 0.7708 (m90) REVERT: C 826 ASP cc_start: 0.8550 (OUTLIER) cc_final: 0.8174 (t0) REVERT: C 844 LYS cc_start: 0.8717 (ptpt) cc_final: 0.8296 (ptpt) REVERT: C 864 LYS cc_start: 0.8577 (OUTLIER) cc_final: 0.8369 (mtmm) REVERT: C 954 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8844 (tptp) REVERT: C 1021 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8669 (tp) REVERT: C 1022 LYS cc_start: 0.9463 (OUTLIER) cc_final: 0.9114 (pttp) REVERT: C 1024 GLU cc_start: 0.9417 (OUTLIER) cc_final: 0.9112 (mm-30) REVERT: C 1032 LYS cc_start: 0.9375 (OUTLIER) cc_final: 0.8740 (ttpt) REVERT: C 1038 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.8366 (tm-30) REVERT: D 159 ILE cc_start: 0.8918 (OUTLIER) cc_final: 0.8699 (tp) REVERT: D 222 LYS cc_start: 0.9116 (mtpt) cc_final: 0.8728 (mmtm) REVERT: D 298 MET cc_start: 0.9051 (OUTLIER) cc_final: 0.8690 (mtp) REVERT: D 321 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8537 (tppt) REVERT: D 466 MET cc_start: 0.8971 (tpt) cc_final: 0.8605 (tpt) REVERT: D 643 ASP cc_start: 0.8121 (m-30) cc_final: 0.7834 (m-30) REVERT: D 695 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8665 (tptm) REVERT: D 697 MET cc_start: 0.8021 (tmm) cc_final: 0.7027 (tmm) REVERT: D 788 LEU cc_start: 0.8806 (tp) cc_final: 0.8584 (tt) REVERT: D 802 ASP cc_start: 0.8785 (m-30) cc_final: 0.8552 (m-30) REVERT: D 868 TRP cc_start: 0.8564 (m-90) cc_final: 0.8135 (m-90) REVERT: D 1040 MET cc_start: 0.5237 (mtp) cc_final: 0.3520 (mmm) REVERT: D 1143 ASP cc_start: 0.7749 (m-30) cc_final: 0.7130 (t0) REVERT: E 62 GLN cc_start: 0.8765 (tm-30) cc_final: 0.8540 (tm-30) REVERT: M 180 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8696 (tptp) REVERT: M 297 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7409 (mm) REVERT: M 362 MET cc_start: 0.8785 (ptm) cc_final: 0.8186 (ppp) REVERT: M 423 LEU cc_start: 0.8839 (tp) cc_final: 0.8487 (pp) outliers start: 199 outliers final: 141 residues processed: 450 average time/residue: 0.1909 time to fit residues: 137.6925 Evaluate side-chains 412 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 159 poor density : 253 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 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 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 A residue 287 VAL Chi-restraints excluded: chain A residue 289 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 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 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 27 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 46 GLN 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 146 VAL Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 208 ILE 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 414 ILE Chi-restraints excluded: chain C residue 455 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 635 THR Chi-restraints excluded: chain C residue 660 VAL 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 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 864 LYS 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 922 ASN 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 1009 ASN 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 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 1096 ILE Chi-restraints excluded: chain C residue 1114 GLU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1191 LYS 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 1337 ILE Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 37 GLU Chi-restraints excluded: chain D residue 93 THR 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 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 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 622 ASP Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 672 LEU 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 743 MET Chi-restraints excluded: chain D residue 746 LEU Chi-restraints excluded: chain D residue 801 VAL 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 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 D residue 1328 THR Chi-restraints excluded: chain D residue 1337 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 49 ILE 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 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 179 LEU 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 203 LEU Chi-restraints excluded: chain M residue 257 ASP Chi-restraints excluded: chain M residue 273 ILE Chi-restraints excluded: chain M residue 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 294 ILE 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 43 optimal weight: 30.0000 chunk 44 optimal weight: 5.9990 chunk 28 optimal weight: 5.9990 chunk 184 optimal weight: 0.6980 chunk 189 optimal weight: 1.9990 chunk 183 optimal weight: 2.9990 chunk 348 optimal weight: 3.9990 chunk 263 optimal weight: 0.6980 chunk 367 optimal weight: 50.0000 chunk 262 optimal weight: 0.8980 chunk 126 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 952 GLN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D1252 HIS ** M 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 337 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.150070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.095707 restraints weight = 59776.362| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.00 r_work: 0.3254 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3118 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.5021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29487 Z= 0.140 Angle : 0.665 16.172 40324 Z= 0.326 Chirality : 0.044 0.397 4762 Planarity : 0.004 0.073 5045 Dihedral : 14.715 174.063 4834 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.72 % Favored : 92.20 % Rotamer: Outliers : 5.37 % Allowed : 21.61 % Favored : 73.02 % 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: -2.03 (0.13), residues: 3655 helix: 0.42 (0.15), residues: 1293 sheet: -1.49 (0.29), residues: 297 loop : -2.64 (0.12), residues: 2065 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG C1033 TYR 0.014 0.001 TYR C1231 PHE 0.024 0.001 PHE C 186 TRP 0.022 0.001 TRP A 321 HIS 0.010 0.001 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (29487) covalent geometry : angle 0.66470 / 0.33 (40324) hydrogen bonds : bond 0.03874 / 2.68 ( 1008) hydrogen bonds : angle 4.16235 / 2.89 ( 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 441 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 291 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 GLN cc_start: 0.9174 (mp10) cc_final: 0.8888 (mp10) REVERT: A 313 SER cc_start: 0.8574 (t) cc_final: 0.7989 (p) REVERT: B 43 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8950 (mp) REVERT: B 145 LYS cc_start: 0.8720 (ptpt) cc_final: 0.8430 (ptpp) REVERT: B 186 ASN cc_start: 0.8744 (t0) cc_final: 0.8442 (t0) REVERT: C 183 TRP cc_start: 0.8545 (m-10) cc_final: 0.8192 (m100) REVERT: C 203 LYS cc_start: 0.8394 (mtmt) cc_final: 0.7979 (mtmt) REVERT: C 352 ARG cc_start: 0.9132 (ptp-170) cc_final: 0.8647 (mtp85) REVERT: C 524 ILE cc_start: 0.9199 (OUTLIER) cc_final: 0.8894 (tt) REVERT: C 542 ARG cc_start: 0.7023 (mmp-170) cc_final: 0.6531 (mmt90) REVERT: C 545 PHE cc_start: 0.7508 (t80) cc_final: 0.7237 (t80) REVERT: C 589 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8845 (t) REVERT: C 628 HIS cc_start: 0.8068 (m90) cc_final: 0.7681 (m90) REVERT: C 835 GLU cc_start: 0.8395 (pp20) cc_final: 0.7947 (pp20) REVERT: C 844 LYS cc_start: 0.8695 (ptpt) cc_final: 0.8382 (ptpt) REVERT: C 954 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8889 (tptp) REVERT: C 1021 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8593 (tp) REVERT: C 1022 LYS cc_start: 0.9463 (OUTLIER) cc_final: 0.9105 (pttp) REVERT: C 1024 GLU cc_start: 0.9427 (OUTLIER) cc_final: 0.9146 (mm-30) REVERT: C 1032 LYS cc_start: 0.9325 (OUTLIER) cc_final: 0.8757 (ttpt) REVERT: C 1200 LYS cc_start: 0.8749 (tptt) cc_final: 0.8378 (ttpt) REVERT: D 222 LYS cc_start: 0.9123 (mtpt) cc_final: 0.8791 (mmtm) REVERT: D 298 MET cc_start: 0.9139 (OUTLIER) cc_final: 0.8760 (mtp) REVERT: D 321 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8474 (tppt) REVERT: D 466 MET cc_start: 0.8914 (tpt) cc_final: 0.8608 (tpt) REVERT: D 643 ASP cc_start: 0.8145 (m-30) cc_final: 0.7802 (m-30) REVERT: D 695 LYS cc_start: 0.8929 (OUTLIER) cc_final: 0.8670 (tptm) REVERT: D 697 MET cc_start: 0.8032 (tmm) cc_final: 0.7638 (tmm) REVERT: D 842 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8431 (mtp85) REVERT: D 868 TRP cc_start: 0.8607 (m-90) cc_final: 0.8138 (m-90) REVERT: D 1040 MET cc_start: 0.5392 (mtp) cc_final: 0.3571 (mmm) REVERT: D 1260 MET cc_start: 0.8982 (mtm) cc_final: 0.8705 (mtp) REVERT: M 180 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.8816 (tptp) REVERT: M 362 MET cc_start: 0.8764 (ptm) cc_final: 0.8279 (ppp) REVERT: M 423 LEU cc_start: 0.8827 (tp) cc_final: 0.8397 (pp) outliers start: 150 outliers final: 107 residues processed: 411 average time/residue: 0.1801 time to fit residues: 119.0548 Evaluate side-chains 384 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 264 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 289 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 77 ASP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 121 VAL 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 27 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 46 GLN 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 208 ILE 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 524 ILE Chi-restraints excluded: chain C residue 538 LEU Chi-restraints excluded: chain C residue 589 THR Chi-restraints excluded: chain C residue 699 LEU 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 864 LYS 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 922 ASN 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 1009 ASN 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 1032 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1289 GLU 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 218 THR Chi-restraints excluded: chain D residue 252 LEU Chi-restraints excluded: chain D residue 266 ASN Chi-restraints excluded: chain D residue 285 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 421 VAL Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 672 LEU 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 803 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 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 179 LEU 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 203 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 279 ARG Chi-restraints excluded: chain M residue 285 TRP Chi-restraints excluded: chain M residue 294 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 354 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 302 optimal weight: 20.0000 chunk 166 optimal weight: 0.9980 chunk 254 optimal weight: 7.9990 chunk 268 optimal weight: 20.0000 chunk 15 optimal weight: 2.9990 chunk 214 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN C 387 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN M 337 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.147805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.093662 restraints weight = 59928.885| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 3.44 r_work: 0.3167 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 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 = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 29487 Z= 0.241 Angle : 0.713 16.062 40324 Z= 0.354 Chirality : 0.046 0.390 4762 Planarity : 0.005 0.060 5045 Dihedral : 14.680 174.443 4831 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.89 % Favored : 91.03 % Rotamer: Outliers : 5.77 % Allowed : 21.28 % Favored : 72.95 % 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: -2.06 (0.13), residues: 3655 helix: 0.36 (0.15), residues: 1299 sheet: -1.45 (0.29), residues: 297 loop : -2.66 (0.12), residues: 2059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 255 TYR 0.014 0.002 TYR C1231 PHE 0.023 0.002 PHE C 186 TRP 0.028 0.002 TRP A 321 HIS 0.009 0.001 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00570 / 0.24 (29487) covalent geometry : angle 0.71310 / 0.35 (40324) hydrogen bonds : bond 0.04329 / 2.97 ( 1008) hydrogen bonds : angle 4.25944 / 2.96 ( 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 424 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 263 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6952 (mp0) REVERT: A 127 GLN cc_start: 0.9197 (mp10) cc_final: 0.8963 (mp10) REVERT: A 255 ARG cc_start: 0.7716 (mpp-170) cc_final: 0.7387 (mpp-170) REVERT: A 313 SER cc_start: 0.8536 (t) cc_final: 0.7873 (m) REVERT: B 43 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8912 (mp) REVERT: B 145 LYS cc_start: 0.8717 (ptpt) cc_final: 0.8423 (ptpp) REVERT: B 147 GLN cc_start: 0.7965 (tt0) cc_final: 0.7708 (mt0) REVERT: B 186 ASN cc_start: 0.8621 (t0) cc_final: 0.8346 (t0) REVERT: C 183 TRP cc_start: 0.8606 (m-10) cc_final: 0.8211 (m100) REVERT: C 203 LYS cc_start: 0.8533 (mtmt) cc_final: 0.8111 (mtmt) REVERT: C 204 LEU cc_start: 0.7854 (tp) cc_final: 0.7249 (tt) REVERT: C 352 ARG cc_start: 0.9141 (ptp-170) cc_final: 0.8676 (mtp85) REVERT: C 488 MET cc_start: 0.7889 (ppp) cc_final: 0.7353 (ppp) REVERT: C 524 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8862 (tt) REVERT: C 542 ARG cc_start: 0.7141 (mmp-170) cc_final: 0.6554 (mmt90) REVERT: C 545 PHE cc_start: 0.7483 (t80) cc_final: 0.7219 (t80) REVERT: C 589 THR cc_start: 0.8996 (OUTLIER) cc_final: 0.8735 (t) REVERT: C 628 HIS cc_start: 0.8039 (m90) cc_final: 0.7659 (m90) REVERT: C 704 MET cc_start: 0.7540 (pmm) cc_final: 0.6906 (ptp) REVERT: C 826 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.8136 (t0) REVERT: C 835 GLU cc_start: 0.8305 (pp20) cc_final: 0.7929 (pp20) REVERT: C 844 LYS cc_start: 0.8696 (ptpt) cc_final: 0.8328 (ptpt) REVERT: C 936 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6381 (ttm170) REVERT: C 954 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8841 (tptp) REVERT: C 1021 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8616 (tp) REVERT: C 1022 LYS cc_start: 0.9447 (OUTLIER) cc_final: 0.9071 (pttp) REVERT: C 1024 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.9106 (mm-30) REVERT: C 1032 LYS cc_start: 0.9339 (OUTLIER) cc_final: 0.8749 (ttpt) REVERT: C 1222 GLU cc_start: 0.7440 (pm20) cc_final: 0.7047 (pm20) REVERT: D 222 LYS cc_start: 0.9129 (mtpt) cc_final: 0.8751 (mmtm) REVERT: D 298 MET cc_start: 0.9063 (OUTLIER) cc_final: 0.8703 (mtp) REVERT: D 466 MET cc_start: 0.8946 (tpt) cc_final: 0.8654 (tpt) REVERT: D 643 ASP cc_start: 0.8088 (m-30) cc_final: 0.7765 (m-30) REVERT: D 695 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8658 (tptm) REVERT: D 697 MET cc_start: 0.8075 (tmm) cc_final: 0.7466 (tmm) REVERT: D 747 MET cc_start: 0.8192 (mmt) cc_final: 0.7755 (mmm) REVERT: D 842 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8419 (mtp85) REVERT: D 868 TRP cc_start: 0.8519 (m-90) cc_final: 0.8070 (m-90) REVERT: D 1040 MET cc_start: 0.5448 (mtp) cc_final: 0.3662 (mmm) REVERT: E 62 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8435 (tm-30) REVERT: M 180 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8752 (tptp) REVERT: M 362 MET cc_start: 0.8810 (ptm) cc_final: 0.8308 (ppp) REVERT: M 423 LEU cc_start: 0.8836 (tp) cc_final: 0.8397 (pp) outliers start: 161 outliers final: 120 residues processed: 396 average time/residue: 0.1850 time to fit residues: 118.6591 Evaluate side-chains 394 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 259 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 64 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 117 HIS 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 287 VAL Chi-restraints excluded: chain A residue 289 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 77 ASP Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 121 VAL 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 27 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 46 GLN 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 208 ILE 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 508 SER Chi-restraints excluded: chain C residue 524 ILE Chi-restraints excluded: chain C residue 538 LEU 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 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 864 LYS 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 922 ASN 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 1009 ASN 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 1032 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1114 GLU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1180 MET Chi-restraints excluded: chain C residue 1289 GLU Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 144 TYR Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 183 GLU 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 285 LEU Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 341 ASN 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 429 LEU Chi-restraints excluded: chain D residue 453 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 552 ILE Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 672 LEU 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 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 D residue 1328 THR 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 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 160 ASP 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 188 VAL Chi-restraints excluded: chain M residue 203 LEU 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 294 ILE Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 455 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 345 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 285 optimal weight: 50.0000 chunk 120 optimal weight: 0.5980 chunk 178 optimal weight: 2.9990 chunk 270 optimal weight: 10.0000 chunk 205 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 70 optimal weight: 0.0170 overall best weight: 2.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 194 GLN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.142352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.091101 restraints weight = 59945.223| |-----------------------------------------------------------------------------| r_work (start): 0.3268 rms_B_bonded: 3.46 r_work: 0.3064 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.5375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 29487 Z= 0.200 Angle : 0.701 16.388 40324 Z= 0.344 Chirality : 0.046 0.397 4762 Planarity : 0.005 0.060 5045 Dihedral : 14.651 174.829 4821 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.40 % Favored : 91.55 % Rotamer: Outliers : 5.77 % Allowed : 21.21 % Favored : 73.02 % 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: -2.00 (0.13), residues: 3655 helix: 0.41 (0.15), residues: 1296 sheet: -1.47 (0.29), residues: 297 loop : -2.60 (0.12), residues: 2062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 255 TYR 0.014 0.001 TYR C1231 PHE 0.028 0.002 PHE C 186 TRP 0.025 0.001 TRP A 321 HIS 0.009 0.001 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00471 / 0.20 (29487) covalent geometry : angle 0.70052 / 0.34 (40324) hydrogen bonds : bond 0.04104 / 2.82 ( 1008) hydrogen bonds : angle 4.24419 / 2.95 ( 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 423 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 161 poor density : 262 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 7 GLU cc_start: 0.7362 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: A 127 GLN cc_start: 0.9222 (mp10) cc_final: 0.8924 (mp10) REVERT: A 255 ARG cc_start: 0.7843 (mpp-170) cc_final: 0.7566 (mpp-170) REVERT: A 313 SER cc_start: 0.8458 (t) cc_final: 0.7758 (m) REVERT: B 18 GLN cc_start: 0.8964 (pm20) cc_final: 0.8434 (pp30) REVERT: B 43 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8822 (mp) REVERT: B 145 LYS cc_start: 0.8576 (ptpt) cc_final: 0.8302 (ptpp) REVERT: B 147 GLN cc_start: 0.8055 (tt0) cc_final: 0.7788 (mt0) REVERT: B 186 ASN cc_start: 0.8704 (t0) cc_final: 0.8398 (t0) REVERT: C 183 TRP cc_start: 0.8637 (m-10) cc_final: 0.8217 (m100) REVERT: C 203 LYS cc_start: 0.8535 (mtmt) cc_final: 0.8086 (mtmt) REVERT: C 352 ARG cc_start: 0.9208 (ptp-170) cc_final: 0.8718 (mtp85) REVERT: C 488 MET cc_start: 0.7981 (ppp) cc_final: 0.7724 (ppp) REVERT: C 524 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8821 (tt) REVERT: C 542 ARG cc_start: 0.7121 (mmp-170) cc_final: 0.6546 (mmt90) REVERT: C 545 PHE cc_start: 0.7647 (t80) cc_final: 0.7391 (t80) REVERT: C 589 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8637 (t) REVERT: C 628 HIS cc_start: 0.7963 (m90) cc_final: 0.7579 (m90) REVERT: C 704 MET cc_start: 0.7459 (pmm) cc_final: 0.7051 (ptp) REVERT: C 826 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8065 (t0) REVERT: C 835 GLU cc_start: 0.8382 (pp20) cc_final: 0.7998 (pp20) REVERT: C 844 LYS cc_start: 0.8710 (ptpt) cc_final: 0.8344 (ptpt) REVERT: C 936 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.6276 (ttm170) REVERT: C 954 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8837 (tptp) REVERT: C 1011 LEU cc_start: 0.9517 (mp) cc_final: 0.8902 (tp) REVERT: C 1021 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8608 (tp) REVERT: C 1022 LYS cc_start: 0.9463 (OUTLIER) cc_final: 0.9082 (pttp) REVERT: C 1024 GLU cc_start: 0.9500 (OUTLIER) cc_final: 0.9235 (mm-30) REVERT: C 1032 LYS cc_start: 0.9324 (OUTLIER) cc_final: 0.8731 (ttpt) REVERT: C 1200 LYS cc_start: 0.8748 (tptt) cc_final: 0.8399 (ttpt) REVERT: C 1222 GLU cc_start: 0.7478 (pm20) cc_final: 0.7229 (pm20) REVERT: D 130 MET cc_start: 0.8539 (OUTLIER) cc_final: 0.7932 (tmm) REVERT: D 222 LYS cc_start: 0.9175 (mtpt) cc_final: 0.8779 (mmtm) REVERT: D 298 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8708 (mtp) REVERT: D 466 MET cc_start: 0.9010 (tpt) cc_final: 0.8716 (tpt) REVERT: D 643 ASP cc_start: 0.8056 (m-30) cc_final: 0.7750 (m-30) REVERT: D 697 MET cc_start: 0.8087 (tmm) cc_final: 0.7473 (tmm) REVERT: D 747 MET cc_start: 0.8255 (mmt) cc_final: 0.7846 (mmm) REVERT: D 842 ARG cc_start: 0.8809 (OUTLIER) cc_final: 0.8454 (mtp85) REVERT: D 868 TRP cc_start: 0.8546 (m-90) cc_final: 0.8088 (m-90) REVERT: D 1040 MET cc_start: 0.5823 (mtp) cc_final: 0.4012 (mmm) REVERT: E 62 GLN cc_start: 0.8741 (tm-30) cc_final: 0.8463 (tm-30) REVERT: M 180 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8674 (tptp) REVERT: M 362 MET cc_start: 0.8822 (ptm) cc_final: 0.8303 (ppp) REVERT: M 423 LEU cc_start: 0.8834 (tp) cc_final: 0.8380 (pp) outliers start: 161 outliers final: 131 residues processed: 396 average time/residue: 0.1830 time to fit residues: 116.5310 Evaluate side-chains 405 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 259 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 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 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 289 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 31 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 VAL 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 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 27 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 46 GLN Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 129 LEU Chi-restraints excluded: chain C residue 133 ASN Chi-restraints excluded: chain C residue 171 LEU Chi-restraints excluded: chain C residue 208 ILE 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 508 SER Chi-restraints excluded: chain C residue 524 ILE 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 603 ILE Chi-restraints excluded: chain C residue 630 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 864 LYS 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 922 ASN 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 1022 LYS Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1114 GLU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1180 MET 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 20 ILE Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 130 MET 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 299 LEU Chi-restraints excluded: chain D residue 303 VAL Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 353 SER 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 453 VAL Chi-restraints excluded: chain D residue 454 CYS Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 622 ASP Chi-restraints excluded: chain D residue 635 SER Chi-restraints excluded: chain D residue 672 LEU Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 685 ILE Chi-restraints excluded: chain D residue 698 MET Chi-restraints excluded: chain D residue 743 MET 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 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 39 VAL Chi-restraints excluded: chain E residue 49 ILE Chi-restraints excluded: chain E residue 64 LEU Chi-restraints excluded: chain E residue 66 VAL 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 160 ASP 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 188 VAL Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 203 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 337 ASN Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 455 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 258 optimal weight: 3.9990 chunk 355 optimal weight: 0.0000 chunk 127 optimal weight: 0.9990 chunk 100 optimal weight: 7.9990 chunk 201 optimal weight: 6.9990 chunk 76 optimal weight: 30.0000 chunk 213 optimal weight: 0.9990 chunk 236 optimal weight: 0.9980 chunk 286 optimal weight: 50.0000 chunk 70 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN M 337 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.143926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.091705 restraints weight = 59327.653| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.36 r_work: 0.3117 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.5373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 29487 Z= 0.124 Angle : 0.664 13.492 40324 Z= 0.322 Chirality : 0.044 0.389 4762 Planarity : 0.004 0.059 5045 Dihedral : 14.524 175.027 4813 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.99 % Favored : 91.96 % Rotamer: Outliers : 4.73 % Allowed : 22.54 % 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: -1.81 (0.13), residues: 3655 helix: 0.57 (0.15), residues: 1297 sheet: -1.37 (0.29), residues: 301 loop : -2.50 (0.12), residues: 2057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG M 336 TYR 0.013 0.001 TYR C1231 PHE 0.032 0.001 PHE C 186 TRP 0.022 0.001 TRP A 321 HIS 0.010 0.001 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (29487) covalent geometry : angle 0.66390 / 0.32 (40324) hydrogen bonds : bond 0.03600 / 2.49 ( 1008) hydrogen bonds : angle 4.10879 / 2.85 ( 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 415 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 283 time to evaluate : 1.080 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 127 GLN cc_start: 0.9154 (mp10) cc_final: 0.8812 (mp10) REVERT: A 313 SER cc_start: 0.8420 (t) cc_final: 0.7749 (m) REVERT: B 18 GLN cc_start: 0.8947 (pm20) cc_final: 0.8435 (pp30) REVERT: B 43 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8760 (mp) REVERT: B 145 LYS cc_start: 0.8525 (ptpt) cc_final: 0.8277 (ptpp) REVERT: B 147 GLN cc_start: 0.8033 (tt0) cc_final: 0.7778 (tt0) REVERT: B 186 ASN cc_start: 0.8649 (t0) cc_final: 0.8325 (t0) REVERT: C 183 TRP cc_start: 0.8561 (m-10) cc_final: 0.8186 (m100) REVERT: C 203 LYS cc_start: 0.8290 (mtmt) cc_final: 0.7838 (mtmt) REVERT: C 488 MET cc_start: 0.7998 (ppp) cc_final: 0.7726 (ppp) REVERT: C 542 ARG cc_start: 0.7116 (mmp-170) cc_final: 0.6585 (mmt90) REVERT: C 545 PHE cc_start: 0.7590 (t80) cc_final: 0.7309 (t80) REVERT: C 589 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8583 (t) REVERT: C 628 HIS cc_start: 0.7878 (m90) cc_final: 0.7507 (m90) REVERT: C 644 LEU cc_start: 0.8798 (tp) cc_final: 0.8489 (tp) REVERT: C 704 MET cc_start: 0.7279 (pmm) cc_final: 0.6904 (ptp) REVERT: C 835 GLU cc_start: 0.8327 (pp20) cc_final: 0.7942 (pp20) REVERT: C 936 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.6295 (ttm170) REVERT: C 954 LYS cc_start: 0.9130 (OUTLIER) cc_final: 0.8830 (tptp) REVERT: C 1021 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8561 (tp) REVERT: C 1022 LYS cc_start: 0.9456 (OUTLIER) cc_final: 0.9090 (pttp) REVERT: C 1024 GLU cc_start: 0.9486 (OUTLIER) cc_final: 0.9113 (mm-30) REVERT: C 1032 LYS cc_start: 0.9310 (OUTLIER) cc_final: 0.8716 (ttpt) REVERT: C 1200 LYS cc_start: 0.8737 (tptt) cc_final: 0.8400 (ttpt) REVERT: D 130 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7962 (tmm) REVERT: D 222 LYS cc_start: 0.9160 (mtpt) cc_final: 0.8763 (mmtm) REVERT: D 298 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8702 (mtp) REVERT: D 404 GLU cc_start: 0.8613 (tm-30) cc_final: 0.8394 (tm-30) REVERT: D 466 MET cc_start: 0.8894 (tpt) cc_final: 0.8624 (tpt) REVERT: D 643 ASP cc_start: 0.8025 (m-30) cc_final: 0.7660 (m-30) REVERT: D 697 MET cc_start: 0.8028 (tmm) cc_final: 0.7397 (tmm) REVERT: D 747 MET cc_start: 0.8165 (mmt) cc_final: 0.7773 (mmm) REVERT: D 842 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8418 (mtp85) REVERT: D 868 TRP cc_start: 0.8482 (m-90) cc_final: 0.8011 (m-90) REVERT: D 1040 MET cc_start: 0.5847 (mtp) cc_final: 0.4024 (mmm) REVERT: E 62 GLN cc_start: 0.8719 (tm-30) cc_final: 0.8426 (tm-30) REVERT: M 180 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8617 (tptp) REVERT: M 362 MET cc_start: 0.8808 (ptm) cc_final: 0.8293 (ppp) REVERT: M 383 ARG cc_start: 0.7731 (mpt180) cc_final: 0.6725 (mmt90) REVERT: M 423 LEU cc_start: 0.8836 (tp) cc_final: 0.8374 (pp) outliers start: 132 outliers final: 104 residues processed: 388 average time/residue: 0.1893 time to fit residues: 116.9030 Evaluate side-chains 386 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 270 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 287 VAL Chi-restraints excluded: chain A residue 289 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 83 LEU Chi-restraints excluded: chain B residue 121 VAL 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 27 LEU Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 129 LEU 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 321 LEU Chi-restraints excluded: chain C residue 414 ILE Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 538 LEU 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 699 LEU Chi-restraints excluded: chain C residue 717 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 836 LEU Chi-restraints excluded: chain C residue 856 ASN Chi-restraints excluded: chain C residue 864 LYS 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 1022 LYS Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1096 ILE Chi-restraints excluded: chain C residue 1114 GLU Chi-restraints excluded: chain C residue 1151 LEU Chi-restraints excluded: chain C residue 1180 MET 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 130 MET 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 341 ASN Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 428 THR Chi-restraints excluded: chain D residue 454 CYS 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 672 LEU Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 698 MET 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 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 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 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 193 LYS Chi-restraints excluded: chain M residue 203 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 337 ASN Chi-restraints excluded: chain M residue 386 THR Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 455 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 140 optimal weight: 0.9990 chunk 235 optimal weight: 2.9990 chunk 249 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 223 optimal weight: 1.9990 chunk 196 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 221 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS ** M 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.143746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.093131 restraints weight = 59636.747| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 3.42 r_work: 0.3104 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3105 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3105 r_free = 0.3105 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3105 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.5421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29487 Z= 0.140 Angle : 0.677 14.879 40324 Z= 0.328 Chirality : 0.044 0.387 4762 Planarity : 0.004 0.059 5045 Dihedral : 14.476 175.198 4810 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.88 % Favored : 92.07 % Rotamer: Outliers : 4.37 % Allowed : 23.15 % Favored : 72.48 % 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: 0.65 (0.15), residues: 1296 sheet: -1.36 (0.29), residues: 303 loop : -2.46 (0.12), residues: 2056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 336 TYR 0.016 0.001 TYR C 872 PHE 0.018 0.001 PHE D 57 TRP 0.020 0.001 TRP A 321 HIS 0.010 0.001 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (29487) covalent geometry : angle 0.67690 / 0.33 (40324) hydrogen bonds : bond 0.03624 / 2.50 ( 1008) hydrogen bonds : angle 4.10901 / 2.85 ( 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: 122 poor density : 275 time to evaluate : 1.078 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 127 GLN cc_start: 0.9152 (mp10) cc_final: 0.8812 (mp10) REVERT: A 313 SER cc_start: 0.8284 (t) cc_final: 0.7578 (m) REVERT: B 18 GLN cc_start: 0.8955 (pm20) cc_final: 0.8436 (pp30) REVERT: B 43 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8747 (mp) REVERT: B 145 LYS cc_start: 0.8531 (ptpt) cc_final: 0.8276 (ptpp) REVERT: B 147 GLN cc_start: 0.8049 (tt0) cc_final: 0.7822 (mt0) REVERT: B 186 ASN cc_start: 0.8697 (t0) cc_final: 0.8375 (t0) REVERT: C 183 TRP cc_start: 0.8574 (m-10) cc_final: 0.8215 (m100) REVERT: C 203 LYS cc_start: 0.8437 (mtmt) cc_final: 0.7934 (mtmt) REVERT: C 488 MET cc_start: 0.7942 (ppp) cc_final: 0.7719 (ppp) REVERT: C 542 ARG cc_start: 0.7107 (mmp-170) cc_final: 0.6624 (mmt90) REVERT: C 545 PHE cc_start: 0.7736 (t80) cc_final: 0.7434 (t80) REVERT: C 589 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8595 (t) REVERT: C 628 HIS cc_start: 0.7879 (m90) cc_final: 0.7506 (m90) REVERT: C 704 MET cc_start: 0.7337 (pmm) cc_final: 0.6955 (ptp) REVERT: C 768 MET cc_start: 0.8352 (mtm) cc_final: 0.7646 (mmt) REVERT: C 835 GLU cc_start: 0.8344 (pp20) cc_final: 0.7974 (pp20) REVERT: C 844 LYS cc_start: 0.8698 (ptpt) cc_final: 0.8395 (ptpt) REVERT: C 936 ARG cc_start: 0.7380 (OUTLIER) cc_final: 0.6217 (ttm170) REVERT: C 954 LYS cc_start: 0.9108 (OUTLIER) cc_final: 0.8799 (tptp) REVERT: C 1021 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8583 (tp) REVERT: C 1022 LYS cc_start: 0.9461 (OUTLIER) cc_final: 0.9091 (pttp) REVERT: C 1024 GLU cc_start: 0.9484 (OUTLIER) cc_final: 0.9087 (mm-30) REVERT: C 1032 LYS cc_start: 0.9313 (OUTLIER) cc_final: 0.8720 (ttpt) REVERT: C 1161 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8385 (tt) REVERT: C 1200 LYS cc_start: 0.8745 (tptt) cc_final: 0.8430 (ttpt) REVERT: D 130 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.7957 (tmm) REVERT: D 222 LYS cc_start: 0.9143 (mtpt) cc_final: 0.8747 (mmtm) REVERT: D 270 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.8083 (ptp90) REVERT: D 298 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8730 (mtp) REVERT: D 342 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7665 (tp) REVERT: D 466 MET cc_start: 0.8872 (tpt) cc_final: 0.8585 (tpt) REVERT: D 643 ASP cc_start: 0.8063 (m-30) cc_final: 0.7726 (m-30) REVERT: D 747 MET cc_start: 0.8233 (mmt) cc_final: 0.7834 (mmm) REVERT: D 842 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8430 (mtp85) REVERT: D 868 TRP cc_start: 0.8511 (m-90) cc_final: 0.7990 (m-90) REVERT: D 1040 MET cc_start: 0.5868 (mtp) cc_final: 0.4009 (mmm) REVERT: E 62 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8393 (tm-30) REVERT: M 180 LYS cc_start: 0.8993 (OUTLIER) cc_final: 0.8695 (tptp) REVERT: M 423 LEU cc_start: 0.8838 (tp) cc_final: 0.8384 (pp) outliers start: 122 outliers final: 101 residues processed: 375 average time/residue: 0.1901 time to fit residues: 114.4940 Evaluate side-chains 383 residues out of total 3158 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 267 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 289 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 83 LEU Chi-restraints excluded: chain B residue 121 VAL 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 27 LEU Chi-restraints excluded: chain C residue 37 LYS Chi-restraints excluded: chain C residue 123 TYR Chi-restraints excluded: chain C residue 129 LEU 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 508 SER Chi-restraints excluded: chain C residue 538 LEU 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 699 LEU 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 864 LYS 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 1022 LYS Chi-restraints excluded: chain C residue 1024 GLU Chi-restraints excluded: chain C residue 1032 LYS Chi-restraints excluded: chain C residue 1052 VAL Chi-restraints excluded: chain C residue 1060 ILE Chi-restraints excluded: chain C residue 1096 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 1180 MET 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 130 MET 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 270 ARG Chi-restraints excluded: chain D residue 298 MET Chi-restraints excluded: chain D residue 341 ASN Chi-restraints excluded: chain D residue 342 LEU 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 454 CYS 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 672 LEU Chi-restraints excluded: chain D residue 679 TYR Chi-restraints excluded: chain D residue 698 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 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 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 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 180 LYS Chi-restraints excluded: chain M residue 184 ARG Chi-restraints excluded: chain M residue 193 LYS Chi-restraints excluded: chain M residue 203 LEU 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 386 THR Chi-restraints excluded: chain M residue 390 LEU Chi-restraints excluded: chain M residue 455 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 372 random chunks: chunk 342 optimal weight: 0.8980 chunk 318 optimal weight: 0.4980 chunk 19 optimal weight: 6.9990 chunk 264 optimal weight: 0.9980 chunk 262 optimal weight: 0.0870 chunk 5 optimal weight: 5.9990 chunk 187 optimal weight: 8.9990 chunk 333 optimal weight: 0.0270 chunk 122 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 235 optimal weight: 3.9990 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 214 ASN ** C 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1023 HIS C1146 GLN ** D 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 337 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.145088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.093217 restraints weight = 59905.334| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 3.29 r_work: 0.3151 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3154 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 : 0.002 0.043 29487 Z= 0.112 Angle : 0.660 15.327 40324 Z= 0.317 Chirality : 0.043 0.388 4762 Planarity : 0.004 0.057 5045 Dihedral : 14.407 175.325 4810 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.66 % Favored : 92.28 % Rotamer: Outliers : 4.05 % Allowed : 23.50 % 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: -1.60 (0.14), residues: 3655 helix: 0.81 (0.15), residues: 1283 sheet: -1.28 (0.29), residues: 303 loop : -2.39 (0.12), residues: 2069 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 473 TYR 0.014 0.001 TYR M 389 PHE 0.018 0.001 PHE D 57 TRP 0.019 0.001 TRP A 321 HIS 0.011 0.001 HIS B 132 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 (29487) covalent geometry : angle 0.65983 / 0.32 (40324) hydrogen bonds : bond 0.03289 / 2.28 ( 1008) hydrogen bonds : angle 4.00745 / 2.78 ( 2785) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9046.52 seconds wall clock time: 154 minutes 37.13 seconds (9277.13 seconds total)