Starting phenix.real_space_refine on Sat Aug 8 13:39:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r6p_18956/08_2026/8r6p_18956.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r6p_18956/08_2026/8r6p_18956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r6p_18956/08_2026/8r6p_18956.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r6p_18956/08_2026/8r6p_18956.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r6p_18956/08_2026/8r6p_18956.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r6p_18956/08_2026/8r6p_18956.map" } resolution = 3.16 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= 0.003 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 85 5.49 5 Mg 1 5.21 5 S 94 5.16 5 C 17720 2.51 5 N 5126 2.21 5 O 5704 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28732 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1716 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1716 Classifications: {'peptide': 226} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 211} Chain: "B" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1783 Classifications: {'peptide': 235} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 220} Chain: "C" Number of atoms: 8602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1110, 8602 Classifications: {'peptide': 1110} Link IDs: {'PCIS': 1, 'PTRANS': 58, 'TRANS': 1050} Chain: "F" Number of atoms: 2443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2443 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 296} Chain: "H" Number of atoms: 1141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1141 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 4, 'TRANS': 136} Chain: "J" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 826 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 7, 'TRANS': 94} Chain: "D" Number of atoms: 9877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1263, 9877 Classifications: {'peptide': 1263} Link IDs: {'PCIS': 2, 'PTRANS': 55, 'TRANS': 1205} Chain breaks: 1 Chain: "E" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 595 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 69} Chain breaks: 1 Chain: "O" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 973 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain breaks: 1 Chain: "P" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 773 Classifications: {'DNA': 38} Link IDs: {'rna3p': 37} Chain breaks: 1 Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' ZN': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23543 SG CYS D 890 33.503 60.254 69.469 1.00 29.77 S ATOM 24105 SG CYS D 967 36.504 62.511 70.260 1.00 30.10 S ATOM 24147 SG CYS D 974 34.133 61.359 73.017 1.00 21.97 S ATOM 24166 SG CYS D 977 36.403 58.939 71.480 1.00 27.80 S ATOM 16970 SG CYS D 60 36.492 124.824 85.965 1.00 51.84 S ATOM 16988 SG CYS D 62 37.111 128.503 86.424 1.00 52.50 S ATOM 17097 SG CYS D 75 34.703 127.309 83.797 1.00 49.13 S ATOM 17123 SG CYS D 78 38.386 126.369 83.422 1.00 50.57 S Residues with excluded nonbonded symmetry interactions: 141 residue: pdb=" N ASP H 5 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP H 5 " occ=0.50 residue: pdb=" N TYR H 6 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR H 6 " occ=0.50 residue: pdb=" N GLU H 7 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU H 7 " occ=0.50 residue: pdb=" N ASP H 8 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP H 8 " occ=0.50 residue: pdb=" N GLU H 9 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU H 9 " occ=0.50 residue: pdb=" N LEU H 10 " occ=0.50 ... (6 atoms not shown) pdb=" CD2 LEU H 10 " occ=0.50 residue: pdb=" N GLN H 11 " occ=0.50 ... (7 atoms not shown) pdb=" NE2 GLN H 11 " occ=0.50 residue: pdb=" N SER H 12 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER H 12 " occ=0.50 residue: pdb=" N GLU H 13 " occ=0.50 ... (7 atoms not shown) pdb=" OE2 GLU H 13 " occ=0.50 residue: pdb=" N ARG H 14 " occ=0.50 ... (9 atoms not shown) pdb=" NH2 ARG H 14 " occ=0.50 residue: pdb=" N ASP H 15 " occ=0.50 ... (6 atoms not shown) pdb=" OD2 ASP H 15 " occ=0.50 residue: pdb=" N TYR H 16 " occ=0.50 ... (10 atoms not shown) pdb=" OH TYR H 16 " occ=0.50 ... (remaining 129 not shown) Time building chain proxies: 5.09, per 1000 atoms: 0.18 Number of scatterers: 28732 At special positions: 0 Unit cell: (127.541, 169.221, 164.219, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 94 16.00 P 85 15.00 Mg 1 11.99 O 5704 8.00 N 5126 7.00 C 17720 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: 2.18 Conformation dependent library (CDL) restraints added in 903.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D2001 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 977 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 974 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 890 " pdb="ZN ZN D2001 " - pdb=" SG CYS D 967 " pdb=" ZN D2002 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 60 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 78 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 75 " pdb="ZN ZN D2002 " - pdb=" SG CYS D 62 " Number of angles added : 12 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6376 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 42 sheets defined 43.9% alpha, 16.3% beta 35 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 2.93 Creating SS restraints... Processing helix chain 'A' and resid 29 through 46 removed outlier: 4.509A pdb=" N THR A 33 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ILE A 46 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 82 removed outlier: 3.717A pdb=" N GLY A 82 " --> pdb=" O LEU A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 110 No H-bonds generated for 'chain 'A' and resid 108 through 110' Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'A' and resid 203 through 224 removed outlier: 4.396A pdb=" N LEU A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ALA A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 223 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 45 removed outlier: 3.719A pdb=" N THR B 33 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN B 36 " --> pdb=" O TYR B 32 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N SER B 37 " --> pdb=" O THR B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 82 removed outlier: 3.675A pdb=" N GLY B 82 " --> pdb=" O LEU B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 110 No H-bonds generated for 'chain 'B' and resid 108 through 110' Processing helix chain 'B' and resid 203 through 224 removed outlier: 3.990A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 57 removed outlier: 4.241A pdb=" N SER C 51 " --> pdb=" O VAL C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 68 Processing helix chain 'C' and resid 75 through 85 Processing helix chain 'C' and resid 109 through 117 Processing helix chain 'C' and resid 224 through 232 removed outlier: 4.013A pdb=" N LEU C 228 " --> pdb=" O PRO C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 243 Processing helix chain 'C' and resid 247 through 256 Processing helix chain 'C' and resid 262 through 273 removed outlier: 3.732A pdb=" N LEU C 266 " --> pdb=" O ASP C 262 " (cutoff:3.500A) Processing helix chain 'C' and resid 279 through 290 removed outlier: 3.616A pdb=" N LEU C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLU C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 312 Processing helix chain 'C' and resid 326 through 342 removed outlier: 3.621A pdb=" N VAL C 330 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 398 removed outlier: 3.725A pdb=" N GLU C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR C 396 " --> pdb=" O ARG C 392 " (cutoff:3.500A) Processing helix chain 'C' and resid 404 through 409 Processing helix chain 'C' and resid 411 through 425 removed outlier: 3.566A pdb=" N PHE C 422 " --> pdb=" O ILE C 418 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 444 removed outlier: 3.524A pdb=" N ARG C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 467 through 471 Processing helix chain 'C' and resid 523 through 529 removed outlier: 3.751A pdb=" N ARG C 529 " --> pdb=" O ASP C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 565 through 567 No H-bonds generated for 'chain 'C' and resid 565 through 567' Processing helix chain 'C' and resid 573 through 578 removed outlier: 4.334A pdb=" N MET C 577 " --> pdb=" O PRO C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 585 Processing helix chain 'C' and resid 587 through 591 Processing helix chain 'C' and resid 592 through 604 removed outlier: 3.856A pdb=" N ARG C 604 " --> pdb=" O ALA C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 630 removed outlier: 4.647A pdb=" N ARG C 624 " --> pdb=" O GLY C 620 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLY C 630 " --> pdb=" O ALA C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 730 through 735 Processing helix chain 'C' and resid 806 through 816 Processing helix chain 'C' and resid 847 through 849 No H-bonds generated for 'chain 'C' and resid 847 through 849' Processing helix chain 'C' and resid 891 through 895 Processing helix chain 'C' and resid 911 through 917 removed outlier: 4.718A pdb=" N ARG C 915 " --> pdb=" O HIS C 911 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG C 916 " --> pdb=" O GLY C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 933 removed outlier: 3.504A pdb=" N LEU C 923 " --> pdb=" O ILE C 919 " (cutoff:3.500A) Processing helix chain 'C' and resid 944 through 948 Processing helix chain 'C' and resid 951 through 954 Processing helix chain 'C' and resid 972 through 982 Processing helix chain 'C' and resid 1060 through 1071 Processing helix chain 'C' and resid 1072 through 1081 Processing helix chain 'C' and resid 1086 through 1100 removed outlier: 3.809A pdb=" N VAL C1091 " --> pdb=" O THR C1087 " (cutoff:3.500A) Processing helix chain 'C' and resid 1109 through 1122 removed outlier: 3.559A pdb=" N LYS C1113 " --> pdb=" O PRO C1109 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 171 Processing helix chain 'F' and resid 172 through 176 removed outlier: 3.929A pdb=" N VAL F 176 " --> pdb=" O ILE F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 180 through 208 removed outlier: 3.808A pdb=" N VAL F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N GLU F 186 " --> pdb=" O GLU F 182 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU F 187 " --> pdb=" O GLU F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 246 removed outlier: 4.691A pdb=" N ARG F 239 " --> pdb=" O GLU F 235 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N LEU F 240 " --> pdb=" O ALA F 236 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL F 241 " --> pdb=" O ASN F 237 " (cutoff:3.500A) Processing helix chain 'F' and resid 247 through 249 No H-bonds generated for 'chain 'F' and resid 247 through 249' Processing helix chain 'F' and resid 254 through 272 Processing helix chain 'F' and resid 274 through 278 removed outlier: 3.654A pdb=" N LYS F 277 " --> pdb=" O ASP F 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 280 through 301 removed outlier: 3.535A pdb=" N THR F 286 " --> pdb=" O SER F 282 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TRP F 287 " --> pdb=" O THR F 283 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N TRP F 288 " --> pdb=" O TYR F 284 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 329 Processing helix chain 'F' and resid 333 through 342 Processing helix chain 'F' and resid 344 through 355 Processing helix chain 'F' and resid 372 through 377 removed outlier: 3.566A pdb=" N PHE F 376 " --> pdb=" O LEU F 373 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE F 377 " --> pdb=" O GLY F 374 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 397 removed outlier: 3.605A pdb=" N THR F 392 " --> pdb=" O ALA F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 405 Processing helix chain 'F' and resid 407 through 417 removed outlier: 4.471A pdb=" N VAL F 413 " --> pdb=" O GLU F 409 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU F 415 " --> pdb=" O GLY F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 426 through 433 removed outlier: 4.039A pdb=" N VAL F 433 " --> pdb=" O GLU F 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 453 removed outlier: 3.503A pdb=" N SER F 446 " --> pdb=" O ARG F 442 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 459 Processing helix chain 'F' and resid 460 through 465 removed outlier: 4.200A pdb=" N ASP F 463 " --> pdb=" O VAL F 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 42 removed outlier: 3.532A pdb=" N HIS H 42 " --> pdb=" O ALA H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 66 removed outlier: 3.686A pdb=" N ALA H 66 " --> pdb=" O ARG H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 96 Processing helix chain 'H' and resid 110 through 115 removed outlier: 3.617A pdb=" N VAL H 114 " --> pdb=" O ARG H 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 89 removed outlier: 4.206A pdb=" N ARG J 88 " --> pdb=" O MET J 84 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG J 89 " --> pdb=" O LEU J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 107 removed outlier: 3.555A pdb=" N LEU J 94 " --> pdb=" O SER J 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 48 through 53 Processing helix chain 'D' and resid 67 through 71 Processing helix chain 'D' and resid 84 through 90 Processing helix chain 'D' and resid 103 through 108 Processing helix chain 'D' and resid 112 through 119 Processing helix chain 'D' and resid 124 through 130 Processing helix chain 'D' and resid 140 through 147 removed outlier: 4.110A pdb=" N ARG D 144 " --> pdb=" O ASP D 140 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 148 through 182 removed outlier: 3.714A pdb=" N LEU D 181 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ALA D 182 " --> pdb=" O GLU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 228 removed outlier: 3.783A pdb=" N LYS D 196 " --> pdb=" O ASP D 192 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL D 197 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ALA D 212 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 249 Processing helix chain 'D' and resid 257 through 268 removed outlier: 3.558A pdb=" N ILE D 261 " --> pdb=" O GLY D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 283 removed outlier: 4.361A pdb=" N GLU D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 287 through 303 removed outlier: 3.869A pdb=" N ARG D 291 " --> pdb=" O GLN D 287 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL D 298 " --> pdb=" O LYS D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 311 removed outlier: 3.761A pdb=" N GLY D 311 " --> pdb=" O SER D 308 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 308 through 311' Processing helix chain 'D' and resid 321 through 325 Processing helix chain 'D' and resid 338 through 361 removed outlier: 4.121A pdb=" N ASP D 342 " --> pdb=" O SER D 338 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL D 347 " --> pdb=" O LEU D 343 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG D 350 " --> pdb=" O ARG D 346 " (cutoff:3.500A) Processing helix chain 'D' and resid 363 through 383 removed outlier: 3.575A pdb=" N VAL D 367 " --> pdb=" O PRO D 363 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 408 removed outlier: 4.277A pdb=" N GLY D 408 " --> pdb=" O ASP D 404 " (cutoff:3.500A) Processing helix chain 'D' and resid 445 through 452 Processing helix chain 'D' and resid 452 through 463 Processing helix chain 'D' and resid 468 through 479 Processing helix chain 'D' and resid 480 through 491 removed outlier: 4.263A pdb=" N TRP D 484 " --> pdb=" O ARG D 480 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ASP D 485 " --> pdb=" O PRO D 481 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL D 486 " --> pdb=" O GLN D 482 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLU D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) Processing helix chain 'D' and resid 505 through 507 No H-bonds generated for 'chain 'D' and resid 505 through 507' Processing helix chain 'D' and resid 528 through 533 Processing helix chain 'D' and resid 548 through 558 Processing helix chain 'D' and resid 560 through 564 Processing helix chain 'D' and resid 579 through 590 Processing helix chain 'D' and resid 614 through 624 Processing helix chain 'D' and resid 643 through 651 removed outlier: 4.184A pdb=" N GLN D 649 " --> pdb=" O ASP D 645 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 651 " --> pdb=" O GLU D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 676 removed outlier: 3.861A pdb=" N LEU D 675 " --> pdb=" O MET D 671 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU D 676 " --> pdb=" O PHE D 672 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 701 Processing helix chain 'D' and resid 704 through 725 removed outlier: 3.720A pdb=" N THR D 724 " --> pdb=" O PHE D 720 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ARG D 725 " --> pdb=" O TYR D 721 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 761 removed outlier: 4.209A pdb=" N ARG D 761 " --> pdb=" O ARG D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 765 through 792 Processing helix chain 'D' and resid 796 through 804 removed outlier: 3.591A pdb=" N VAL D 802 " --> pdb=" O ILE D 798 " (cutoff:3.500A) Processing helix chain 'D' and resid 809 through 818 Processing helix chain 'D' and resid 844 through 880 removed outlier: 3.517A pdb=" N THR D 852 " --> pdb=" O TYR D 848 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N HIS D 853 " --> pdb=" O PHE D 849 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N GLY D 854 " --> pdb=" O ILE D 850 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N ALA D 855 " --> pdb=" O ASN D 851 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA D 863 " --> pdb=" O LEU D 859 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N LEU D 864 " --> pdb=" O ALA D 860 " (cutoff:3.500A) Processing helix chain 'D' and resid 944 through 953 Processing helix chain 'D' and resid 963 through 967 Processing helix chain 'D' and resid 975 through 979 Processing helix chain 'D' and resid 993 through 1004 Processing helix chain 'D' and resid 1005 through 1009 Processing helix chain 'D' and resid 1028 through 1037 Processing helix chain 'D' and resid 1118 through 1146 Proline residue: D1128 - end of helix removed outlier: 4.032A pdb=" N VAL D1131 " --> pdb=" O GLY D1127 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLN D1132 " --> pdb=" O PRO D1128 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL D1142 " --> pdb=" O GLU D1138 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N TYR D1143 " --> pdb=" O VAL D1139 " (cutoff:3.500A) Processing helix chain 'D' and resid 1151 through 1163 removed outlier: 3.922A pdb=" N ILE D1155 " --> pdb=" O HIS D1151 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE D1158 " --> pdb=" O HIS D1154 " (cutoff:3.500A) Processing helix chain 'D' and resid 1184 through 1198 removed outlier: 3.944A pdb=" N ALA D1189 " --> pdb=" O ALA D1185 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA D1196 " --> pdb=" O ARG D1192 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N GLU D1197 " --> pdb=" O ARG D1193 " (cutoff:3.500A) Processing helix chain 'D' and resid 1210 through 1217 Processing helix chain 'D' and resid 1220 through 1228 removed outlier: 4.144A pdb=" N SER D1226 " --> pdb=" O LEU D1222 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE D1227 " --> pdb=" O SER D1223 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN D1228 " --> pdb=" O ALA D1224 " (cutoff:3.500A) Processing helix chain 'D' and resid 1229 through 1241 Processing helix chain 'D' and resid 1248 through 1256 removed outlier: 3.833A pdb=" N VAL D1253 " --> pdb=" O LEU D1249 " (cutoff:3.500A) Processing helix chain 'D' and resid 1261 through 1264 Processing helix chain 'D' and resid 1265 through 1270 Processing helix chain 'D' and resid 1276 through 1283 Processing helix chain 'E' and resid 30 through 34 Processing helix chain 'E' and resid 36 through 42 Processing helix chain 'E' and resid 46 through 67 Processing helix chain 'E' and resid 87 through 98 Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 13 removed outlier: 6.626A pdb=" N ASP A 190 " --> pdb=" O PRO A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 93 through 100 removed outlier: 7.445A pdb=" N GLU A 135 " --> pdb=" O ILE A 56 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ILE A 56 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU A 137 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE A 54 " --> pdb=" O GLU A 137 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N VAL A 139 " --> pdb=" O THR A 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 85 through 87 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 Processing sheet with id=AA5, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA6, first strand: chain 'B' and resid 8 through 15 removed outlier: 6.594A pdb=" N ARG B 18 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N ARG B 18 " --> pdb=" O THR B 198 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N THR B 198 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ARG B 20 " --> pdb=" O VAL B 196 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL B 196 " --> pdb=" O ARG B 20 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL B 22 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ILE B 194 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLU B 24 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU B 192 " --> pdb=" O GLU B 24 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N THR B 187 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL B 183 " --> pdb=" O THR B 187 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 93 through 100 removed outlier: 7.533A pdb=" N GLU B 135 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N ILE B 56 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLU B 137 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ILE B 54 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 139 " --> pdb=" O THR B 52 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 85 through 87 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 106 Processing sheet with id=AB1, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB2, first strand: chain 'C' and resid 30 through 31 removed outlier: 6.445A pdb=" N VAL C 30 " --> pdb=" O ALA C 964 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 87 through 88 removed outlier: 6.560A pdb=" N PHE C 125 " --> pdb=" O PRO C 101 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N PHE C 103 " --> pdb=" O PRO C 123 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N GLY C 146 " --> pdb=" O LEU C 124 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N VAL C 126 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N PHE C 144 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N ALA C 128 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR C 142 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 7.387A pdb=" N PHE C 130 " --> pdb=" O SER C 140 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N SER C 140 " --> pdb=" O PHE C 130 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N ASN C 132 " --> pdb=" O ILE C 138 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ILE C 138 " --> pdb=" O ASN C 132 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 157 through 159 Processing sheet with id=AB5, first strand: chain 'C' and resid 367 through 370 removed outlier: 3.685A pdb=" N SER C 168 " --> pdb=" O ARG C 445 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 175 through 183 removed outlier: 5.899A pdb=" N HIS C 191 " --> pdb=" O VAL C 207 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU C 203 " --> pdb=" O VAL C 195 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 345 through 346 Processing sheet with id=AB8, first strand: chain 'C' and resid 496 through 497 removed outlier: 6.939A pdb=" N ILE C 503 " --> pdb=" O LEU C 522 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU C 522 " --> pdb=" O ILE C 503 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N THR C 505 " --> pdb=" O ASP C 520 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ASP C 520 " --> pdb=" O THR C 505 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N TYR C 507 " --> pdb=" O GLN C 518 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLN C 518 " --> pdb=" O TYR C 507 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS C 509 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 496 through 497 Processing sheet with id=AC1, first strand: chain 'C' and resid 633 through 634 removed outlier: 6.665A pdb=" N VAL C 633 " --> pdb=" O ILE C 693 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 658 through 662 removed outlier: 6.958A pdb=" N TYR C 648 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 5.022A pdb=" N VAL C 644 " --> pdb=" O TYR C 648 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N THR C 650 " --> pdb=" O GLU C 642 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 699 through 700 Processing sheet with id=AC4, first strand: chain 'C' and resid 998 through 999 removed outlier: 6.586A pdb=" N ILE C 726 " --> pdb=" O LYS C 888 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N LEU C 890 " --> pdb=" O ILE C 726 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N LEU C 728 " --> pdb=" O LEU C 890 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE C 727 " --> pdb=" O ILE C 907 " (cutoff:3.500A) removed outlier: 9.184A pdb=" N ILE C 906 " --> pdb=" O ASN C 709 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU C 711 " --> pdb=" O ILE C 906 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N LEU C 908 " --> pdb=" O LEU C 711 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA C 713 " --> pdb=" O LEU C 908 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR C1015 " --> pdb=" O ILE C 714 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 740 through 751 removed outlier: 3.691A pdb=" N GLY C 840 " --> pdb=" O TYR C 863 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N ALA C 865 " --> pdb=" O VAL C 838 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N VAL C 838 " --> pdb=" O ALA C 865 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N LYS C 867 " --> pdb=" O GLY C 836 " (cutoff:3.500A) removed outlier: 8.672A pdb=" N GLY C 836 " --> pdb=" O LYS C 867 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 759 through 760 Processing sheet with id=AC7, first strand: chain 'C' and resid 792 through 794 removed outlier: 6.579A pdb=" N LEU C 828 " --> pdb=" O LEU C 793 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 935 through 936 Processing sheet with id=AC9, first strand: chain 'C' and resid 1033 through 1035 removed outlier: 3.592A pdb=" N HIS C1033 " --> pdb=" O ARG D 427 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 1057 through 1059 removed outlier: 3.871A pdb=" N GLN C1057 " --> pdb=" O VAL D 422 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 1124 through 1129 removed outlier: 3.526A pdb=" N GLU D 9 " --> pdb=" O LEU C1129 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 359 through 360 removed outlier: 6.500A pdb=" N ILE F 359 " --> pdb=" O THR D 337 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLN D 329 " --> pdb=" O SER J 9 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N GLU F 378 " --> pdb=" O GLY J 8 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 90 through 92 removed outlier: 6.223A pdb=" N ILE H 90 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 10.337A pdb=" N ARG H 82 " --> pdb=" O GLU H 98 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N LEU H 100 " --> pdb=" O ARG H 82 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR H 84 " --> pdb=" O LEU H 100 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU H 83 " --> pdb=" O LEU H 75 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY H 73 " --> pdb=" O ILE H 85 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N PHE H 72 " --> pdb=" O PHE H 129 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG H 74 " --> pdb=" O ARG H 127 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG H 125 " --> pdb=" O ASP H 76 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ASP H 138 " --> pdb=" O HIS H 130 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU H 132 " --> pdb=" O VAL H 136 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N VAL H 136 " --> pdb=" O LEU H 132 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 39 through 45 removed outlier: 3.656A pdb=" N PHE J 44 " --> pdb=" O GLN J 28 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'D' and resid 93 through 102 removed outlier: 10.475A pdb=" N LEU D 97 " --> pdb=" O PRO D 318 " (cutoff:3.500A) removed outlier: 10.301A pdb=" N ALA D 99 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N ALA D 316 " --> pdb=" O ALA D 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 234 through 235 removed outlier: 5.013A pdb=" N ILE D 136 " --> pdb=" O ALA D 255 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA D 255 " --> pdb=" O ILE D 136 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 611 through 612 Processing sheet with id=AD9, first strand: chain 'D' and resid 885 through 887 Processing sheet with id=AE1, first strand: chain 'D' and resid 896 through 899 Processing sheet with id=AE2, first strand: chain 'D' and resid 901 through 902 Processing sheet with id=AE3, first strand: chain 'D' and resid 928 through 929 removed outlier: 6.713A pdb=" N ALA D 928 " --> pdb=" O ILE D 936 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 1076 through 1078 Processing sheet with id=AE5, first strand: chain 'D' and resid 1181 through 1183 removed outlier: 7.861A pdb=" N ALA D1203 " --> pdb=" O ILE D1169 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 1272 through 1275 1228 hydrogen bonds defined for protein. 3447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 85 hydrogen bonds 170 hydrogen bond angles 0 basepair planarities 35 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 6.21 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9443 1.34 - 1.46: 3812 1.46 - 1.57: 15793 1.57 - 1.69: 166 1.69 - 1.81: 167 Bond restraints: 29381 Sorted by residual: bond pdb=" C3' DG P 26 " pdb=" C2' DG P 26 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.84e+00 bond pdb=" C3' DC O 41 " pdb=" C2' DC O 41 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.51e+00 bond pdb=" C1' DT O 13 " pdb=" N1 DT O 13 " ideal model delta sigma weight residual 1.468 1.506 -0.038 1.40e-02 5.10e+03 7.42e+00 bond pdb=" C3' DT O 16 " pdb=" C2' DT O 16 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.24e+00 bond pdb=" C3' DA O 19 " pdb=" C2' DA O 19 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.95e+00 ... (remaining 29376 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 38439 1.10 - 2.19: 1226 2.19 - 3.29: 362 3.29 - 4.39: 95 4.39 - 5.49: 7 Bond angle restraints: 40129 Sorted by residual: angle pdb=" C GLU F 407 " pdb=" CA GLU F 407 " pdb=" CB GLU F 407 " ideal model delta sigma weight residual 116.63 111.61 5.02 1.16e+00 7.43e-01 1.88e+01 angle pdb=" N3 DT O 4 " pdb=" C4 DT O 4 " pdb=" O4 DT O 4 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" N3 DT O 15 " pdb=" C4 DT O 15 " pdb=" O4 DT O 15 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.80e+01 angle pdb=" N3 DT P 41 " pdb=" C4 DT P 41 " pdb=" O4 DT P 41 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.77e+01 angle pdb=" N3 DT O 3 " pdb=" C4 DT O 3 " pdb=" O4 DT O 3 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 ... (remaining 40124 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.61: 17026 32.61 - 65.23: 697 65.23 - 97.84: 59 97.84 - 130.46: 0 130.46 - 163.07: 3 Dihedral angle restraints: 17785 sinusoidal: 7879 harmonic: 9906 Sorted by residual: dihedral pdb=" CA GLN F 423 " pdb=" C GLN F 423 " pdb=" N PRO F 424 " pdb=" CA PRO F 424 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C4' DA O 19 " pdb=" C3' DA O 19 " pdb=" O3' DA O 19 " pdb=" P DT O 20 " ideal model delta sinusoidal sigma weight residual 220.00 56.93 163.07 1 3.50e+01 8.16e-04 1.53e+01 dihedral pdb=" C4' DA P 35 " pdb=" C3' DA P 35 " pdb=" O3' DA P 35 " pdb=" P DA P 36 " ideal model delta sinusoidal sigma weight residual 220.00 61.37 158.63 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 17782 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 3096 0.032 - 0.064: 901 0.064 - 0.096: 258 0.096 - 0.128: 216 0.128 - 0.160: 81 Chirality restraints: 4552 Sorted by residual: chirality pdb=" C3' DT P 43 " pdb=" C4' DT P 43 " pdb=" O3' DT P 43 " pdb=" C2' DT P 43 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" C3' DT O 13 " pdb=" C4' DT O 13 " pdb=" O3' DT O 13 " pdb=" C2' DT O 13 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" C3' DC P 6 " pdb=" C4' DC P 6 " pdb=" O3' DC P 6 " pdb=" C2' DC P 6 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 4549 not shown) Planarity restraints: 4993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 98 " 0.052 5.00e-02 4.00e+02 7.85e-02 9.87e+00 pdb=" N PRO H 99 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO H 99 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO H 99 " 0.043 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 397 " -0.009 2.00e-02 2.50e+03 1.84e-02 3.39e+00 pdb=" C GLN F 397 " 0.032 2.00e-02 2.50e+03 pdb=" O GLN F 397 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU F 398 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 196 " -0.010 2.00e-02 2.50e+03 1.21e-02 2.94e+00 pdb=" CG TYR F 196 " 0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR F 196 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR F 196 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 196 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 196 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR F 196 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR F 196 " 0.003 2.00e-02 2.50e+03 ... (remaining 4990 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 164 2.58 - 3.16: 23480 3.16 - 3.74: 43413 3.74 - 4.32: 60098 4.32 - 4.90: 100443 Nonbonded interactions: 227598 Sorted by model distance: nonbonded pdb=" O ILE F 365 " pdb=" OG SER F 371 " model vdw 1.998 3.040 nonbonded pdb=" OD1 ASP C1029 " pdb=" NZ LYS D 520 " model vdw 2.036 3.120 nonbonded pdb=" O ALA D 301 " pdb=" OG SER D 305 " model vdw 2.049 3.040 nonbonded pdb=" NH2 ARG J 27 " pdb=" O LYS D 71 " model vdw 2.075 3.120 nonbonded pdb=" OD1 ASP C 298 " pdb=" OG SER C 322 " model vdw 2.131 3.040 ... (remaining 227593 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and resid 1 through 226) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.98 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: 2.930 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: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 28.480 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 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 : 0.003 0.072 29389 Z= 0.200 Angle : 0.527 7.844 40141 Z= 0.347 Chirality : 0.043 0.160 4552 Planarity : 0.003 0.079 4993 Dihedral : 16.263 163.071 11409 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.26 (0.15), residues: 3438 helix: 1.91 (0.15), residues: 1281 sheet: 0.33 (0.25), residues: 427 loop : 0.24 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 77 TYR 0.030 0.001 TYR F 196 PHE 0.015 0.001 PHE C 364 TRP 0.011 0.001 TRP D 777 HIS 0.005 0.001 HIS D 748 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.20 (29381) covalent geometry : angle 0.52427 / 0.35 (40129) hydrogen bonds : bond 0.15356 / 10.68 ( 1311) hydrogen bonds : angle 5.84288 / 4.20 ( 3617) metal coordination : bond 0.03821 / 1.81 ( 8) metal coordination : angle 3.05948 / 1.57 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 385 time to evaluate : 1.007 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: C 209 LYS cc_start: 0.7582 (ptmm) cc_final: 0.7352 (tttp) REVERT: F 415 LEU cc_start: 0.8059 (mt) cc_final: 0.7714 (mp) REVERT: H 63 LEU cc_start: 0.6840 (mt) cc_final: 0.6581 (mt) REVERT: J 29 VAL cc_start: 0.8723 (p) cc_final: 0.6812 (p) REVERT: D 270 ILE cc_start: 0.7424 (tp) cc_final: 0.6777 (tp) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.2151 time to fit residues: 123.5355 Evaluate side-chains 213 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 0.3980 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 4.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 5 GLN A 152 ASN ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 223 GLN C 434 ASN C 470 HIS C 866 GLN C1045 GLN F 326 GLN F 454 HIS D 233 GLN D 686 GLN ** D1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.079266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.056775 restraints weight = 87867.725| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.11 r_work: 0.2896 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 29389 Z= 0.212 Angle : 0.631 12.486 40141 Z= 0.337 Chirality : 0.045 0.294 4552 Planarity : 0.005 0.046 4993 Dihedral : 14.904 167.470 4736 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.76 % Allowed : 6.67 % Favored : 92.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.07 (0.14), residues: 3438 helix: 1.66 (0.15), residues: 1321 sheet: 0.51 (0.26), residues: 423 loop : 0.09 (0.15), residues: 1694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 77 TYR 0.016 0.002 TYR C 722 PHE 0.026 0.002 PHE D 268 TRP 0.010 0.001 TRP D 223 HIS 0.009 0.001 HIS F 454 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.21 (29381) covalent geometry : angle 0.62742 / 0.34 (40129) hydrogen bonds : bond 0.04838 / 3.32 ( 1311) hydrogen bonds : angle 4.69693 / 3.39 ( 3617) metal coordination : bond 0.01061 / 0.51 ( 8) metal coordination : angle 3.95672 / 2.10 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 215 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 209 LYS cc_start: 0.8304 (ptmm) cc_final: 0.7505 (tttp) REVERT: C 296 ARG cc_start: 0.8033 (ttp80) cc_final: 0.7720 (ttp80) REVERT: F 182 GLU cc_start: 0.9050 (tp30) cc_final: 0.8679 (tp30) REVERT: F 196 TYR cc_start: 0.8791 (t80) cc_final: 0.8418 (t80) REVERT: F 204 LEU cc_start: 0.8495 (tt) cc_final: 0.8236 (mp) REVERT: F 415 LEU cc_start: 0.8810 (mt) cc_final: 0.8554 (mp) REVERT: H 138 ASP cc_start: 0.6103 (OUTLIER) cc_final: 0.5567 (t0) REVERT: D 764 LEU cc_start: 0.7832 (tp) cc_final: 0.7372 (mp) outliers start: 22 outliers final: 13 residues processed: 228 average time/residue: 0.1922 time to fit residues: 69.3371 Evaluate side-chains 200 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 186 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 ASN Chi-restraints excluded: chain B residue 60 LEU Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain D residue 118 LEU Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain E residue 63 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 135 optimal weight: 0.8980 chunk 121 optimal weight: 0.9980 chunk 153 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 129 optimal weight: 0.9990 chunk 141 optimal weight: 8.9990 chunk 316 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 88 optimal weight: 0.2980 chunk 0 optimal weight: 8.9990 chunk 321 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 284 GLN F 454 HIS ** D1146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.079684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.057370 restraints weight = 87677.675| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 3.13 r_work: 0.2910 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2911 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 29389 Z= 0.111 Angle : 0.527 11.914 40141 Z= 0.283 Chirality : 0.042 0.304 4552 Planarity : 0.004 0.052 4993 Dihedral : 15.007 168.796 4736 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.69 % Allowed : 7.80 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.26 (0.15), residues: 3438 helix: 1.82 (0.15), residues: 1325 sheet: 0.69 (0.26), residues: 413 loop : 0.17 (0.15), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 31 TYR 0.014 0.001 TYR D 36 PHE 0.017 0.001 PHE D 268 TRP 0.028 0.001 TRP J 82 HIS 0.007 0.001 HIS D 941 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 (29381) covalent geometry : angle 0.52555 / 0.28 (40129) hydrogen bonds : bond 0.04081 / 2.79 ( 1311) hydrogen bonds : angle 4.39314 / 3.17 ( 3617) metal coordination : bond 0.00448 / 0.21 ( 8) metal coordination : angle 2.60188 / 1.38 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 207 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 100 GLN cc_start: 0.8328 (tp40) cc_final: 0.8114 (tp-100) REVERT: C 209 LYS cc_start: 0.8296 (ptmm) cc_final: 0.7456 (tttp) REVERT: C 296 ARG cc_start: 0.8069 (ttp80) cc_final: 0.7533 (mtm110) REVERT: F 196 TYR cc_start: 0.8746 (t80) cc_final: 0.8210 (t80) REVERT: F 204 LEU cc_start: 0.8400 (tt) cc_final: 0.8046 (mp) REVERT: F 354 TYR cc_start: 0.8381 (m-80) cc_final: 0.8177 (m-80) REVERT: F 415 LEU cc_start: 0.8834 (mt) cc_final: 0.8585 (mp) REVERT: J 28 GLN cc_start: 0.8093 (mp10) cc_final: 0.7801 (pm20) REVERT: J 84 MET cc_start: 0.8829 (mtm) cc_final: 0.8572 (mtt) REVERT: D 366 ILE cc_start: 0.7264 (mp) cc_final: 0.6922 (mt) outliers start: 20 outliers final: 13 residues processed: 221 average time/residue: 0.1772 time to fit residues: 63.0386 Evaluate side-chains 195 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 182 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain E residue 63 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 130 optimal weight: 8.9990 chunk 111 optimal weight: 0.6980 chunk 349 optimal weight: 30.0000 chunk 327 optimal weight: 7.9990 chunk 199 optimal weight: 30.0000 chunk 90 optimal weight: 4.9990 chunk 194 optimal weight: 10.0000 chunk 341 optimal weight: 8.9990 chunk 156 optimal weight: 7.9990 chunk 248 optimal weight: 6.9990 chunk 186 optimal weight: 7.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 921 GLN F 454 HIS D 224 ASN D1105 HIS D1146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.074788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.052436 restraints weight = 88917.326| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 3.10 r_work: 0.2780 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2783 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2783 r_free = 0.2783 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2783 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 29389 Z= 0.349 Angle : 0.706 11.638 40141 Z= 0.371 Chirality : 0.048 0.311 4552 Planarity : 0.005 0.047 4993 Dihedral : 15.322 166.362 4736 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.11 % Favored : 96.86 % Rotamer: Outliers : 1.65 % Allowed : 10.03 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.72 (0.14), residues: 3438 helix: 1.37 (0.14), residues: 1330 sheet: 0.46 (0.27), residues: 385 loop : -0.15 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 223 TYR 0.018 0.002 TYR C 120 PHE 0.027 0.002 PHE C 364 TRP 0.028 0.002 TRP J 82 HIS 0.010 0.002 HIS H 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00820 / 0.35 (29381) covalent geometry : angle 0.70265 / 0.37 (40129) hydrogen bonds : bond 0.05713 / 3.90 ( 1311) hydrogen bonds : angle 4.70770 / 3.37 ( 3617) metal coordination : bond 0.01781 / 0.87 ( 8) metal coordination : angle 3.91714 / 1.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 1.056 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: C 209 LYS cc_start: 0.8390 (ptmm) cc_final: 0.7513 (tttp) REVERT: C 296 ARG cc_start: 0.8035 (ttp80) cc_final: 0.7570 (mtm180) REVERT: C 551 MET cc_start: 0.8563 (mmm) cc_final: 0.8314 (tpt) REVERT: F 182 GLU cc_start: 0.9031 (tp30) cc_final: 0.8597 (tp30) REVERT: F 204 LEU cc_start: 0.8448 (tt) cc_final: 0.8177 (mt) REVERT: F 221 TRP cc_start: 0.8899 (t60) cc_final: 0.8447 (t60) REVERT: F 354 TYR cc_start: 0.8571 (m-80) cc_final: 0.8338 (m-80) REVERT: F 415 LEU cc_start: 0.8830 (mt) cc_final: 0.8545 (mp) REVERT: H 138 ASP cc_start: 0.6030 (OUTLIER) cc_final: 0.5545 (t0) REVERT: D 764 LEU cc_start: 0.7874 (tp) cc_final: 0.7607 (mp) outliers start: 48 outliers final: 27 residues processed: 224 average time/residue: 0.1677 time to fit residues: 60.9900 Evaluate side-chains 197 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 559 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1122 LEU Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain D residue 1273 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 93 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 264 optimal weight: 0.8980 chunk 250 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 298 optimal weight: 4.9990 chunk 243 optimal weight: 0.7980 chunk 277 optimal weight: 0.0050 chunk 138 optimal weight: 2.9990 chunk 280 optimal weight: 0.7980 chunk 305 optimal weight: 3.9990 chunk 319 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 454 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.077421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.055137 restraints weight = 87258.181| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 3.11 r_work: 0.2856 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8819 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 29389 Z= 0.110 Angle : 0.540 13.360 40141 Z= 0.286 Chirality : 0.042 0.295 4552 Planarity : 0.004 0.089 4993 Dihedral : 15.241 169.332 4736 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.20 % Allowed : 10.93 % Favored : 87.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.11 (0.15), residues: 3438 helix: 1.79 (0.15), residues: 1322 sheet: 0.50 (0.26), residues: 407 loop : 0.03 (0.15), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 223 TYR 0.016 0.001 TYR F 196 PHE 0.016 0.001 PHE D 268 TRP 0.032 0.001 TRP J 82 HIS 0.008 0.001 HIS D 941 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.11 (29381) covalent geometry : angle 0.53788 / 0.29 (40129) hydrogen bonds : bond 0.04010 / 2.72 ( 1311) hydrogen bonds : angle 4.29100 / 3.09 ( 3617) metal coordination : bond 0.00495 / 0.23 ( 8) metal coordination : angle 2.85421 / 1.37 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 192 time to evaluate : 0.740 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: C 209 LYS cc_start: 0.8303 (ptmm) cc_final: 0.7340 (tttp) REVERT: C 296 ARG cc_start: 0.8067 (ttp80) cc_final: 0.7844 (ttp80) REVERT: C 551 MET cc_start: 0.8545 (mmm) cc_final: 0.8264 (tpt) REVERT: C 1119 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.6786 (mp) REVERT: F 182 GLU cc_start: 0.9014 (tp30) cc_final: 0.8507 (tp30) REVERT: F 354 TYR cc_start: 0.8498 (m-80) cc_final: 0.8292 (m-80) REVERT: F 415 LEU cc_start: 0.8852 (mt) cc_final: 0.8586 (mp) REVERT: H 138 ASP cc_start: 0.6075 (OUTLIER) cc_final: 0.5643 (t0) REVERT: J 28 GLN cc_start: 0.8017 (mp10) cc_final: 0.7736 (pm20) REVERT: J 99 LYS cc_start: 0.9217 (tppp) cc_final: 0.8708 (tptt) REVERT: D 170 LEU cc_start: 0.5971 (OUTLIER) cc_final: 0.5456 (mm) REVERT: D 205 MET cc_start: 0.7946 (tpp) cc_final: 0.7668 (mmm) REVERT: D 366 ILE cc_start: 0.7514 (mp) cc_final: 0.7277 (mt) REVERT: D 1088 ARG cc_start: 0.7801 (tpt-90) cc_final: 0.7110 (tpt170) outliers start: 35 outliers final: 18 residues processed: 218 average time/residue: 0.1681 time to fit residues: 60.0018 Evaluate side-chains 197 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 176 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 248 ILE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1122 LEU Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain D residue 1273 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 216 optimal weight: 9.9990 chunk 344 optimal weight: 40.0000 chunk 278 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 150 optimal weight: 6.9990 chunk 154 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 331 optimal weight: 0.8980 chunk 91 optimal weight: 6.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 454 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.074964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.052673 restraints weight = 88355.679| |-----------------------------------------------------------------------------| r_work (start): 0.2928 rms_B_bonded: 3.07 r_work: 0.2791 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2795 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2795 r_free = 0.2795 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2794 r_free = 0.2794 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2794 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 29389 Z= 0.286 Angle : 0.643 13.171 40141 Z= 0.336 Chirality : 0.046 0.311 4552 Planarity : 0.005 0.047 4993 Dihedral : 15.384 166.952 4736 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 1.65 % Allowed : 11.37 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.84 (0.14), residues: 3438 helix: 1.55 (0.14), residues: 1328 sheet: 0.43 (0.27), residues: 380 loop : -0.13 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 223 TYR 0.022 0.002 TYR F 196 PHE 0.022 0.002 PHE C 130 TRP 0.039 0.002 TRP J 82 HIS 0.007 0.001 HIS H 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.29 (29381) covalent geometry : angle 0.64014 / 0.34 (40129) hydrogen bonds : bond 0.05052 / 3.44 ( 1311) hydrogen bonds : angle 4.51416 / 3.23 ( 3617) metal coordination : bond 0.01524 / 0.74 ( 8) metal coordination : angle 3.31046 / 1.52 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 0.683 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: C 296 ARG cc_start: 0.8025 (ttp80) cc_final: 0.7815 (ttp80) REVERT: C 1119 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.6888 (mp) REVERT: F 182 GLU cc_start: 0.9073 (tp30) cc_final: 0.8658 (tp30) REVERT: F 196 TYR cc_start: 0.9019 (t80) cc_final: 0.8368 (t80) REVERT: F 221 TRP cc_start: 0.8901 (t60) cc_final: 0.8632 (t60) REVERT: F 354 TYR cc_start: 0.8630 (m-80) cc_final: 0.8351 (m-80) REVERT: H 138 ASP cc_start: 0.6130 (OUTLIER) cc_final: 0.5686 (t0) REVERT: J 99 LYS cc_start: 0.9186 (tppp) cc_final: 0.8654 (tptt) REVERT: D 143 MET cc_start: 0.3201 (ptm) cc_final: 0.2480 (tmm) outliers start: 48 outliers final: 32 residues processed: 213 average time/residue: 0.1654 time to fit residues: 57.1480 Evaluate side-chains 203 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1122 LEU Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 398 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 135 VAL Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 461 VAL Chi-restraints excluded: chain D residue 765 ASN Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain D residue 1273 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 93 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 150 optimal weight: 0.9980 chunk 234 optimal weight: 10.0000 chunk 123 optimal weight: 5.9990 chunk 286 optimal weight: 4.9990 chunk 211 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 chunk 304 optimal weight: 2.9990 chunk 170 optimal weight: 5.9990 chunk 257 optimal weight: 0.0980 chunk 236 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 454 HIS ** H 64 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 = 0.3534 r_free = 0.3534 target = 0.076618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.054494 restraints weight = 86873.909| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 3.08 r_work: 0.2842 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2845 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29389 Z= 0.123 Angle : 0.539 13.431 40141 Z= 0.284 Chirality : 0.042 0.298 4552 Planarity : 0.004 0.044 4993 Dihedral : 15.330 169.400 4736 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.55 % Allowed : 11.55 % Favored : 86.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.07 (0.15), residues: 3438 helix: 1.77 (0.15), residues: 1331 sheet: 0.49 (0.28), residues: 385 loop : -0.02 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 223 TYR 0.014 0.001 TYR F 354 PHE 0.017 0.001 PHE D 268 TRP 0.036 0.001 TRP J 82 HIS 0.005 0.001 HIS D 941 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (29381) covalent geometry : angle 0.53660 / 0.28 (40129) hydrogen bonds : bond 0.03962 / 2.69 ( 1311) hydrogen bonds : angle 4.24680 / 3.05 ( 3617) metal coordination : bond 0.00651 / 0.31 ( 8) metal coordination : angle 2.84138 / 1.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 176 time to evaluate : 0.829 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: C 296 ARG cc_start: 0.8058 (ttp80) cc_final: 0.7580 (mtm110) REVERT: C 1119 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.6827 (mp) REVERT: F 182 GLU cc_start: 0.9062 (tp30) cc_final: 0.8618 (tp30) REVERT: F 196 TYR cc_start: 0.8968 (t80) cc_final: 0.8262 (t80) REVERT: F 221 TRP cc_start: 0.8856 (t60) cc_final: 0.8564 (t60) REVERT: H 138 ASP cc_start: 0.6108 (OUTLIER) cc_final: 0.5629 (t0) REVERT: J 28 GLN cc_start: 0.7916 (mp10) cc_final: 0.7605 (pm20) REVERT: J 99 LYS cc_start: 0.9194 (tppp) cc_final: 0.8676 (tptt) REVERT: D 167 ASP cc_start: 0.8902 (t0) cc_final: 0.8627 (m-30) REVERT: D 205 MET cc_start: 0.7907 (tpp) cc_final: 0.7687 (mmm) REVERT: D 976 MET cc_start: 0.9085 (mmm) cc_final: 0.8533 (mmm) REVERT: D 1080 LYS cc_start: 0.9206 (mttp) cc_final: 0.8986 (tmtt) outliers start: 45 outliers final: 34 residues processed: 213 average time/residue: 0.1639 time to fit residues: 57.7300 Evaluate side-chains 206 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1122 LEU Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 900 LEU Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain D residue 1273 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 96 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 14 optimal weight: 8.9990 chunk 326 optimal weight: 9.9990 chunk 116 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 186 optimal weight: 10.0000 chunk 193 optimal weight: 6.9990 chunk 332 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 81 optimal weight: 3.9990 chunk 209 optimal weight: 9.9990 chunk 103 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 423 GLN ** H 64 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 = 0.3522 r_free = 0.3522 target = 0.076047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.054010 restraints weight = 87402.910| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 3.07 r_work: 0.2828 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2831 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2831 r_free = 0.2831 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2831 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 29389 Z= 0.165 Angle : 0.559 13.828 40141 Z= 0.292 Chirality : 0.043 0.305 4552 Planarity : 0.004 0.044 4993 Dihedral : 15.345 168.082 4736 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.72 % Allowed : 12.10 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.06 (0.15), residues: 3438 helix: 1.76 (0.15), residues: 1334 sheet: 0.47 (0.28), residues: 385 loop : -0.02 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.012 0.001 TYR C 120 PHE 0.015 0.001 PHE D 268 TRP 0.054 0.001 TRP J 82 HIS 0.009 0.001 HIS D 941 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (29381) covalent geometry : angle 0.55656 / 0.29 (40129) hydrogen bonds : bond 0.04161 / 2.84 ( 1311) hydrogen bonds : angle 4.25956 / 3.06 ( 3617) metal coordination : bond 0.00887 / 0.43 ( 8) metal coordination : angle 2.75405 / 1.26 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 178 time to evaluate : 0.796 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: C 1119 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.6826 (mp) REVERT: F 182 GLU cc_start: 0.9067 (tp30) cc_final: 0.8634 (tp30) REVERT: F 196 TYR cc_start: 0.8998 (t80) cc_final: 0.8294 (t80) REVERT: F 221 TRP cc_start: 0.8889 (t60) cc_final: 0.8576 (t60) REVERT: F 423 GLN cc_start: 0.7869 (OUTLIER) cc_final: 0.7014 (mp10) REVERT: H 138 ASP cc_start: 0.6072 (OUTLIER) cc_final: 0.5636 (t0) REVERT: J 28 GLN cc_start: 0.7880 (mp10) cc_final: 0.7593 (pm20) REVERT: J 99 LYS cc_start: 0.9162 (tppp) cc_final: 0.8634 (tptt) REVERT: D 143 MET cc_start: 0.3125 (ptm) cc_final: 0.2547 (tmm) REVERT: D 170 LEU cc_start: 0.5915 (OUTLIER) cc_final: 0.4951 (tp) REVERT: D 176 LYS cc_start: 0.6082 (mttm) cc_final: 0.5721 (tppt) REVERT: D 205 MET cc_start: 0.8037 (tpp) cc_final: 0.7672 (mmt) REVERT: D 976 MET cc_start: 0.9074 (mmm) cc_final: 0.8506 (mmm) REVERT: D 1080 LYS cc_start: 0.9200 (mttp) cc_final: 0.8986 (tmtt) outliers start: 50 outliers final: 40 residues processed: 218 average time/residue: 0.1542 time to fit residues: 54.9258 Evaluate side-chains 215 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 171 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 MET Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 LEU Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1119 LEU Chi-restraints excluded: chain C residue 1122 LEU Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain F residue 423 GLN Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 900 LEU Chi-restraints excluded: chain D residue 971 THR Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain D residue 1273 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 96 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 114 optimal weight: 0.9980 chunk 122 optimal weight: 0.6980 chunk 144 optimal weight: 0.9980 chunk 234 optimal weight: 9.9990 chunk 62 optimal weight: 9.9990 chunk 45 optimal weight: 0.0980 chunk 93 optimal weight: 0.9980 chunk 159 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 191 optimal weight: 8.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.077541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.055466 restraints weight = 87372.826| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.06 r_work: 0.2869 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8836 moved from start: 0.2969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 29389 Z= 0.106 Angle : 0.534 13.557 40141 Z= 0.279 Chirality : 0.041 0.299 4552 Planarity : 0.004 0.042 4993 Dihedral : 15.304 169.295 4736 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 1.34 % Allowed : 12.44 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.16 (0.15), residues: 3438 helix: 1.86 (0.15), residues: 1331 sheet: 0.57 (0.28), residues: 385 loop : 0.03 (0.15), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 425 TYR 0.012 0.001 TYR C 335 PHE 0.015 0.001 PHE D 268 TRP 0.082 0.002 TRP J 82 HIS 0.009 0.001 HIS D 941 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 (29381) covalent geometry : angle 0.53253 / 0.28 (40129) hydrogen bonds : bond 0.03665 / 2.48 ( 1311) hydrogen bonds : angle 4.14307 / 2.98 ( 3617) metal coordination : bond 0.00451 / 0.21 ( 8) metal coordination : angle 2.62110 / 1.23 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 176 time to evaluate : 0.939 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: C 250 MET cc_start: 0.6086 (mmm) cc_final: 0.5761 (mmm) REVERT: F 182 GLU cc_start: 0.9090 (tp30) cc_final: 0.8683 (tp30) REVERT: F 196 TYR cc_start: 0.8909 (t80) cc_final: 0.8200 (t80) REVERT: F 221 TRP cc_start: 0.8870 (t60) cc_final: 0.8559 (t60) REVERT: H 138 ASP cc_start: 0.6060 (OUTLIER) cc_final: 0.5632 (t0) REVERT: J 28 GLN cc_start: 0.7908 (mp10) cc_final: 0.7665 (pm20) REVERT: J 99 LYS cc_start: 0.9170 (tppp) cc_final: 0.8638 (tptt) REVERT: D 143 MET cc_start: 0.3137 (ptm) cc_final: 0.2470 (tmm) REVERT: D 167 ASP cc_start: 0.8914 (t0) cc_final: 0.8660 (m-30) REVERT: D 170 LEU cc_start: 0.5825 (OUTLIER) cc_final: 0.5377 (mm) REVERT: D 176 LYS cc_start: 0.6067 (mttm) cc_final: 0.5720 (tppt) REVERT: D 976 MET cc_start: 0.9085 (mmm) cc_final: 0.8538 (mmm) REVERT: D 1080 LYS cc_start: 0.9106 (mttp) cc_final: 0.8752 (tptt) outliers start: 39 outliers final: 35 residues processed: 208 average time/residue: 0.1569 time to fit residues: 54.3510 Evaluate side-chains 207 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 170 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1122 LEU Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 170 LEU Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 900 LEU Chi-restraints excluded: chain D residue 971 THR Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain D residue 1273 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 258 optimal weight: 6.9990 chunk 276 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 142 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 262 optimal weight: 5.9990 chunk 239 optimal weight: 0.9990 chunk 236 optimal weight: 1.9990 chunk 166 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.077063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.054894 restraints weight = 87551.222| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.07 r_work: 0.2854 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8850 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29389 Z= 0.138 Angle : 0.549 14.142 40141 Z= 0.284 Chirality : 0.042 0.305 4552 Planarity : 0.004 0.042 4993 Dihedral : 15.303 168.487 4736 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.48 % Allowed : 12.54 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 1.17 (0.15), residues: 3438 helix: 1.86 (0.15), residues: 1330 sheet: 0.54 (0.27), residues: 395 loop : 0.04 (0.15), residues: 1713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 203 TYR 0.019 0.001 TYR F 354 PHE 0.015 0.001 PHE C 130 TRP 0.082 0.002 TRP J 82 HIS 0.009 0.001 HIS D 941 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 (29381) covalent geometry : angle 0.54765 / 0.28 (40129) hydrogen bonds : bond 0.03810 / 2.59 ( 1311) hydrogen bonds : angle 4.15852 / 2.98 ( 3617) metal coordination : bond 0.00717 / 0.35 ( 8) metal coordination : angle 2.50803 / 1.16 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6876 Ramachandran restraints generated. 3438 Oldfield, 0 Emsley, 3438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 1.088 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: C 250 MET cc_start: 0.6244 (mmm) cc_final: 0.5947 (mmm) REVERT: F 182 GLU cc_start: 0.9095 (tp30) cc_final: 0.8693 (tp30) REVERT: F 196 TYR cc_start: 0.8975 (t80) cc_final: 0.8755 (t80) REVERT: F 221 TRP cc_start: 0.8907 (t60) cc_final: 0.8589 (t60) REVERT: H 138 ASP cc_start: 0.6067 (OUTLIER) cc_final: 0.5618 (t0) REVERT: J 28 GLN cc_start: 0.7880 (mp10) cc_final: 0.7637 (pm20) REVERT: J 99 LYS cc_start: 0.9148 (tppp) cc_final: 0.8609 (tptt) REVERT: D 167 ASP cc_start: 0.8936 (t0) cc_final: 0.8640 (m-30) REVERT: D 176 LYS cc_start: 0.6082 (mttm) cc_final: 0.5740 (tppt) REVERT: D 976 MET cc_start: 0.9105 (mmm) cc_final: 0.8559 (mmm) outliers start: 43 outliers final: 37 residues processed: 211 average time/residue: 0.1540 time to fit residues: 53.4157 Evaluate side-chains 211 residues out of total 2910 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 173 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain C residue 138 ILE Chi-restraints excluded: chain C residue 176 VAL Chi-restraints excluded: chain C residue 212 THR Chi-restraints excluded: chain C residue 245 PHE Chi-restraints excluded: chain C residue 279 THR Chi-restraints excluded: chain C residue 337 VAL Chi-restraints excluded: chain C residue 364 PHE Chi-restraints excluded: chain C residue 388 GLU Chi-restraints excluded: chain C residue 390 VAL Chi-restraints excluded: chain C residue 551 MET Chi-restraints excluded: chain C residue 570 MET Chi-restraints excluded: chain C residue 617 VAL Chi-restraints excluded: chain C residue 806 THR Chi-restraints excluded: chain C residue 965 THR Chi-restraints excluded: chain C residue 967 VAL Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1082 ILE Chi-restraints excluded: chain C residue 1122 LEU Chi-restraints excluded: chain F residue 173 ILE Chi-restraints excluded: chain F residue 383 VAL Chi-restraints excluded: chain F residue 415 LEU Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 138 ASP Chi-restraints excluded: chain J residue 16 TYR Chi-restraints excluded: chain D residue 92 MET Chi-restraints excluded: chain D residue 216 LEU Chi-restraints excluded: chain D residue 799 ILE Chi-restraints excluded: chain D residue 900 LEU Chi-restraints excluded: chain D residue 971 THR Chi-restraints excluded: chain D residue 1181 LEU Chi-restraints excluded: chain D residue 1273 VAL Chi-restraints excluded: chain E residue 28 THR Chi-restraints excluded: chain E residue 93 LEU Chi-restraints excluded: chain E residue 96 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 350 random chunks: chunk 149 optimal weight: 4.9990 chunk 64 optimal weight: 9.9990 chunk 307 optimal weight: 10.0000 chunk 196 optimal weight: 6.9990 chunk 295 optimal weight: 9.9990 chunk 174 optimal weight: 0.9980 chunk 263 optimal weight: 7.9990 chunk 129 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 247 optimal weight: 0.7980 chunk 97 optimal weight: 10.0000 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 423 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.075070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.052983 restraints weight = 87876.806| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 3.07 r_work: 0.2800 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2804 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2804 r_free = 0.2804 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.2804 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 29389 Z= 0.239 Angle : 0.612 13.541 40141 Z= 0.317 Chirality : 0.044 0.312 4552 Planarity : 0.004 0.045 4993 Dihedral : 15.397 168.123 4736 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.55 % Allowed : 12.65 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.55 % 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: 0.97 (0.15), residues: 3438 helix: 1.68 (0.15), residues: 1337 sheet: 0.44 (0.27), residues: 393 loop : -0.07 (0.15), residues: 1708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 223 TYR 0.017 0.002 TYR F 354 PHE 0.019 0.002 PHE C 130 TRP 0.042 0.002 TRP J 82 HIS 0.009 0.001 HIS D 941 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.24 (29381) covalent geometry : angle 0.60953 / 0.32 (40129) hydrogen bonds : bond 0.04569 / 3.10 ( 1311) hydrogen bonds : angle 4.36155 / 3.12 ( 3617) metal coordination : bond 0.01321 / 0.64 ( 8) metal coordination : angle 2.99907 / 1.31 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6189.96 seconds wall clock time: 106 minutes 30.58 seconds (6390.58 seconds total)