Starting phenix.real_space_refine on Thu Mar 5 05:42:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rdd_4814/03_2026/6rdd_4814.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rdd_4814/03_2026/6rdd_4814.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rdd_4814/03_2026/6rdd_4814.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rdd_4814/03_2026/6rdd_4814.map" model { file = "/net/cci-nas-00/data/ceres_data/6rdd_4814/03_2026/6rdd_4814.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rdd_4814/03_2026/6rdd_4814.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 33 5.16 5 C 12734 2.51 5 N 3312 2.21 5 O 3776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19856 Number of models: 1 Model: "" Number of chains: 19 Chain: "0" Number of atoms: 607 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 607 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 8, 'TRANS': 72} Chain: "1" Number of atoms: 4661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 595, 4661 Classifications: {'peptide': 595} Link IDs: {'PTRANS': 31, 'TRANS': 563} Chain: "2" Number of atoms: 3163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3163 Classifications: {'peptide': 441} Link IDs: {'PTRANS': 17, 'TRANS': 423} Chain: "3" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1874 Classifications: {'peptide': 245} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 239} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 7 Chain: "4" Number of atoms: 2177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 2177 Classifications: {'peptide': 290} Link IDs: {'PTRANS': 9, 'TRANS': 280} Chain: "5" Number of atoms: 986 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 986 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "6" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 926 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "7" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1347 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 5, 'TRANS': 170} Chain: "8" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 692 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 7, 'TRANS': 80} Chain: "9" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 776 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "M" Number of atoms: 1640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1640 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 204} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "P" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 646 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "T" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 330 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "6" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Time building chain proxies: 3.72, per 1000 atoms: 0.19 Number of scatterers: 19856 At special positions: 0 Unit cell: (180.063, 120.042, 249.561, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 33 16.00 O 3776 8.00 N 3312 7.00 C 12734 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: 1.80 Conformation dependent library (CDL) restraints added in 878.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN M 600 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 248 " pdb="ZN ZN M 600 " - pdb=" NE2 HIS M 252 " 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4918 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 7 sheets defined 67.8% alpha, 2.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.57 Creating SS restraints... Processing helix chain '0' and resid 17 through 30 removed outlier: 3.618A pdb=" N LEU 0 21 " --> pdb=" O GLY 0 17 " (cutoff:3.500A) Processing helix chain '0' and resid 43 through 50 Processing helix chain '0' and resid 51 through 56 Processing helix chain '1' and resid 45 through 73 removed outlier: 3.573A pdb=" N ASN 1 51 " --> pdb=" O VAL 1 47 " (cutoff:3.500A) Processing helix chain '1' and resid 96 through 100 removed outlier: 3.683A pdb=" N THR 1 99 " --> pdb=" O ASP 1 96 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLN 1 100 " --> pdb=" O PHE 1 97 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 96 through 100' Processing helix chain '1' and resid 105 through 124 removed outlier: 4.450A pdb=" N LYS 1 109 " --> pdb=" O GLY 1 105 " (cutoff:3.500A) Processing helix chain '1' and resid 126 through 139 removed outlier: 3.982A pdb=" N THR 1 135 " --> pdb=" O ALA 1 131 " (cutoff:3.500A) Processing helix chain '1' and resid 163 through 176 removed outlier: 3.990A pdb=" N THR 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '1' and resid 190 through 204 removed outlier: 4.414A pdb=" N ALA 1 196 " --> pdb=" O GLY 1 192 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL 1 197 " --> pdb=" O VAL 1 193 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP 1 199 " --> pdb=" O LYS 1 195 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N PHE 1 200 " --> pdb=" O ALA 1 196 " (cutoff:3.500A) Processing helix chain '1' and resid 206 through 208 No H-bonds generated for 'chain '1' and resid 206 through 208' Processing helix chain '1' and resid 209 through 224 removed outlier: 3.609A pdb=" N VAL 1 213 " --> pdb=" O ASN 1 209 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU 1 221 " --> pdb=" O LEU 1 217 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LYS 1 224 " --> pdb=" O SER 1 220 " (cutoff:3.500A) Processing helix chain '1' and resid 241 through 271 removed outlier: 3.517A pdb=" N ALA 1 250 " --> pdb=" O ALA 1 246 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU 1 258 " --> pdb=" O ALA 1 254 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG 1 259 " --> pdb=" O GLU 1 255 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL 1 270 " --> pdb=" O LYS 1 266 " (cutoff:3.500A) Processing helix chain '1' and resid 272 through 277 removed outlier: 3.644A pdb=" N ALA 1 275 " --> pdb=" O PRO 1 272 " (cutoff:3.500A) Processing helix chain '1' and resid 282 through 286 Processing helix chain '1' and resid 289 through 293 Processing helix chain '1' and resid 297 through 305 Processing helix chain '1' and resid 310 through 316 removed outlier: 3.545A pdb=" N ASN 1 316 " --> pdb=" O ALA 1 312 " (cutoff:3.500A) Processing helix chain '1' and resid 323 through 327 removed outlier: 3.701A pdb=" N LYS 1 327 " --> pdb=" O PHE 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 330 through 334 Processing helix chain '1' and resid 338 through 351 removed outlier: 3.581A pdb=" N GLU 1 350 " --> pdb=" O GLN 1 346 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU 1 351 " --> pdb=" O LYS 1 347 " (cutoff:3.500A) Processing helix chain '1' and resid 353 through 362 removed outlier: 3.649A pdb=" N LEU 1 358 " --> pdb=" O PRO 1 354 " (cutoff:3.500A) Processing helix chain '1' and resid 363 through 367 removed outlier: 3.875A pdb=" N GLU 1 367 " --> pdb=" O PRO 1 364 " (cutoff:3.500A) Processing helix chain '1' and resid 375 through 388 removed outlier: 3.541A pdb=" N ARG 1 381 " --> pdb=" O SER 1 377 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL 1 382 " --> pdb=" O GLU 1 378 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS 1 386 " --> pdb=" O VAL 1 382 " (cutoff:3.500A) Processing helix chain '1' and resid 392 through 421 removed outlier: 3.531A pdb=" N LYS 1 396 " --> pdb=" O ARG 1 392 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU 1 401 " --> pdb=" O GLU 1 397 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N VAL 1 418 " --> pdb=" O GLU 1 414 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ILE 1 419 " --> pdb=" O GLU 1 415 " (cutoff:3.500A) Processing helix chain '1' and resid 425 through 432 removed outlier: 3.953A pdb=" N PHE 1 429 " --> pdb=" O ASP 1 425 " (cutoff:3.500A) Processing helix chain '1' and resid 435 through 441 Processing helix chain '1' and resid 446 through 458 removed outlier: 3.646A pdb=" N ARG 1 453 " --> pdb=" O ALA 1 449 " (cutoff:3.500A) Processing helix chain '1' and resid 463 through 478 removed outlier: 3.658A pdb=" N TYR 1 468 " --> pdb=" O PRO 1 464 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLN 1 474 " --> pdb=" O VAL 1 470 " (cutoff:3.500A) Processing helix chain '1' and resid 479 through 483 Processing helix chain '1' and resid 485 through 490 Processing helix chain '1' and resid 490 through 495 Processing helix chain '1' and resid 495 through 515 removed outlier: 3.889A pdb=" N GLU 1 501 " --> pdb=" O LEU 1 497 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA 1 511 " --> pdb=" O GLU 1 507 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU 1 512 " --> pdb=" O ASP 1 508 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA 1 515 " --> pdb=" O ALA 1 511 " (cutoff:3.500A) Processing helix chain '1' and resid 518 through 536 removed outlier: 3.657A pdb=" N THR 1 526 " --> pdb=" O LEU 1 522 " (cutoff:3.500A) Processing helix chain '1' and resid 541 through 549 removed outlier: 3.515A pdb=" N VAL 1 545 " --> pdb=" O PRO 1 541 " (cutoff:3.500A) Processing helix chain '1' and resid 549 through 562 removed outlier: 3.571A pdb=" N GLU 1 559 " --> pdb=" O LYS 1 555 " (cutoff:3.500A) Processing helix chain '1' and resid 566 through 574 Processing helix chain '1' and resid 577 through 588 Processing helix chain '1' and resid 589 through 591 No H-bonds generated for 'chain '1' and resid 589 through 591' Processing helix chain '1' and resid 592 through 606 removed outlier: 3.664A pdb=" N LYS 1 605 " --> pdb=" O ASP 1 601 " (cutoff:3.500A) Processing helix chain '1' and resid 610 through 614 Processing helix chain '2' and resid 8 through 17 removed outlier: 3.824A pdb=" N LYS 2 13 " --> pdb=" O PRO 2 9 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU 2 14 " --> pdb=" O ALA 2 10 " (cutoff:3.500A) Processing helix chain '2' and resid 25 through 38 Processing helix chain '2' and resid 44 through 58 removed outlier: 3.619A pdb=" N TRP 2 48 " --> pdb=" O ASN 2 44 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY 2 56 " --> pdb=" O LEU 2 52 " (cutoff:3.500A) Processing helix chain '2' and resid 62 through 76 removed outlier: 3.528A pdb=" N THR 2 67 " --> pdb=" O ALA 2 63 " (cutoff:3.500A) Processing helix chain '2' and resid 80 through 86 Processing helix chain '2' and resid 87 through 94 Processing helix chain '2' and resid 99 through 113 removed outlier: 3.602A pdb=" N SER 2 104 " --> pdb=" O PRO 2 100 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE 2 105 " --> pdb=" O VAL 2 101 " (cutoff:3.500A) Processing helix chain '2' and resid 117 through 131 removed outlier: 3.559A pdb=" N VAL 2 127 " --> pdb=" O LYS 2 123 " (cutoff:3.500A) Processing helix chain '2' and resid 136 through 150 removed outlier: 3.555A pdb=" N ALA 2 141 " --> pdb=" O PRO 2 137 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL 2 143 " --> pdb=" O GLU 2 139 " (cutoff:3.500A) Processing helix chain '2' and resid 154 through 166 removed outlier: 3.659A pdb=" N ALA 2 158 " --> pdb=" O ASP 2 154 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL 2 164 " --> pdb=" O ALA 2 160 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA 2 166 " --> pdb=" O GLY 2 162 " (cutoff:3.500A) Processing helix chain '2' and resid 171 through 186 Processing helix chain '2' and resid 189 through 198 removed outlier: 3.856A pdb=" N ALA 2 195 " --> pdb=" O ALA 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 209 through 221 removed outlier: 3.534A pdb=" N LEU 2 220 " --> pdb=" O ALA 2 216 " (cutoff:3.500A) Processing helix chain '2' and resid 227 through 235 removed outlier: 3.823A pdb=" N ALA 2 234 " --> pdb=" O ASP 2 230 " (cutoff:3.500A) Processing helix chain '2' and resid 240 through 254 removed outlier: 3.702A pdb=" N GLU 2 246 " --> pdb=" O ALA 2 242 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLY 2 250 " --> pdb=" O GLU 2 246 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER 2 254 " --> pdb=" O GLY 2 250 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 276 removed outlier: 3.568A pdb=" N VAL 2 268 " --> pdb=" O ALA 2 264 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL 2 269 " --> pdb=" O LEU 2 265 " (cutoff:3.500A) Proline residue: 2 271 - end of helix removed outlier: 3.504A pdb=" N GLU 2 274 " --> pdb=" O ALA 2 270 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS 2 275 " --> pdb=" O PRO 2 271 " (cutoff:3.500A) Processing helix chain '2' and resid 281 through 295 removed outlier: 3.534A pdb=" N SER 2 295 " --> pdb=" O ALA 2 291 " (cutoff:3.500A) Processing helix chain '2' and resid 300 through 321 removed outlier: 3.911A pdb=" N SER 2 305 " --> pdb=" O ALA 2 301 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE 2 306 " --> pdb=" O ALA 2 302 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY 2 312 " --> pdb=" O ALA 2 308 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA 2 318 " --> pdb=" O ALA 2 314 " (cutoff:3.500A) Processing helix chain '2' and resid 326 through 339 Processing helix chain '2' and resid 345 through 353 removed outlier: 3.624A pdb=" N ALA 2 350 " --> pdb=" O ARG 2 346 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N SER 2 351 " --> pdb=" O PRO 2 347 " (cutoff:3.500A) Processing helix chain '2' and resid 396 through 408 removed outlier: 4.185A pdb=" N ALA 2 400 " --> pdb=" O LEU 2 396 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA 2 408 " --> pdb=" O LYS 2 404 " (cutoff:3.500A) Processing helix chain '2' and resid 418 through 422 Processing helix chain '2' and resid 426 through 440 removed outlier: 3.690A pdb=" N ALA 2 436 " --> pdb=" O GLN 2 432 " (cutoff:3.500A) Processing helix chain '3' and resid 78 through 87 Processing helix chain '3' and resid 91 through 99 removed outlier: 3.620A pdb=" N ASN 3 97 " --> pdb=" O GLU 3 93 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA 3 99 " --> pdb=" O LEU 3 95 " (cutoff:3.500A) Processing helix chain '3' and resid 102 through 113 removed outlier: 3.942A pdb=" N TRP 3 106 " --> pdb=" O ASP 3 102 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER 3 111 " --> pdb=" O SER 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 119 through 128 removed outlier: 3.960A pdb=" N LYS 3 123 " --> pdb=" O ASP 3 119 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA 3 127 " --> pdb=" O LYS 3 123 " (cutoff:3.500A) Processing helix chain '3' and resid 131 through 135 Processing helix chain '3' and resid 136 through 150 removed outlier: 3.520A pdb=" N VAL 3 145 " --> pdb=" O THR 3 141 " (cutoff:3.500A) Processing helix chain '3' and resid 154 through 166 removed outlier: 3.693A pdb=" N GLY 3 160 " --> pdb=" O ASP 3 156 " (cutoff:3.500A) Processing helix chain '3' and resid 168 through 172 removed outlier: 3.628A pdb=" N PHE 3 172 " --> pdb=" O PHE 3 169 " (cutoff:3.500A) Processing helix chain '3' and resid 173 through 185 removed outlier: 4.074A pdb=" N GLN 3 179 " --> pdb=" O GLU 3 175 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALA 3 182 " --> pdb=" O LEU 3 178 " (cutoff:3.500A) Processing helix chain '3' and resid 191 through 204 removed outlier: 3.537A pdb=" N SER 3 201 " --> pdb=" O ASP 3 197 " (cutoff:3.500A) Processing helix chain '3' and resid 215 through 229 removed outlier: 3.624A pdb=" N LEU 3 219 " --> pdb=" O GLY 3 215 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N THR 3 221 " --> pdb=" O ASP 3 217 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN 3 229 " --> pdb=" O TYR 3 225 " (cutoff:3.500A) Processing helix chain '3' and resid 233 through 241 removed outlier: 3.513A pdb=" N THR 3 239 " --> pdb=" O ASP 3 235 " (cutoff:3.500A) Processing helix chain '3' and resid 242 through 244 No H-bonds generated for 'chain '3' and resid 242 through 244' Processing helix chain '3' and resid 245 through 251 Processing helix chain '3' and resid 253 through 271 removed outlier: 3.526A pdb=" N LYS 3 258 " --> pdb=" O ALA 3 254 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP 3 259 " --> pdb=" O ALA 3 255 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA 3 267 " --> pdb=" O SER 3 263 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE 3 271 " --> pdb=" O ALA 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 275 through 277 No H-bonds generated for 'chain '3' and resid 275 through 277' Processing helix chain '3' and resid 278 through 287 removed outlier: 3.888A pdb=" N ALA 3 285 " --> pdb=" O VAL 3 281 " (cutoff:3.500A) Processing helix chain '3' and resid 293 through 299 Processing helix chain '3' and resid 300 through 312 Processing helix chain '4' and resid 8 through 14 removed outlier: 3.649A pdb=" N TYR 4 13 " --> pdb=" O LYS 4 9 " (cutoff:3.500A) Processing helix chain '4' and resid 19 through 35 removed outlier: 3.903A pdb=" N ALA 4 25 " --> pdb=" O GLU 4 21 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER 4 28 " --> pdb=" O THR 4 24 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER 4 32 " --> pdb=" O SER 4 28 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR 4 34 " --> pdb=" O LEU 4 30 " (cutoff:3.500A) Processing helix chain '4' and resid 47 through 69 removed outlier: 3.580A pdb=" N ALA 4 51 " --> pdb=" O SER 4 47 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS 4 56 " --> pdb=" O GLN 4 52 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALA 4 60 " --> pdb=" O LYS 4 56 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLN 4 61 " --> pdb=" O TYR 4 57 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL 4 62 " --> pdb=" O LEU 4 58 " (cutoff:3.500A) Proline residue: 4 65 - end of helix removed outlier: 3.675A pdb=" N HIS 4 68 " --> pdb=" O GLU 4 64 " (cutoff:3.500A) Processing helix chain '4' and resid 79 through 96 Processing helix chain '4' and resid 100 through 113 Processing helix chain '4' and resid 118 through 126 removed outlier: 3.502A pdb=" N ASN 4 124 " --> pdb=" O LYS 4 120 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR 4 126 " --> pdb=" O VAL 4 122 " (cutoff:3.500A) Processing helix chain '4' and resid 131 through 136 Processing helix chain '4' and resid 138 through 150 removed outlier: 3.540A pdb=" N ALA 4 147 " --> pdb=" O SER 4 143 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 177 removed outlier: 3.808A pdb=" N LYS 4 168 " --> pdb=" O LYS 4 164 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS 4 170 " --> pdb=" O ALA 4 166 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA 4 171 " --> pdb=" O ALA 4 167 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER 4 175 " --> pdb=" O ALA 4 171 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY 4 177 " --> pdb=" O ALA 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 179 through 188 Processing helix chain '4' and resid 192 through 234 removed outlier: 3.564A pdb=" N LYS 4 198 " --> pdb=" O ASP 4 194 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VAL 4 199 " --> pdb=" O ALA 4 195 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU 4 202 " --> pdb=" O LYS 4 198 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR 4 205 " --> pdb=" O LYS 4 201 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N TRP 4 206 " --> pdb=" O GLU 4 202 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA 4 213 " --> pdb=" O SER 4 209 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ASP 4 214 " --> pdb=" O ALA 4 210 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA 4 221 " --> pdb=" O ALA 4 217 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE 4 222 " --> pdb=" O GLU 4 218 " (cutoff:3.500A) Processing helix chain '4' and resid 237 through 259 removed outlier: 3.570A pdb=" N ALA 4 256 " --> pdb=" O LEU 4 252 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA 4 259 " --> pdb=" O ARG 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 283 Processing helix chain '5' and resid 7 through 29 removed outlier: 3.616A pdb=" N GLU 5 11 " --> pdb=" O SER 5 7 " (cutoff:3.500A) Processing helix chain '5' and resid 30 through 59 removed outlier: 3.614A pdb=" N ARG 5 36 " --> pdb=" O PRO 5 32 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU 5 37 " --> pdb=" O THR 5 33 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N HIS 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N LYS 5 49 " --> pdb=" O ALA 5 45 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ARG 5 50 " --> pdb=" O ALA 5 46 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASN 5 52 " --> pdb=" O ALA 5 48 " (cutoff:3.500A) Processing helix chain '5' and resid 63 through 67 Processing helix chain '5' and resid 73 through 81 removed outlier: 3.531A pdb=" N ASN 5 79 " --> pdb=" O GLN 5 75 " (cutoff:3.500A) Processing helix chain '5' and resid 88 through 106 removed outlier: 3.963A pdb=" N LEU 5 92 " --> pdb=" O PRO 5 88 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N SER 5 97 " --> pdb=" O GLU 5 93 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS 5 101 " --> pdb=" O SER 5 97 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL 5 102 " --> pdb=" O ALA 5 98 " (cutoff:3.500A) Processing helix chain '5' and resid 114 through 119 Processing helix chain '6' and resid 30 through 41 Processing helix chain '6' and resid 48 through 50 No H-bonds generated for 'chain '6' and resid 48 through 50' Processing helix chain '6' and resid 51 through 58 Processing helix chain '6' and resid 72 through 94 removed outlier: 3.548A pdb=" N ALA 6 78 " --> pdb=" O GLN 6 74 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU 6 79 " --> pdb=" O ALA 6 75 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 104 Processing helix chain '6' and resid 105 through 118 removed outlier: 3.683A pdb=" N TRP 6 112 " --> pdb=" O LEU 6 108 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER 6 117 " --> pdb=" O LEU 6 113 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER 6 118 " --> pdb=" O ILE 6 114 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 130 Processing helix chain '6' and resid 133 through 138 removed outlier: 4.006A pdb=" N SER 6 138 " --> pdb=" O PRO 6 134 " (cutoff:3.500A) Processing helix chain '7' and resid 63 through 68 removed outlier: 3.840A pdb=" N ARG 7 67 " --> pdb=" O ALA 7 63 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS 7 68 " --> pdb=" O ALA 7 64 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 63 through 68' Processing helix chain '7' and resid 69 through 72 removed outlier: 4.102A pdb=" N SER 7 72 " --> pdb=" O LEU 7 69 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 69 through 72' Processing helix chain '7' and resid 83 through 102 removed outlier: 3.506A pdb=" N TYR 7 92 " --> pdb=" O SER 7 88 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLU 7 99 " --> pdb=" O SER 7 95 " (cutoff:3.500A) Processing helix chain '7' and resid 109 through 114 removed outlier: 3.836A pdb=" N THR 7 112 " --> pdb=" O ASP 7 109 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N TYR 7 114 " --> pdb=" O THR 7 111 " (cutoff:3.500A) Processing helix chain '7' and resid 115 through 120 Processing helix chain '7' and resid 124 through 145 removed outlier: 3.625A pdb=" N PHE 7 130 " --> pdb=" O ASP 7 126 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP 7 135 " --> pdb=" O TYR 7 131 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR 7 137 " --> pdb=" O ALA 7 133 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TYR 7 138 " --> pdb=" O ALA 7 134 " (cutoff:3.500A) Processing helix chain '7' and resid 146 through 149 Processing helix chain '7' and resid 150 through 155 removed outlier: 3.640A pdb=" N SER 7 155 " --> pdb=" O SER 7 151 " (cutoff:3.500A) Processing helix chain '7' and resid 157 through 163 Processing helix chain '7' and resid 174 through 187 removed outlier: 3.576A pdb=" N ASN 7 184 " --> pdb=" O GLY 7 180 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE 7 185 " --> pdb=" O ALA 7 181 " (cutoff:3.500A) Processing helix chain '8' and resid 26 through 31 removed outlier: 3.840A pdb=" N SER 8 31 " --> pdb=" O PRO 8 27 " (cutoff:3.500A) Processing helix chain '8' and resid 31 through 39 removed outlier: 3.556A pdb=" N TYR 8 35 " --> pdb=" O SER 8 31 " (cutoff:3.500A) Processing helix chain '8' and resid 39 through 78 removed outlier: 3.751A pdb=" N TRP 8 45 " --> pdb=" O ILE 8 41 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N TYR 8 46 " --> pdb=" O PRO 8 42 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N LEU 8 47 " --> pdb=" O ARG 8 43 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA 8 76 " --> pdb=" O ALA 8 72 " (cutoff:3.500A) Processing helix chain '9' and resid 5 through 17 Processing helix chain '9' and resid 36 through 55 removed outlier: 4.208A pdb=" N VAL 9 42 " --> pdb=" O ALA 9 38 " (cutoff:3.500A) Processing helix chain '9' and resid 82 through 97 removed outlier: 4.288A pdb=" N GLU 9 88 " --> pdb=" O ALA 9 84 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N MET 9 89 " --> pdb=" O LYS 9 85 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS 9 91 " --> pdb=" O LEU 9 87 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER 9 96 " --> pdb=" O GLU 9 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 118 Processing helix chain 'M' and resid 134 through 145 Processing helix chain 'M' and resid 147 through 164 removed outlier: 3.653A pdb=" N THR M 153 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER M 161 " --> pdb=" O CYS M 157 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N CYS M 162 " --> pdb=" O THR M 158 " (cutoff:3.500A) Processing helix chain 'M' and resid 165 through 168 Processing helix chain 'M' and resid 173 through 176 Processing helix chain 'M' and resid 177 through 199 removed outlier: 3.581A pdb=" N SER M 187 " --> pdb=" O GLY M 183 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LYS M 199 " --> pdb=" O LEU M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 231 Processing helix chain 'M' and resid 231 through 265 removed outlier: 4.106A pdb=" N GLY M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLY M 247 " --> pdb=" O ASN M 243 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N HIS M 248 " --> pdb=" O MET M 244 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU M 250 " --> pdb=" O ALA M 246 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU M 261 " --> pdb=" O MET M 257 " (cutoff:3.500A) Proline residue: M 262 - end of helix Processing helix chain 'M' and resid 270 through 308 removed outlier: 3.678A pdb=" N VAL M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU M 280 " --> pdb=" O GLY M 276 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU M 290 " --> pdb=" O GLY M 286 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER M 296 " --> pdb=" O ALA M 292 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER M 300 " --> pdb=" O SER M 296 " (cutoff:3.500A) Processing helix chain 'P' and resid 163 through 175 removed outlier: 3.773A pdb=" N VAL P 168 " --> pdb=" O LYS P 164 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU P 170 " --> pdb=" O GLU P 166 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS P 172 " --> pdb=" O VAL P 168 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS P 173 " --> pdb=" O GLU P 169 " (cutoff:3.500A) Processing helix chain 'P' and resid 210 through 226 removed outlier: 3.871A pdb=" N GLU P 216 " --> pdb=" O ALA P 212 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASN P 219 " --> pdb=" O VAL P 215 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 67 removed outlier: 3.652A pdb=" N ILE T 67 " --> pdb=" O SER T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 67 through 75 removed outlier: 3.668A pdb=" N GLU T 72 " --> pdb=" O PRO T 68 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N TRP T 73 " --> pdb=" O ALA T 69 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU T 74 " --> pdb=" O VAL T 70 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS T 75 " --> pdb=" O LYS T 71 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '1' and resid 183 through 184 Processing sheet with id=AA2, first strand: chain '2' and resid 369 through 372 removed outlier: 8.110A pdb=" N ALA 2 414 " --> pdb=" O LYS 2 376 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU 2 378 " --> pdb=" O ALA 2 414 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N VAL 2 416 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN 2 380 " --> pdb=" O VAL 2 416 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '3' and resid 314 through 317 Processing sheet with id=AA4, first strand: chain '7' and resid 36 through 41 Processing sheet with id=AA5, first strand: chain '7' and resid 36 through 41 Processing sheet with id=AA6, first strand: chain 'P' and resid 151 through 152 Processing sheet with id=AA7, first strand: chain 'P' and resid 188 through 190 1059 hydrogen bonds defined for protein. 3087 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.28 Time building geometry restraints manager: 2.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5210 1.33 - 1.45: 3678 1.45 - 1.57: 11297 1.57 - 1.69: 0 1.69 - 1.81: 54 Bond restraints: 20239 Sorted by residual: bond pdb=" N THR M 200 " pdb=" CA THR M 200 " ideal model delta sigma weight residual 1.457 1.485 -0.029 6.40e-03 2.44e+04 2.04e+01 bond pdb=" CB THR M 153 " pdb=" CG2 THR M 153 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.65e+00 bond pdb=" N ILE 3 101 " pdb=" CA ILE 3 101 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 7.12e+00 bond pdb=" CB PRO 4 65 " pdb=" CG PRO 4 65 " ideal model delta sigma weight residual 1.492 1.360 0.132 5.00e-02 4.00e+02 6.99e+00 bond pdb=" CG1 ILE 5 34 " pdb=" CD1 ILE 5 34 " ideal model delta sigma weight residual 1.513 1.414 0.099 3.90e-02 6.57e+02 6.49e+00 ... (remaining 20234 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.72: 26760 2.72 - 5.44: 618 5.44 - 8.16: 75 8.16 - 10.88: 14 10.88 - 13.60: 2 Bond angle restraints: 27469 Sorted by residual: angle pdb=" N PRO 3 77 " pdb=" CA PRO 3 77 " pdb=" CB PRO 3 77 " ideal model delta sigma weight residual 103.00 110.34 -7.34 1.10e+00 8.26e-01 4.45e+01 angle pdb=" C THR M 200 " pdb=" CA THR M 200 " pdb=" CB THR M 200 " ideal model delta sigma weight residual 117.07 107.48 9.59 1.44e+00 4.82e-01 4.43e+01 angle pdb=" C VAL 7 157 " pdb=" N VAL 7 158 " pdb=" CA VAL 7 158 " ideal model delta sigma weight residual 120.33 125.36 -5.03 8.00e-01 1.56e+00 3.96e+01 angle pdb=" N ILE 8 11 " pdb=" CA ILE 8 11 " pdb=" C ILE 8 11 " ideal model delta sigma weight residual 111.62 107.68 3.94 7.90e-01 1.60e+00 2.48e+01 angle pdb=" C VAL P 185 " pdb=" N MET P 186 " pdb=" CA MET P 186 " ideal model delta sigma weight residual 121.54 130.69 -9.15 1.91e+00 2.74e-01 2.29e+01 ... (remaining 27464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 11104 17.59 - 35.17: 866 35.17 - 52.76: 167 52.76 - 70.34: 30 70.34 - 87.93: 15 Dihedral angle restraints: 12182 sinusoidal: 4595 harmonic: 7587 Sorted by residual: dihedral pdb=" CA MET P 186 " pdb=" C MET P 186 " pdb=" N GLN P 187 " pdb=" CA GLN P 187 " ideal model delta harmonic sigma weight residual 180.00 140.10 39.90 0 5.00e+00 4.00e-02 6.37e+01 dihedral pdb=" CA VAL P 185 " pdb=" C VAL P 185 " pdb=" N MET P 186 " pdb=" CA MET P 186 " ideal model delta harmonic sigma weight residual 180.00 144.47 35.53 0 5.00e+00 4.00e-02 5.05e+01 dihedral pdb=" CA SER 4 47 " pdb=" C SER 4 47 " pdb=" N GLU 4 48 " pdb=" CA GLU 4 48 " ideal model delta harmonic sigma weight residual -180.00 -148.99 -31.01 0 5.00e+00 4.00e-02 3.85e+01 ... (remaining 12179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2594 0.077 - 0.155: 514 0.155 - 0.232: 51 0.232 - 0.309: 3 0.309 - 0.386: 1 Chirality restraints: 3163 Sorted by residual: chirality pdb=" CB ILE 3 90 " pdb=" CA ILE 3 90 " pdb=" CG1 ILE 3 90 " pdb=" CG2 ILE 3 90 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CB ILE P 200 " pdb=" CA ILE P 200 " pdb=" CG1 ILE P 200 " pdb=" CG2 ILE P 200 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB VAL 1 94 " pdb=" CA VAL 1 94 " pdb=" CG1 VAL 1 94 " pdb=" CG2 VAL 1 94 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.27 2.00e-01 2.50e+01 1.88e+00 ... (remaining 3160 not shown) Planarity restraints: 3505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR 1 92 " 0.048 5.00e-02 4.00e+02 7.27e-02 8.46e+00 pdb=" N PRO 1 93 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO 1 93 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO 1 93 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU M 135 " 0.046 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO M 136 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO M 136 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO M 136 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA 3 210 " 0.045 5.00e-02 4.00e+02 6.68e-02 7.13e+00 pdb=" N PRO 3 211 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO 3 211 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO 3 211 " 0.038 5.00e-02 4.00e+02 ... (remaining 3502 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 470 2.68 - 3.24: 18793 3.24 - 3.79: 31442 3.79 - 4.35: 43455 4.35 - 4.90: 71365 Nonbonded interactions: 165525 Sorted by model distance: nonbonded pdb="ZN ZN M 600 " pdb=" O HOH M 715 " model vdw 2.126 2.230 nonbonded pdb=" O GLY M 183 " pdb=" OG SER M 187 " model vdw 2.234 3.040 nonbonded pdb=" O THR 5 83 " pdb=" OH TYR 7 119 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR 5 62 " pdb=" O PHE 6 146 " model vdw 2.250 3.040 nonbonded pdb=" OH TYR 6 126 " pdb=" O HOH 6 201 " model vdw 2.263 3.040 ... (remaining 165520 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.270 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 19.790 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:1.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 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 : 0.012 0.155 20241 Z= 0.524 Angle : 1.028 13.598 27469 Z= 0.565 Chirality : 0.062 0.386 3163 Planarity : 0.008 0.073 3505 Dihedral : 13.794 87.928 7264 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.27 % Allowed : 4.94 % Favored : 94.78 % Rotamer: Outliers : 0.19 % Allowed : 6.64 % Favored : 93.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -5.88 (0.11), residues: 2569 helix: -4.52 (0.05), residues: 1675 sheet: -2.05 (0.58), residues: 70 loop : -2.02 (0.18), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG P 206 TYR 0.034 0.003 TYR 4 211 PHE 0.029 0.003 PHE 3 121 TRP 0.024 0.003 TRP 7 107 HIS 0.014 0.002 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.01237 (20239) covalent geometry : angle 1.02809 (27469) hydrogen bonds : bond 0.29886 ( 1053) hydrogen bonds : angle 11.25089 ( 3087) metal coordination : bond 0.11377 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 329 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8947 (ttpt) cc_final: 0.7786 (tppt) REVERT: 1 101 ASN cc_start: 0.8172 (t0) cc_final: 0.7938 (t0) REVERT: 1 242 LYS cc_start: 0.8249 (tttt) cc_final: 0.8018 (mmtm) REVERT: 1 504 ASP cc_start: 0.7889 (t0) cc_final: 0.7532 (t0) REVERT: 2 68 ASN cc_start: 0.8857 (m110) cc_final: 0.8270 (m110) REVERT: 2 74 ASN cc_start: 0.9047 (t0) cc_final: 0.8818 (t0) REVERT: 2 346 ARG cc_start: 0.7549 (mtm-85) cc_final: 0.7265 (mtt180) REVERT: 4 117 GLU cc_start: 0.7559 (pm20) cc_final: 0.7316 (pm20) REVERT: 4 121 ASP cc_start: 0.8323 (t70) cc_final: 0.8119 (t0) REVERT: 4 255 ARG cc_start: 0.8307 (ttm170) cc_final: 0.8021 (ttm170) REVERT: 7 135 ASP cc_start: 0.8515 (m-30) cc_final: 0.8129 (m-30) REVERT: 7 160 ASN cc_start: 0.8866 (m-40) cc_final: 0.8665 (m-40) REVERT: 8 33 TYR cc_start: 0.9103 (t80) cc_final: 0.8844 (t80) REVERT: 8 38 LYS cc_start: 0.8983 (mttt) cc_final: 0.8676 (mtpp) REVERT: 9 12 GLU cc_start: 0.8137 (tt0) cc_final: 0.7925 (tt0) REVERT: M 140 ASP cc_start: 0.8381 (t70) cc_final: 0.8069 (t70) outliers start: 4 outliers final: 1 residues processed: 333 average time/residue: 0.1675 time to fit residues: 82.1009 Evaluate side-chains 241 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 144 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.8980 chunk 227 optimal weight: 0.5980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.0980 chunk 247 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 0 48 ASN 1 65 GLN 1 100 GLN 1 101 ASN 1 285 GLN 1 298 GLN 1 316 ASN 1 365 GLN 1 423 ASN 1 430 GLN 1 482 ASN 1 562 ASN 1 587 ASN 1 590 HIS 2 68 ASN 2 122 ASN 2 243 GLN 2 289 HIS 2 380 GLN 2 427 GLN 3 189 HIS 3 206 ASN 4 135 ASN 4 240 GLN 5 107 ASN 6 40 ASN 7 38 ASN 7 86 HIS 7 98 ASN 7 123 HIS 7 170 HIS 7 184 ASN 8 26 HIS 9 23 GLN ** 9 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 120 GLN M 163 ASN T 64 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.123319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.096115 restraints weight = 28346.216| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.63 r_work: 0.2958 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 20241 Z= 0.135 Angle : 0.605 12.843 27469 Z= 0.320 Chirality : 0.041 0.240 3163 Planarity : 0.006 0.061 3505 Dihedral : 5.545 35.575 2747 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.78 % Favored : 96.19 % Rotamer: Outliers : 1.70 % Allowed : 9.60 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.14), residues: 2569 helix: -2.35 (0.10), residues: 1676 sheet: -1.45 (0.69), residues: 52 loop : -1.54 (0.19), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG 1 609 TYR 0.026 0.001 TYR 4 211 PHE 0.016 0.001 PHE 1 529 TRP 0.019 0.002 TRP 4 206 HIS 0.006 0.001 HIS 7 123 Details of bonding type rmsd covalent geometry : bond 0.00300 (20239) covalent geometry : angle 0.60471 (27469) hydrogen bonds : bond 0.04483 ( 1053) hydrogen bonds : angle 4.95941 ( 3087) metal coordination : bond 0.00271 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 290 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.9024 (ttpt) cc_final: 0.7505 (tppt) REVERT: 0 41 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7768 (pm20) REVERT: 1 69 ASP cc_start: 0.7852 (m-30) cc_final: 0.7298 (m-30) REVERT: 1 101 ASN cc_start: 0.8674 (t0) cc_final: 0.8389 (t0) REVERT: 1 456 LYS cc_start: 0.8198 (tmmt) cc_final: 0.7884 (tptt) REVERT: 1 504 ASP cc_start: 0.8382 (t0) cc_final: 0.8110 (t0) REVERT: 2 68 ASN cc_start: 0.9043 (m-40) cc_final: 0.8567 (m110) REVERT: 2 74 ASN cc_start: 0.9137 (t0) cc_final: 0.8922 (t0) REVERT: 4 117 GLU cc_start: 0.7898 (pm20) cc_final: 0.7431 (pm20) REVERT: 8 3 LEU cc_start: 0.9215 (OUTLIER) cc_final: 0.8999 (tt) REVERT: 8 38 LYS cc_start: 0.9082 (mttt) cc_final: 0.8866 (mtpp) REVERT: 9 88 GLU cc_start: 0.7367 (mp0) cc_final: 0.7013 (mp0) REVERT: P 205 ARG cc_start: 0.6976 (ptt-90) cc_final: 0.2580 (mmt-90) outliers start: 35 outliers final: 16 residues processed: 308 average time/residue: 0.1541 time to fit residues: 71.8211 Evaluate side-chains 253 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 236 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 356 VAL Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 578 ASP Chi-restraints excluded: chain 2 residue 155 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 3 LEU Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 92 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 220 optimal weight: 0.6980 chunk 176 optimal weight: 2.9990 chunk 166 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 119 optimal weight: 0.4980 chunk 88 optimal weight: 6.9990 chunk 105 optimal weight: 0.0570 chunk 169 optimal weight: 0.2980 chunk 91 optimal weight: 4.9990 chunk 162 optimal weight: 2.9990 chunk 87 optimal weight: 0.0170 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 0 48 ASN 0 56 GLN 0 60 GLN 1 430 GLN 2 153 ASN ** 6 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.099090 restraints weight = 28285.940| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.36 r_work: 0.3028 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 20241 Z= 0.102 Angle : 0.528 11.890 27469 Z= 0.271 Chirality : 0.039 0.217 3163 Planarity : 0.004 0.050 3505 Dihedral : 4.782 31.205 2747 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.81 % Favored : 96.15 % Rotamer: Outliers : 1.70 % Allowed : 11.20 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.56 (0.16), residues: 2569 helix: -0.81 (0.12), residues: 1680 sheet: -0.69 (0.73), residues: 51 loop : -1.22 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 1 387 TYR 0.027 0.001 TYR 4 211 PHE 0.015 0.001 PHE 1 529 TRP 0.022 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00224 (20239) covalent geometry : angle 0.52838 (27469) hydrogen bonds : bond 0.03315 ( 1053) hydrogen bonds : angle 4.05874 ( 3087) metal coordination : bond 0.00008 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 277 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.8993 (ttpt) cc_final: 0.7522 (tppt) REVERT: 0 41 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7742 (pm20) REVERT: 1 69 ASP cc_start: 0.7570 (m-30) cc_final: 0.6786 (m-30) REVERT: 1 87 PHE cc_start: 0.8617 (m-80) cc_final: 0.8391 (m-80) REVERT: 1 456 LYS cc_start: 0.8213 (tmmt) cc_final: 0.7992 (tptt) REVERT: 1 504 ASP cc_start: 0.8431 (t0) cc_final: 0.8149 (t0) REVERT: 4 117 GLU cc_start: 0.7736 (pm20) cc_final: 0.7285 (pm20) REVERT: 7 119 TYR cc_start: 0.9364 (t80) cc_final: 0.9085 (t80) REVERT: M 154 THR cc_start: 0.8978 (m) cc_final: 0.8738 (m) REVERT: P 191 ASP cc_start: 0.7075 (t0) cc_final: 0.6680 (p0) REVERT: P 205 ARG cc_start: 0.6902 (ptt-90) cc_final: 0.2606 (mmt-90) outliers start: 35 outliers final: 25 residues processed: 298 average time/residue: 0.1442 time to fit residues: 65.1886 Evaluate side-chains 267 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 242 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 277 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 356 VAL Chi-restraints excluded: chain 1 residue 501 GLU Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 1 residue 578 ASP Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 155 VAL Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 7 LEU Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 11 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 204 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 130 optimal weight: 0.9990 chunk 146 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 161 optimal weight: 2.9990 chunk 178 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 0 48 ASN 1 531 HIS 1 542 HIS 2 153 ASN 3 229 ASN 4 52 GLN 4 111 GLN T 64 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.126040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.099095 restraints weight = 28382.828| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 2.43 r_work: 0.2699 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2572 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 20241 Z= 0.221 Angle : 0.603 14.979 27469 Z= 0.308 Chirality : 0.043 0.162 3163 Planarity : 0.004 0.054 3505 Dihedral : 4.874 34.227 2747 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.56 % Rotamer: Outliers : 2.33 % Allowed : 11.92 % Favored : 85.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.16), residues: 2569 helix: -0.39 (0.13), residues: 1698 sheet: -0.65 (0.74), residues: 51 loop : -1.07 (0.20), residues: 820 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 206 TYR 0.026 0.002 TYR 4 211 PHE 0.033 0.002 PHE 3 115 TRP 0.013 0.002 TRP 7 107 HIS 0.008 0.001 HIS 7 123 Details of bonding type rmsd covalent geometry : bond 0.00522 (20239) covalent geometry : angle 0.60334 (27469) hydrogen bonds : bond 0.03708 ( 1053) hydrogen bonds : angle 4.10242 ( 3087) metal coordination : bond 0.00180 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 251 time to evaluate : 0.655 Fit side-chains revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.9064 (ttpt) cc_final: 0.7542 (tppt) REVERT: 0 41 GLU cc_start: 0.8534 (mt-10) cc_final: 0.7829 (pm20) REVERT: 1 69 ASP cc_start: 0.7928 (m-30) cc_final: 0.7123 (m-30) REVERT: 1 456 LYS cc_start: 0.8300 (tmmt) cc_final: 0.8054 (tptt) REVERT: 1 504 ASP cc_start: 0.8762 (t0) cc_final: 0.8424 (t0) REVERT: 2 68 ASN cc_start: 0.9127 (m-40) cc_final: 0.8661 (m110) REVERT: 7 24 GLN cc_start: 0.8545 (tm-30) cc_final: 0.8288 (tm-30) REVERT: 9 88 GLU cc_start: 0.7493 (mp0) cc_final: 0.7143 (mp0) REVERT: P 186 MET cc_start: 0.5810 (tpp) cc_final: 0.5558 (tpp) outliers start: 48 outliers final: 35 residues processed: 281 average time/residue: 0.1421 time to fit residues: 61.7739 Evaluate side-chains 270 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 0 residue 82 HIS Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 574 MET Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 121 PHE Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 3 residue 319 GLN Chi-restraints excluded: chain 4 residue 21 GLU Chi-restraints excluded: chain 4 residue 52 GLN Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 38 SER Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 25 ASP Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain T residue 67 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 42 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 233 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 49 optimal weight: 0.0770 chunk 130 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 150 optimal weight: 0.7980 chunk 236 optimal weight: 0.9980 chunk 109 optimal weight: 6.9990 chunk 224 optimal weight: 0.6980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 0 48 ASN 2 122 ASN 2 153 ASN 4 52 GLN 4 111 GLN 9 80 GLN T 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.130499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.103650 restraints weight = 27938.858| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.04 r_work: 0.2773 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2651 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 20241 Z= 0.121 Angle : 0.535 12.829 27469 Z= 0.271 Chirality : 0.040 0.336 3163 Planarity : 0.004 0.052 3505 Dihedral : 4.630 31.191 2747 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.89 % Favored : 96.07 % Rotamer: Outliers : 2.28 % Allowed : 13.18 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.17), residues: 2569 helix: 0.08 (0.13), residues: 1696 sheet: -0.33 (0.78), residues: 51 loop : -0.89 (0.21), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 1 387 TYR 0.025 0.001 TYR 4 211 PHE 0.019 0.001 PHE 3 121 TRP 0.018 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00281 (20239) covalent geometry : angle 0.53469 (27469) hydrogen bonds : bond 0.03209 ( 1053) hydrogen bonds : angle 3.86829 ( 3087) metal coordination : bond 0.00106 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 255 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.9030 (ttpt) cc_final: 0.7539 (tppt) REVERT: 0 41 GLU cc_start: 0.8494 (mt-10) cc_final: 0.7823 (pm20) REVERT: 1 69 ASP cc_start: 0.7857 (m-30) cc_final: 0.7008 (m-30) REVERT: 1 87 PHE cc_start: 0.8750 (m-80) cc_final: 0.8443 (m-80) REVERT: 1 504 ASP cc_start: 0.8655 (t0) cc_final: 0.8280 (t0) REVERT: 2 16 ASP cc_start: 0.8770 (t70) cc_final: 0.8325 (t0) REVERT: 2 139 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7471 (mp0) REVERT: 4 229 ILE cc_start: 0.8937 (tt) cc_final: 0.8579 (pt) REVERT: 5 111 LYS cc_start: 0.8771 (ttmm) cc_final: 0.8471 (mmtp) REVERT: 6 52 LYS cc_start: 0.8707 (OUTLIER) cc_final: 0.8476 (mmtt) REVERT: 7 24 GLN cc_start: 0.8505 (tm-30) cc_final: 0.8108 (tm-30) REVERT: 7 119 TYR cc_start: 0.9407 (t80) cc_final: 0.8996 (t80) REVERT: P 191 ASP cc_start: 0.7031 (t0) cc_final: 0.6644 (p0) outliers start: 47 outliers final: 32 residues processed: 285 average time/residue: 0.1345 time to fit residues: 59.5872 Evaluate side-chains 269 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 235 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 0 residue 82 HIS Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 277 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 139 GLU Chi-restraints excluded: chain 2 residue 155 VAL Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 154 LEU Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain M residue 148 ILE Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 323 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 84 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 170 optimal weight: 0.7980 chunk 243 optimal weight: 7.9990 chunk 223 optimal weight: 1.9990 chunk 247 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 0 48 ASN 2 122 ASN 2 153 ASN 4 111 GLN 9 80 GLN T 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.124083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.096800 restraints weight = 28270.911| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 2.36 r_work: 0.2745 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2620 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 20241 Z= 0.153 Angle : 0.553 12.583 27469 Z= 0.280 Chirality : 0.041 0.149 3163 Planarity : 0.004 0.051 3505 Dihedral : 4.589 33.344 2747 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.24 % Favored : 95.72 % Rotamer: Outliers : 2.18 % Allowed : 13.62 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.17), residues: 2569 helix: 0.29 (0.13), residues: 1697 sheet: -0.08 (0.80), residues: 51 loop : -0.80 (0.21), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 1 387 TYR 0.025 0.001 TYR 4 211 PHE 0.013 0.001 PHE 1 529 TRP 0.013 0.001 TRP 9 73 HIS 0.006 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00363 (20239) covalent geometry : angle 0.55333 (27469) hydrogen bonds : bond 0.03283 ( 1053) hydrogen bonds : angle 3.84723 ( 3087) metal coordination : bond 0.00137 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 243 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.9044 (ttpt) cc_final: 0.7509 (tppt) REVERT: 0 41 GLU cc_start: 0.8538 (mt-10) cc_final: 0.7807 (pm20) REVERT: 1 69 ASP cc_start: 0.7893 (m-30) cc_final: 0.7003 (m-30) REVERT: 1 87 PHE cc_start: 0.8800 (m-80) cc_final: 0.8449 (m-80) REVERT: 1 504 ASP cc_start: 0.8689 (t0) cc_final: 0.8288 (t0) REVERT: 2 16 ASP cc_start: 0.8754 (t70) cc_final: 0.8310 (t0) REVERT: 2 139 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7478 (mp0) REVERT: 3 115 PHE cc_start: 0.8116 (t80) cc_final: 0.7868 (t80) REVERT: 3 297 LEU cc_start: 0.8182 (mt) cc_final: 0.7757 (mt) REVERT: 4 120 LYS cc_start: 0.8702 (ttpp) cc_final: 0.8477 (ttmm) REVERT: 4 229 ILE cc_start: 0.9026 (tt) cc_final: 0.8644 (pt) REVERT: 5 111 LYS cc_start: 0.8697 (ttmm) cc_final: 0.8401 (mmtp) REVERT: 6 52 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8485 (mmtt) REVERT: 7 24 GLN cc_start: 0.8503 (tm-30) cc_final: 0.8094 (tm-30) REVERT: 9 88 GLU cc_start: 0.7410 (mp0) cc_final: 0.7060 (mp0) REVERT: P 205 ARG cc_start: 0.7162 (ptt-90) cc_final: 0.2726 (mmt-90) outliers start: 45 outliers final: 39 residues processed: 275 average time/residue: 0.1504 time to fit residues: 63.5123 Evaluate side-chains 276 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 235 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 0 residue 82 HIS Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 277 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 139 GLU Chi-restraints excluded: chain 2 residue 155 VAL Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 3 residue 319 GLN Chi-restraints excluded: chain 4 residue 21 GLU Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 154 LEU Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 184 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 106 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 110 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 163 optimal weight: 5.9990 chunk 167 optimal weight: 0.6980 chunk 239 optimal weight: 0.9990 chunk 178 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 0 48 ASN 4 111 GLN 6 74 GLN 9 80 GLN T 64 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.130852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.104832 restraints weight = 27834.299| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.20 r_work: 0.2763 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 20241 Z= 0.127 Angle : 0.535 12.578 27469 Z= 0.269 Chirality : 0.040 0.140 3163 Planarity : 0.004 0.052 3505 Dihedral : 4.459 30.523 2747 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 2.33 % Allowed : 13.72 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.17), residues: 2569 helix: 0.56 (0.13), residues: 1698 sheet: -0.65 (0.88), residues: 41 loop : -0.72 (0.21), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 1 387 TYR 0.025 0.001 TYR 4 211 PHE 0.013 0.001 PHE 1 529 TRP 0.016 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00299 (20239) covalent geometry : angle 0.53476 (27469) hydrogen bonds : bond 0.03115 ( 1053) hydrogen bonds : angle 3.74658 ( 3087) metal coordination : bond 0.00121 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 244 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.9025 (ttpt) cc_final: 0.7510 (tppt) REVERT: 0 41 GLU cc_start: 0.8528 (mt-10) cc_final: 0.7817 (pm20) REVERT: 1 69 ASP cc_start: 0.7880 (m-30) cc_final: 0.7032 (m-30) REVERT: 1 87 PHE cc_start: 0.8807 (m-80) cc_final: 0.8434 (m-80) REVERT: 1 193 VAL cc_start: 0.6943 (OUTLIER) cc_final: 0.6668 (p) REVERT: 1 504 ASP cc_start: 0.8681 (t0) cc_final: 0.8272 (t0) REVERT: 2 16 ASP cc_start: 0.8739 (t70) cc_final: 0.8294 (t0) REVERT: 2 139 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7452 (mp0) REVERT: 3 115 PHE cc_start: 0.8101 (t80) cc_final: 0.7890 (t80) REVERT: 3 297 LEU cc_start: 0.8195 (mt) cc_final: 0.7763 (mt) REVERT: 3 319 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7028 (mm-40) REVERT: 4 229 ILE cc_start: 0.9009 (tt) cc_final: 0.8674 (pt) REVERT: 5 111 LYS cc_start: 0.8717 (ttmm) cc_final: 0.8457 (mmtm) REVERT: 6 52 LYS cc_start: 0.8715 (OUTLIER) cc_final: 0.8504 (mmtt) REVERT: 7 24 GLN cc_start: 0.8483 (tm-30) cc_final: 0.8118 (tm-30) REVERT: 7 25 ASP cc_start: 0.8942 (t0) cc_final: 0.8716 (t0) REVERT: 7 119 TYR cc_start: 0.9414 (t80) cc_final: 0.9017 (t80) REVERT: 7 187 LEU cc_start: 0.8053 (mt) cc_final: 0.7798 (mt) REVERT: 9 13 LYS cc_start: 0.7417 (tttm) cc_final: 0.6578 (mmmt) REVERT: 9 88 GLU cc_start: 0.7421 (mp0) cc_final: 0.7022 (mp0) REVERT: P 191 ASP cc_start: 0.7105 (t0) cc_final: 0.6735 (p0) REVERT: P 205 ARG cc_start: 0.7221 (ptt-90) cc_final: 0.2849 (mmt-90) outliers start: 48 outliers final: 39 residues processed: 278 average time/residue: 0.1467 time to fit residues: 62.5950 Evaluate side-chains 275 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 36 THR Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 0 residue 82 HIS Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 277 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 139 GLU Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 3 residue 319 GLN Chi-restraints excluded: chain 4 residue 21 GLU Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 154 LEU Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 5 residue 110 SER Chi-restraints excluded: chain 6 residue 38 SER Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 184 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 50 optimal weight: 0.0060 chunk 125 optimal weight: 0.9980 chunk 235 optimal weight: 0.6980 chunk 226 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 94 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 224 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 166 optimal weight: 0.7980 chunk 239 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 4 111 GLN 9 80 GLN T 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.132766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.105833 restraints weight = 27851.507| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.15 r_work: 0.2789 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 20241 Z= 0.110 Angle : 0.521 12.600 27469 Z= 0.262 Chirality : 0.039 0.140 3163 Planarity : 0.004 0.052 3505 Dihedral : 4.323 28.818 2747 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 2.33 % Allowed : 13.91 % Favored : 83.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.17), residues: 2569 helix: 0.78 (0.13), residues: 1700 sheet: 0.05 (0.75), residues: 57 loop : -0.70 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 319 TYR 0.025 0.001 TYR 4 211 PHE 0.014 0.001 PHE 1 529 TRP 0.015 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00255 (20239) covalent geometry : angle 0.52116 (27469) hydrogen bonds : bond 0.03003 ( 1053) hydrogen bonds : angle 3.66017 ( 3087) metal coordination : bond 0.00074 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 252 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.9010 (ttpt) cc_final: 0.7491 (tppt) REVERT: 0 41 GLU cc_start: 0.8440 (mt-10) cc_final: 0.7766 (pm20) REVERT: 1 69 ASP cc_start: 0.7816 (m-30) cc_final: 0.6965 (m-30) REVERT: 1 87 PHE cc_start: 0.8779 (m-80) cc_final: 0.8396 (m-80) REVERT: 1 193 VAL cc_start: 0.6664 (OUTLIER) cc_final: 0.6375 (p) REVERT: 1 504 ASP cc_start: 0.8641 (t0) cc_final: 0.8243 (t0) REVERT: 2 16 ASP cc_start: 0.8724 (t70) cc_final: 0.8268 (t0) REVERT: 2 139 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7344 (mp0) REVERT: 3 297 LEU cc_start: 0.8188 (mt) cc_final: 0.7769 (mt) REVERT: 3 319 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7033 (mm110) REVERT: 4 220 LYS cc_start: 0.8488 (mptt) cc_final: 0.8054 (mmmt) REVERT: 4 229 ILE cc_start: 0.8982 (tt) cc_final: 0.8662 (pt) REVERT: 5 111 LYS cc_start: 0.8664 (ttmm) cc_final: 0.8458 (mmtm) REVERT: 6 52 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8399 (mmtp) REVERT: 7 24 GLN cc_start: 0.8476 (tm-30) cc_final: 0.8122 (tm-30) REVERT: 7 119 TYR cc_start: 0.9394 (t80) cc_final: 0.9010 (t80) REVERT: 7 187 LEU cc_start: 0.8018 (mt) cc_final: 0.7792 (mt) REVERT: 9 13 LYS cc_start: 0.7453 (tttm) cc_final: 0.6651 (mmmt) REVERT: 9 88 GLU cc_start: 0.7402 (mp0) cc_final: 0.7013 (mp0) REVERT: P 205 ARG cc_start: 0.7195 (ptt-90) cc_final: 0.2833 (mmt-90) REVERT: P 216 GLU cc_start: 0.8469 (tt0) cc_final: 0.8253 (mm-30) outliers start: 48 outliers final: 39 residues processed: 284 average time/residue: 0.1492 time to fit residues: 64.2898 Evaluate side-chains 284 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 0 residue 82 HIS Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 277 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 139 GLU Chi-restraints excluded: chain 2 residue 228 ILE Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 256 GLN Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 3 residue 319 GLN Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 154 LEU Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 204 PHE Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 6 residue 38 SER Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 184 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 7 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 240 optimal weight: 1.9990 chunk 251 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 100 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 4 95 GLN 4 111 GLN 9 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.131737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.104984 restraints weight = 27670.287| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 2.12 r_work: 0.2772 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 20241 Z= 0.134 Angle : 0.541 12.149 27469 Z= 0.271 Chirality : 0.040 0.166 3163 Planarity : 0.004 0.051 3505 Dihedral : 4.362 29.108 2747 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.95 % Rotamer: Outliers : 2.18 % Allowed : 14.01 % Favored : 83.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.17), residues: 2569 helix: 0.85 (0.13), residues: 1697 sheet: 0.07 (0.80), residues: 51 loop : -0.69 (0.22), residues: 821 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG P 167 TYR 0.025 0.001 TYR 4 211 PHE 0.013 0.001 PHE 1 529 TRP 0.014 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00316 (20239) covalent geometry : angle 0.54143 (27469) hydrogen bonds : bond 0.03105 ( 1053) hydrogen bonds : angle 3.69593 ( 3087) metal coordination : bond 0.00119 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 243 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.9021 (ttpt) cc_final: 0.7563 (tppt) REVERT: 0 41 GLU cc_start: 0.8436 (mt-10) cc_final: 0.7815 (pm20) REVERT: 1 69 ASP cc_start: 0.7819 (m-30) cc_final: 0.6985 (m-30) REVERT: 1 87 PHE cc_start: 0.8784 (m-80) cc_final: 0.8402 (m-80) REVERT: 1 193 VAL cc_start: 0.6809 (OUTLIER) cc_final: 0.6514 (p) REVERT: 1 456 LYS cc_start: 0.8164 (tttt) cc_final: 0.7821 (tptt) REVERT: 1 504 ASP cc_start: 0.8661 (t0) cc_final: 0.8274 (t0) REVERT: 2 16 ASP cc_start: 0.8751 (t70) cc_final: 0.8317 (t0) REVERT: 2 139 GLU cc_start: 0.8073 (OUTLIER) cc_final: 0.7337 (mp0) REVERT: 3 297 LEU cc_start: 0.8259 (mt) cc_final: 0.7861 (mt) REVERT: 3 319 GLN cc_start: 0.7565 (OUTLIER) cc_final: 0.7100 (mm110) REVERT: 4 220 LYS cc_start: 0.8477 (mptt) cc_final: 0.8043 (mmmt) REVERT: 4 229 ILE cc_start: 0.9016 (tt) cc_final: 0.8658 (pt) REVERT: 6 52 LYS cc_start: 0.8771 (OUTLIER) cc_final: 0.8508 (mmtp) REVERT: 7 119 TYR cc_start: 0.9412 (t80) cc_final: 0.9013 (t80) REVERT: 7 187 LEU cc_start: 0.8041 (mt) cc_final: 0.7798 (mt) REVERT: 9 88 GLU cc_start: 0.7423 (mp0) cc_final: 0.7056 (mp0) REVERT: P 205 ARG cc_start: 0.7301 (ptt-90) cc_final: 0.2950 (mmt-90) outliers start: 45 outliers final: 39 residues processed: 275 average time/residue: 0.1421 time to fit residues: 59.5187 Evaluate side-chains 283 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 240 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 0 residue 82 HIS Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 277 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 1 residue 512 LEU Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 139 GLU Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 3 residue 319 GLN Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 154 LEU Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 4 residue 204 PHE Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 6 residue 38 SER Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 216 optimal weight: 8.9990 chunk 174 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 232 optimal weight: 2.9990 chunk 162 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 4 111 GLN 9 80 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.129476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.102492 restraints weight = 27908.621| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.12 r_work: 0.2729 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 20241 Z= 0.190 Angle : 0.586 13.840 27469 Z= 0.294 Chirality : 0.043 0.161 3163 Planarity : 0.004 0.051 3505 Dihedral : 4.541 30.635 2747 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.40 % Favored : 95.56 % Rotamer: Outliers : 2.13 % Allowed : 14.20 % Favored : 83.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.17), residues: 2569 helix: 0.75 (0.13), residues: 1696 sheet: 0.01 (0.81), residues: 51 loop : -0.74 (0.22), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 187 TYR 0.024 0.002 TYR 4 211 PHE 0.034 0.001 PHE 3 115 TRP 0.013 0.001 TRP 3 109 HIS 0.007 0.001 HIS 7 123 Details of bonding type rmsd covalent geometry : bond 0.00452 (20239) covalent geometry : angle 0.58628 (27469) hydrogen bonds : bond 0.03406 ( 1053) hydrogen bonds : angle 3.84145 ( 3087) metal coordination : bond 0.00200 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5138 Ramachandran restraints generated. 2569 Oldfield, 0 Emsley, 2569 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 231 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: 0 40 LYS cc_start: 0.9051 (ttpt) cc_final: 0.7562 (tppt) REVERT: 0 41 GLU cc_start: 0.8469 (mt-10) cc_final: 0.7824 (pm20) REVERT: 1 69 ASP cc_start: 0.7862 (m-30) cc_final: 0.6943 (m-30) REVERT: 1 87 PHE cc_start: 0.8812 (m-80) cc_final: 0.8417 (m-80) REVERT: 1 193 VAL cc_start: 0.6928 (OUTLIER) cc_final: 0.6630 (p) REVERT: 1 456 LYS cc_start: 0.8182 (tttt) cc_final: 0.7833 (tptt) REVERT: 1 504 ASP cc_start: 0.8724 (t0) cc_final: 0.8316 (t0) REVERT: 2 16 ASP cc_start: 0.8812 (t70) cc_final: 0.8376 (t0) REVERT: 2 139 GLU cc_start: 0.8184 (OUTLIER) cc_final: 0.7472 (mp0) REVERT: 3 297 LEU cc_start: 0.8244 (mt) cc_final: 0.7822 (mt) REVERT: 3 319 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7212 (mm110) REVERT: 6 52 LYS cc_start: 0.8762 (OUTLIER) cc_final: 0.8504 (mmtp) REVERT: 7 187 LEU cc_start: 0.8134 (mt) cc_final: 0.7844 (mt) REVERT: 9 88 GLU cc_start: 0.7458 (mp0) cc_final: 0.7107 (mp0) REVERT: P 205 ARG cc_start: 0.7440 (ptt-90) cc_final: 0.3048 (mmt-90) outliers start: 44 outliers final: 39 residues processed: 265 average time/residue: 0.1421 time to fit residues: 58.0444 Evaluate side-chains 266 residues out of total 2067 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 223 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 19 SER Chi-restraints excluded: chain 0 residue 43 SER Chi-restraints excluded: chain 0 residue 82 HIS Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 92 TYR Chi-restraints excluded: chain 1 residue 193 VAL Chi-restraints excluded: chain 1 residue 234 VAL Chi-restraints excluded: chain 1 residue 277 VAL Chi-restraints excluded: chain 1 residue 310 THR Chi-restraints excluded: chain 1 residue 367 GLU Chi-restraints excluded: chain 1 residue 435 THR Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 2 residue 139 GLU Chi-restraints excluded: chain 2 residue 228 ILE Chi-restraints excluded: chain 2 residue 370 ILE Chi-restraints excluded: chain 2 residue 399 VAL Chi-restraints excluded: chain 2 residue 422 GLU Chi-restraints excluded: chain 3 residue 303 VAL Chi-restraints excluded: chain 3 residue 319 GLN Chi-restraints excluded: chain 4 residue 21 GLU Chi-restraints excluded: chain 4 residue 77 SER Chi-restraints excluded: chain 4 residue 122 VAL Chi-restraints excluded: chain 4 residue 141 VAL Chi-restraints excluded: chain 4 residue 154 LEU Chi-restraints excluded: chain 4 residue 181 ASP Chi-restraints excluded: chain 5 residue 106 LEU Chi-restraints excluded: chain 6 residue 38 SER Chi-restraints excluded: chain 6 residue 52 LYS Chi-restraints excluded: chain 6 residue 73 THR Chi-restraints excluded: chain 6 residue 84 SER Chi-restraints excluded: chain 6 residue 146 PHE Chi-restraints excluded: chain 7 residue 144 VAL Chi-restraints excluded: chain 8 residue 6 VAL Chi-restraints excluded: chain 8 residue 54 THR Chi-restraints excluded: chain 8 residue 77 ILE Chi-restraints excluded: chain 9 residue 3 VAL Chi-restraints excluded: chain 9 residue 65 THR Chi-restraints excluded: chain 9 residue 92 GLU Chi-restraints excluded: chain M residue 261 LEU Chi-restraints excluded: chain M residue 290 LEU Chi-restraints excluded: chain M residue 296 SER Chi-restraints excluded: chain M residue 323 VAL Chi-restraints excluded: chain P residue 184 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 255 random chunks: chunk 166 optimal weight: 0.2980 chunk 244 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 111 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 138 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 12 optimal weight: 0.8980 chunk 222 optimal weight: 0.0470 chunk 58 optimal weight: 1.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 44 ASN 4 111 GLN 6 74 GLN 9 80 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.132935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.106176 restraints weight = 27737.847| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 2.05 r_work: 0.2791 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 20241 Z= 0.108 Angle : 0.526 12.178 27469 Z= 0.263 Chirality : 0.039 0.147 3163 Planarity : 0.004 0.052 3505 Dihedral : 4.312 29.937 2747 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.74 % Favored : 96.22 % Rotamer: Outliers : 2.08 % Allowed : 14.30 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.17), residues: 2569 helix: 1.02 (0.13), residues: 1699 sheet: 0.00 (0.80), residues: 51 loop : -0.64 (0.22), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 2 187 TYR 0.025 0.001 TYR 4 211 PHE 0.030 0.001 PHE 3 115 TRP 0.018 0.001 TRP 9 73 HIS 0.005 0.001 HIS 4 233 Details of bonding type rmsd covalent geometry : bond 0.00249 (20239) covalent geometry : angle 0.52593 (27469) hydrogen bonds : bond 0.02952 ( 1053) hydrogen bonds : angle 3.65275 ( 3087) metal coordination : bond 0.00095 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6592.31 seconds wall clock time: 113 minutes 12.80 seconds (6792.80 seconds total)