Starting phenix.real_space_refine on Sat Aug 8 15:06:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8fni_29314/08_2026/8fni_29314.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fni_29314/08_2026/8fni_29314.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8fni_29314/08_2026/8fni_29314.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fni_29314/08_2026/8fni_29314.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8fni_29314/08_2026/8fni_29314.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8fni_29314/08_2026/8fni_29314.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8fni_29314/08_2026/8fni_29314.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fni_29314/08_2026/8fni_29314.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 37 5.49 5 S 187 5.16 5 C 18136 2.51 5 N 5066 2.21 5 O 5432 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 28858 Number of models: 1 Model: "" Number of chains: 11 Chain: "m" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 453 Classifications: {'RNAv2': 21} Modifications used: {'rna2p_pur': 13, 'rna2p_pyr': 3, 'rna3p_pur': 2, 'rna3p_pyr': 3} Link IDs: {'rna2p': 16, 'rna3p': 4} Chain: "g" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 320 Classifications: {'RNAv2': 16} Modifications used: {'rna2p_pyr': 10, 'rna3p_pyr': 6} Link IDs: {'rna2p': 10, 'rna3p': 5} Chain: "5" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2318 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 15, 'TRANS': 280} Chain: "6" Number of atoms: 3591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 453, 3591 Classifications: {'peptide': 453} Link IDs: {'PTRANS': 11, 'TRANS': 441} Chain: "7" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain breaks: 1 Chain: "8" Number of atoms: 4056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4056 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 24, 'TRANS': 488} Chain: "9" Number of atoms: 6662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 858, 6662 Classifications: {'peptide': 858} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 34, 'TRANS': 823} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "10" Number of atoms: 3290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 416, 3290 Classifications: {'peptide': 416} Link IDs: {'PTRANS': 14, 'TRANS': 401} Chain breaks: 3 Chain: "11" Number of atoms: 4918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 614, 4918 Classifications: {'peptide': 614} Link IDs: {'PTRANS': 34, 'TRANS': 579} Chain breaks: 3 Chain: "13" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 227 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 1, 'TRANS': 28} Chain: "14" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 2505 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 24, 'TRANS': 290} Time building chain proxies: 5.36, per 1000 atoms: 0.19 Number of scatterers: 28858 At special positions: 0 Unit cell: (128.502, 132.75, 204.966, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 187 16.00 P 37 15.00 O 5432 8.00 N 5066 7.00 C 18136 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 858.8 milliseconds 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6782 Finding SS restraints... Secondary structure from input PDB file: 208 helices and 9 sheets defined 73.0% alpha, 3.4% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 2.76 Creating SS restraints... Processing helix chain '5' and resid 34 through 51 Processing helix chain '5' and resid 67 through 71 Processing helix chain '5' and resid 94 through 108 Processing helix chain '5' and resid 147 through 159 removed outlier: 3.648A pdb=" N HIS 5 151 " --> pdb=" O ASN 5 147 " (cutoff:3.500A) Processing helix chain '5' and resid 180 through 184 removed outlier: 3.924A pdb=" N TYR 5 184 " --> pdb=" O PRO 5 180 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 180 through 184' Processing helix chain '5' and resid 198 through 212 Processing helix chain '5' and resid 247 through 256 Processing helix chain '5' and resid 265 through 272 Processing helix chain '5' and resid 275 through 279 removed outlier: 3.863A pdb=" N VAL 5 279 " --> pdb=" O ARG 5 276 " (cutoff:3.500A) Processing helix chain '6' and resid 62 through 80 removed outlier: 3.767A pdb=" N GLU 6 69 " --> pdb=" O ASN 6 65 " (cutoff:3.500A) Processing helix chain '6' and resid 83 through 96 removed outlier: 3.799A pdb=" N ALA 6 96 " --> pdb=" O ARG 6 92 " (cutoff:3.500A) Processing helix chain '6' and resid 105 through 119 Processing helix chain '6' and resid 125 through 138 Processing helix chain '6' and resid 146 through 157 removed outlier: 3.686A pdb=" N VAL 6 150 " --> pdb=" O VAL 6 146 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR 6 156 " --> pdb=" O THR 6 152 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LEU 6 157 " --> pdb=" O ALA 6 153 " (cutoff:3.500A) Processing helix chain '6' and resid 159 through 176 Processing helix chain '6' and resid 181 through 195 removed outlier: 3.676A pdb=" N LYS 6 194 " --> pdb=" O SER 6 190 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR 6 195 " --> pdb=" O ALA 6 191 " (cutoff:3.500A) Processing helix chain '6' and resid 199 through 215 Processing helix chain '6' and resid 220 through 234 Processing helix chain '6' and resid 238 through 252 Processing helix chain '6' and resid 257 through 272 Proline residue: 6 263 - end of helix removed outlier: 3.927A pdb=" N GLY 6 272 " --> pdb=" O PHE 6 268 " (cutoff:3.500A) Processing helix chain '6' and resid 276 through 289 removed outlier: 3.928A pdb=" N LYS 6 280 " --> pdb=" O PRO 6 276 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ARG 6 281 " --> pdb=" O LYS 6 277 " (cutoff:3.500A) Processing helix chain '6' and resid 290 through 293 Processing helix chain '6' and resid 294 through 309 Processing helix chain '6' and resid 313 through 326 Processing helix chain '6' and resid 331 through 346 Processing helix chain '6' and resid 349 through 363 Processing helix chain '6' and resid 368 through 383 Processing helix chain '6' and resid 387 through 400 removed outlier: 3.541A pdb=" N SER 6 399 " --> pdb=" O SER 6 395 " (cutoff:3.500A) Processing helix chain '6' and resid 401 through 404 removed outlier: 3.799A pdb=" N PHE 6 404 " --> pdb=" O ALA 6 401 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 401 through 404' Processing helix chain '6' and resid 405 through 419 removed outlier: 4.013A pdb=" N VAL 6 410 " --> pdb=" O ALA 6 406 " (cutoff:3.500A) Processing helix chain '6' and resid 423 through 434 Processing helix chain '6' and resid 437 through 441 removed outlier: 3.664A pdb=" N LEU 6 441 " --> pdb=" O CYS 6 438 " (cutoff:3.500A) Processing helix chain '6' and resid 442 through 457 Processing helix chain '6' and resid 460 through 474 Proline residue: 6 466 - end of helix Processing helix chain '6' and resid 474 through 480 Processing helix chain '6' and resid 484 through 496 Processing helix chain '6' and resid 500 through 508 Processing helix chain '7' and resid 81 through 97 removed outlier: 3.905A pdb=" N THR 7 97 " --> pdb=" O ARG 7 93 " (cutoff:3.500A) Processing helix chain '7' and resid 112 through 118 removed outlier: 4.023A pdb=" N LEU 7 118 " --> pdb=" O ASP 7 114 " (cutoff:3.500A) Processing helix chain '7' and resid 119 through 125 Processing helix chain '7' and resid 127 through 145 Processing helix chain '8' and resid 22 through 33 Processing helix chain '8' and resid 39 through 53 Processing helix chain '8' and resid 61 through 74 removed outlier: 3.650A pdb=" N MET 8 65 " --> pdb=" O ASP 8 61 " (cutoff:3.500A) Processing helix chain '8' and resid 76 through 80 removed outlier: 3.862A pdb=" N VAL 8 79 " --> pdb=" O ASP 8 76 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE 8 80 " --> pdb=" O GLN 8 77 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 76 through 80' Processing helix chain '8' and resid 81 through 96 removed outlier: 3.779A pdb=" N VAL 8 95 " --> pdb=" O THR 8 91 " (cutoff:3.500A) Processing helix chain '8' and resid 113 through 127 removed outlier: 3.828A pdb=" N ILE 8 118 " --> pdb=" O PRO 8 114 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU 8 119 " --> pdb=" O GLU 8 115 " (cutoff:3.500A) Processing helix chain '8' and resid 131 through 141 Processing helix chain '8' and resid 145 through 149 removed outlier: 3.745A pdb=" N PHE 8 149 " --> pdb=" O LEU 8 146 " (cutoff:3.500A) Processing helix chain '8' and resid 150 through 164 removed outlier: 3.630A pdb=" N SER 8 155 " --> pdb=" O PRO 8 151 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR 8 159 " --> pdb=" O SER 8 155 " (cutoff:3.500A) Processing helix chain '8' and resid 168 through 182 removed outlier: 3.950A pdb=" N VAL 8 172 " --> pdb=" O ASN 8 168 " (cutoff:3.500A) Processing helix chain '8' and resid 183 through 186 Processing helix chain '8' and resid 187 through 201 Processing helix chain '8' and resid 205 through 219 removed outlier: 3.726A pdb=" N LEU 8 209 " --> pdb=" O SER 8 205 " (cutoff:3.500A) Processing helix chain '8' and resid 220 through 223 removed outlier: 3.719A pdb=" N PHE 8 223 " --> pdb=" O MET 8 220 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 220 through 223' Processing helix chain '8' and resid 224 through 239 Processing helix chain '8' and resid 242 through 254 removed outlier: 3.648A pdb=" N PHE 8 246 " --> pdb=" O PHE 8 242 " (cutoff:3.500A) Processing helix chain '8' and resid 261 through 276 Processing helix chain '8' and resid 279 through 293 removed outlier: 4.070A pdb=" N ILE 8 283 " --> pdb=" O GLN 8 279 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ASP 8 284 " --> pdb=" O ARG 8 280 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE 8 285 " --> pdb=" O GLU 8 281 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL 8 293 " --> pdb=" O ALA 8 289 " (cutoff:3.500A) Processing helix chain '8' and resid 294 through 297 removed outlier: 3.566A pdb=" N LEU 8 297 " --> pdb=" O ALA 8 294 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 294 through 297' Processing helix chain '8' and resid 298 through 312 Processing helix chain '8' and resid 316 through 332 removed outlier: 3.625A pdb=" N PHE 8 320 " --> pdb=" O SER 8 316 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY 8 321 " --> pdb=" O ASP 8 317 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ARG 8 329 " --> pdb=" O SER 8 325 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR 8 330 " --> pdb=" O CYS 8 326 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA 8 332 " --> pdb=" O ILE 8 328 " (cutoff:3.500A) Processing helix chain '8' and resid 333 through 334 No H-bonds generated for 'chain '8' and resid 333 through 334' Processing helix chain '8' and resid 335 through 338 Processing helix chain '8' and resid 339 through 349 Processing helix chain '8' and resid 353 through 368 Processing helix chain '8' and resid 372 through 383 Processing helix chain '8' and resid 386 through 390 Processing helix chain '8' and resid 393 through 406 removed outlier: 4.000A pdb=" N LEU 8 397 " --> pdb=" O PRO 8 393 " (cutoff:3.500A) Processing helix chain '8' and resid 410 through 424 removed outlier: 3.769A pdb=" N ALA 8 415 " --> pdb=" O PRO 8 411 " (cutoff:3.500A) Processing helix chain '8' and resid 428 through 443 Processing helix chain '8' and resid 446 through 449 Processing helix chain '8' and resid 450 through 461 removed outlier: 3.848A pdb=" N THR 8 460 " --> pdb=" O GLY 8 456 " (cutoff:3.500A) Processing helix chain '8' and resid 464 through 479 Proline residue: 8 477 - end of helix Processing helix chain '8' and resid 480 through 482 No H-bonds generated for 'chain '8' and resid 480 through 482' Processing helix chain '8' and resid 483 through 498 Processing helix chain '8' and resid 501 through 516 removed outlier: 4.091A pdb=" N TYR 8 505 " --> pdb=" O ASP 8 501 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN 8 514 " --> pdb=" O SER 8 510 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE 8 515 " --> pdb=" O ARG 8 511 " (cutoff:3.500A) Processing helix chain '8' and resid 524 through 533 Processing helix chain '9' and resid 2 through 13 Processing helix chain '9' and resid 20 through 35 Processing helix chain '9' and resid 36 through 38 No H-bonds generated for 'chain '9' and resid 36 through 38' Processing helix chain '9' and resid 39 through 41 No H-bonds generated for 'chain '9' and resid 39 through 41' Processing helix chain '9' and resid 42 through 57 Proline residue: 9 49 - end of helix Processing helix chain '9' and resid 59 through 68 removed outlier: 4.238A pdb=" N SER 9 63 " --> pdb=" O ASP 9 59 " (cutoff:3.500A) Processing helix chain '9' and resid 76 through 88 removed outlier: 4.293A pdb=" N ARG 9 80 " --> pdb=" O THR 9 76 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU 9 84 " --> pdb=" O ARG 9 80 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU 9 85 " --> pdb=" O ALA 9 81 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG 9 86 " --> pdb=" O ALA 9 82 " (cutoff:3.500A) Processing helix chain '9' and resid 94 through 112 removed outlier: 3.635A pdb=" N TRP 9 98 " --> pdb=" O ASP 9 94 " (cutoff:3.500A) Processing helix chain '9' and resid 115 through 130 removed outlier: 3.930A pdb=" N HIS 9 125 " --> pdb=" O VAL 9 121 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ARG 9 128 " --> pdb=" O ALA 9 124 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N GLY 9 129 " --> pdb=" O HIS 9 125 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY 9 130 " --> pdb=" O ALA 9 126 " (cutoff:3.500A) Processing helix chain '9' and resid 134 through 147 removed outlier: 4.418A pdb=" N ALA 9 138 " --> pdb=" O PRO 9 134 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER 9 145 " --> pdb=" O GLU 9 141 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER 9 147 " --> pdb=" O PHE 9 143 " (cutoff:3.500A) Processing helix chain '9' and resid 155 through 164 removed outlier: 3.742A pdb=" N ILE 9 162 " --> pdb=" O ALA 9 158 " (cutoff:3.500A) Processing helix chain '9' and resid 166 through 171 removed outlier: 4.158A pdb=" N ARG 9 171 " --> pdb=" O GLU 9 168 " (cutoff:3.500A) Processing helix chain '9' and resid 172 through 185 removed outlier: 4.198A pdb=" N GLN 9 176 " --> pdb=" O SER 9 172 " (cutoff:3.500A) Processing helix chain '9' and resid 190 through 202 removed outlier: 3.868A pdb=" N GLY 9 195 " --> pdb=" O PRO 9 191 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLN 9 196 " --> pdb=" O ALA 9 192 " (cutoff:3.500A) Processing helix chain '9' and resid 208 through 218 removed outlier: 4.005A pdb=" N GLU 9 218 " --> pdb=" O ALA 9 214 " (cutoff:3.500A) Processing helix chain '9' and resid 218 through 223 Processing helix chain '9' and resid 227 through 241 removed outlier: 3.552A pdb=" N GLN 9 241 " --> pdb=" O PHE 9 237 " (cutoff:3.500A) Processing helix chain '9' and resid 250 through 259 removed outlier: 4.127A pdb=" N LEU 9 254 " --> pdb=" O ALA 9 250 " (cutoff:3.500A) Processing helix chain '9' and resid 265 through 278 Processing helix chain '9' and resid 280 through 282 No H-bonds generated for 'chain '9' and resid 280 through 282' Processing helix chain '9' and resid 283 through 308 removed outlier: 5.967A pdb=" N ARG 9 289 " --> pdb=" O PRO 9 285 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLU 9 290 " --> pdb=" O GLU 9 286 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE 9 297 " --> pdb=" O GLU 9 293 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY 9 300 " --> pdb=" O GLU 9 296 " (cutoff:3.500A) Processing helix chain '9' and resid 309 through 313 Processing helix chain '9' and resid 320 through 337 removed outlier: 3.703A pdb=" N SER 9 326 " --> pdb=" O GLY 9 322 " (cutoff:3.500A) Processing helix chain '9' and resid 347 through 362 removed outlier: 3.811A pdb=" N ALA 9 351 " --> pdb=" O THR 9 347 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG 9 362 " --> pdb=" O TYR 9 358 " (cutoff:3.500A) Processing helix chain '9' and resid 363 through 369 Processing helix chain '9' and resid 375 through 382 removed outlier: 4.190A pdb=" N HIS 9 379 " --> pdb=" O SER 9 375 " (cutoff:3.500A) Processing helix chain '9' and resid 385 through 403 Processing helix chain '9' and resid 407 through 422 Processing helix chain '9' and resid 426 through 439 Processing helix chain '9' and resid 444 through 458 Processing helix chain '9' and resid 469 through 499 removed outlier: 3.686A pdb=" N ASP 9 480 " --> pdb=" O LEU 9 476 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN 9 491 " --> pdb=" O PHE 9 487 " (cutoff:3.500A) Processing helix chain '9' and resid 501 through 516 Processing helix chain '9' and resid 521 through 533 Processing helix chain '9' and resid 543 through 554 Processing helix chain '9' and resid 555 through 562 Processing helix chain '9' and resid 562 through 575 removed outlier: 3.571A pdb=" N HIS 9 566 " --> pdb=" O HIS 9 562 " (cutoff:3.500A) Processing helix chain '9' and resid 584 through 593 Processing helix chain '9' and resid 602 through 618 Processing helix chain '9' and resid 622 through 635 removed outlier: 3.537A pdb=" N LEU 9 626 " --> pdb=" O ASP 9 622 " (cutoff:3.500A) Processing helix chain '9' and resid 636 through 640 Processing helix chain '9' and resid 644 through 655 removed outlier: 3.510A pdb=" N GLY 9 650 " --> pdb=" O LYS 9 646 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE 9 652 " --> pdb=" O PHE 9 648 " (cutoff:3.500A) Processing helix chain '9' and resid 659 through 673 removed outlier: 3.652A pdb=" N LEU 9 663 " --> pdb=" O GLN 9 659 " (cutoff:3.500A) Processing helix chain '9' and resid 680 through 693 Processing helix chain '9' and resid 698 through 709 removed outlier: 3.894A pdb=" N VAL 9 702 " --> pdb=" O TYR 9 698 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE 9 709 " --> pdb=" O PHE 9 705 " (cutoff:3.500A) Processing helix chain '9' and resid 710 through 716 removed outlier: 3.598A pdb=" N TRP 9 714 " --> pdb=" O SER 9 710 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU 9 716 " --> pdb=" O GLU 9 712 " (cutoff:3.500A) Processing helix chain '9' and resid 718 through 732 Processing helix chain '9' and resid 736 through 751 removed outlier: 3.864A pdb=" N VAL 9 741 " --> pdb=" O PRO 9 737 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N HIS 9 742 " --> pdb=" O GLN 9 738 " (cutoff:3.500A) Processing helix chain '9' and resid 752 through 754 No H-bonds generated for 'chain '9' and resid 752 through 754' Processing helix chain '9' and resid 755 through 769 Processing helix chain '9' and resid 774 through 787 Processing helix chain '9' and resid 788 through 791 Processing helix chain '9' and resid 792 through 801 Processing helix chain '9' and resid 804 through 809 removed outlier: 3.956A pdb=" N LEU 9 808 " --> pdb=" O GLY 9 804 " (cutoff:3.500A) Processing helix chain '9' and resid 811 through 826 Proline residue: 9 817 - end of helix Processing helix chain '9' and resid 828 through 842 Processing helix chain '9' and resid 845 through 857 Processing helix chain '10' and resid 117 through 141 removed outlier: 4.150A pdb=" N ALA10 121 " --> pdb=" O THR10 117 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL10 125 " --> pdb=" O ALA10 121 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU10 126 " --> pdb=" O HIS10 122 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA10 137 " --> pdb=" O ALA10 133 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS10 141 " --> pdb=" O ALA10 137 " (cutoff:3.500A) Processing helix chain '10' and resid 155 through 183 Processing helix chain '10' and resid 184 through 189 removed outlier: 3.791A pdb=" N ARG10 188 " --> pdb=" O PRO10 184 " (cutoff:3.500A) Processing helix chain '10' and resid 191 through 207 removed outlier: 3.834A pdb=" N LYS10 205 " --> pdb=" O THR10 201 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU10 206 " --> pdb=" O THR10 202 " (cutoff:3.500A) Processing helix chain '10' and resid 211 through 233 removed outlier: 3.585A pdb=" N MET10 221 " --> pdb=" O ALA10 217 " (cutoff:3.500A) Processing helix chain '10' and resid 236 through 249 removed outlier: 3.988A pdb=" N LEU10 241 " --> pdb=" O ALA10 237 " (cutoff:3.500A) Processing helix chain '10' and resid 254 through 265 Processing helix chain '10' and resid 275 through 289 removed outlier: 3.854A pdb=" N THR10 289 " --> pdb=" O ARG10 285 " (cutoff:3.500A) Processing helix chain '10' and resid 294 through 296 No H-bonds generated for 'chain '10' and resid 294 through 296' Processing helix chain '10' and resid 297 through 308 removed outlier: 3.663A pdb=" N MET10 308 " --> pdb=" O VAL10 304 " (cutoff:3.500A) Processing helix chain '10' and resid 308 through 315 Processing helix chain '10' and resid 320 through 334 removed outlier: 3.505A pdb=" N HIS10 334 " --> pdb=" O CYS10 330 " (cutoff:3.500A) Processing helix chain '10' and resid 338 through 340 No H-bonds generated for 'chain '10' and resid 338 through 340' Processing helix chain '10' and resid 341 through 350 removed outlier: 3.513A pdb=" N ALA10 345 " --> pdb=" O LEU10 341 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ALA10 348 " --> pdb=" O LEU10 344 " (cutoff:3.500A) Processing helix chain '10' and resid 356 through 370 removed outlier: 4.064A pdb=" N ALA10 361 " --> pdb=" O PRO10 357 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR10 362 " --> pdb=" O HIS10 358 " (cutoff:3.500A) Processing helix chain '10' and resid 374 through 387 removed outlier: 3.646A pdb=" N ARG10 380 " --> pdb=" O GLU10 376 " (cutoff:3.500A) Processing helix chain '10' and resid 392 through 408 Processing helix chain '10' and resid 416 through 418 No H-bonds generated for 'chain '10' and resid 416 through 418' Processing helix chain '10' and resid 419 through 436 removed outlier: 3.681A pdb=" N THR10 423 " --> pdb=" O ASN10 419 " (cutoff:3.500A) Processing helix chain '10' and resid 445 through 459 removed outlier: 3.843A pdb=" N ILE10 449 " --> pdb=" O ALA10 445 " (cutoff:3.500A) Processing helix chain '10' and resid 464 through 483 removed outlier: 4.238A pdb=" N ILE10 481 " --> pdb=" O ASP10 477 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N VAL10 482 " --> pdb=" O MET10 478 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N MET10 483 " --> pdb=" O VAL10 479 " (cutoff:3.500A) Processing helix chain '10' and resid 502 through 517 Processing helix chain '10' and resid 521 through 535 removed outlier: 3.687A pdb=" N GLN10 526 " --> pdb=" O PRO10 522 " (cutoff:3.500A) Processing helix chain '11' and resid 194 through 207 Processing helix chain '11' and resid 208 through 213 removed outlier: 6.207A pdb=" N ARG11 211 " --> pdb=" O LYS11 208 " (cutoff:3.500A) Processing helix chain '11' and resid 214 through 229 Proline residue: 11 223 - end of helix Processing helix chain '11' and resid 230 through 232 No H-bonds generated for 'chain '11' and resid 230 through 232' Processing helix chain '11' and resid 233 through 243 removed outlier: 3.719A pdb=" N CYS11 243 " --> pdb=" O ASP11 239 " (cutoff:3.500A) Processing helix chain '11' and resid 246 through 253 Processing helix chain '11' and resid 253 through 277 Processing helix chain '11' and resid 326 through 331 Processing helix chain '11' and resid 332 through 345 removed outlier: 3.835A pdb=" N MET11 345 " --> pdb=" O ILE11 341 " (cutoff:3.500A) Processing helix chain '11' and resid 350 through 367 Processing helix chain '11' and resid 368 through 371 Processing helix chain '11' and resid 373 through 388 removed outlier: 3.889A pdb=" N LEU11 377 " --> pdb=" O ASP11 373 " (cutoff:3.500A) Processing helix chain '11' and resid 392 through 407 Processing helix chain '11' and resid 413 through 427 Processing helix chain '11' and resid 431 through 464 removed outlier: 4.227A pdb=" N PHE11 435 " --> pdb=" O GLN11 431 " (cutoff:3.500A) Processing helix chain '11' and resid 524 through 541 Processing helix chain '11' and resid 543 through 557 Processing helix chain '11' and resid 565 through 570 removed outlier: 4.560A pdb=" N VAL11 570 " --> pdb=" O ARG11 566 " (cutoff:3.500A) Processing helix chain '11' and resid 572 through 577 Processing helix chain '11' and resid 581 through 596 Processing helix chain '11' and resid 599 through 613 Proline residue: 11 605 - end of helix Processing helix chain '11' and resid 620 through 632 Processing helix chain '11' and resid 641 through 656 removed outlier: 3.521A pdb=" N LEU11 645 " --> pdb=" O ASN11 641 " (cutoff:3.500A) Processing helix chain '11' and resid 686 through 701 removed outlier: 3.730A pdb=" N LYS11 701 " --> pdb=" O LYS11 697 " (cutoff:3.500A) Processing helix chain '11' and resid 705 through 729 Proline residue: 11 711 - end of helix removed outlier: 3.511A pdb=" N LYS11 728 " --> pdb=" O TYR11 724 " (cutoff:3.500A) Processing helix chain '11' and resid 733 through 748 removed outlier: 3.557A pdb=" N VAL11 737 " --> pdb=" O SER11 733 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN11 748 " --> pdb=" O CYS11 744 " (cutoff:3.500A) Processing helix chain '11' and resid 754 through 769 Processing helix chain '11' and resid 770 through 777 removed outlier: 3.938A pdb=" N GLU11 774 " --> pdb=" O GLU11 770 " (cutoff:3.500A) Processing helix chain '11' and resid 780 through 795 Processing helix chain '11' and resid 806 through 819 Processing helix chain '11' and resid 821 through 836 Processing helix chain '11' and resid 841 through 858 removed outlier: 4.136A pdb=" N GLY11 858 " --> pdb=" O ALA11 854 " (cutoff:3.500A) Processing helix chain '11' and resid 881 through 895 Processing helix chain '11' and resid 897 through 902 Processing helix chain '11' and resid 903 through 918 removed outlier: 3.567A pdb=" N TRP11 907 " --> pdb=" O SER11 903 " (cutoff:3.500A) Processing helix chain '11' and resid 920 through 934 Processing helix chain '13' and resid 116 through 121 removed outlier: 3.816A pdb=" N ARG13 119 " --> pdb=" O ALA13 116 " (cutoff:3.500A) Processing helix chain '13' and resid 123 through 128 Processing helix chain '14' and resid 39 through 43 removed outlier: 3.655A pdb=" N ARG14 43 " --> pdb=" O LYS14 40 " (cutoff:3.500A) Processing helix chain '14' and resid 49 through 53 Processing helix chain '14' and resid 70 through 74 removed outlier: 3.686A pdb=" N PHE14 73 " --> pdb=" O PHE14 70 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL14 74 " --> pdb=" O GLY14 71 " (cutoff:3.500A) No H-bonds generated for 'chain '14' and resid 70 through 74' Processing helix chain '14' and resid 76 through 87 Processing helix chain '14' and resid 97 through 112 Processing helix chain '14' and resid 120 through 124 Processing helix chain '14' and resid 143 through 146 Processing helix chain '14' and resid 149 through 155 removed outlier: 3.609A pdb=" N ILE14 154 " --> pdb=" O MET14 150 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N TYR14 155 " --> pdb=" O HIS14 151 " (cutoff:3.500A) Processing helix chain '14' and resid 156 through 167 removed outlier: 3.894A pdb=" N ALA14 162 " --> pdb=" O THR14 158 " (cutoff:3.500A) Processing helix chain '14' and resid 194 through 198 removed outlier: 3.530A pdb=" N ARG14 198 " --> pdb=" O ASN14 195 " (cutoff:3.500A) Processing helix chain '14' and resid 229 through 237 removed outlier: 3.510A pdb=" N ARG14 232 " --> pdb=" O GLY14 229 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N TRP14 233 " --> pdb=" O SER14 230 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ARG14 234 " --> pdb=" O HIS14 231 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU14 235 " --> pdb=" O ARG14 232 " (cutoff:3.500A) Processing helix chain '14' and resid 249 through 261 removed outlier: 4.076A pdb=" N GLN14 253 " --> pdb=" O ASP14 249 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N ILE14 257 " --> pdb=" O GLN14 253 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N TRP14 258 " --> pdb=" O LEU14 254 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU14 259 " --> pdb=" O ASN14 255 " (cutoff:3.500A) Processing helix chain '14' and resid 262 through 272 removed outlier: 3.770A pdb=" N ASP14 271 " --> pdb=" O GLU14 267 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR14 272 " --> pdb=" O MET14 268 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '5' and resid 12 through 16 removed outlier: 6.410A pdb=" N ALA 5 13 " --> pdb=" O HIS 5 59 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N MET 5 61 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N VAL 5 15 " --> pdb=" O MET 5 61 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '5' and resid 76 through 79 Processing sheet with id=AA3, first strand: chain '5' and resid 132 through 134 removed outlier: 3.569A pdb=" N ILE 5 138 " --> pdb=" O ASP 5 168 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '5' and resid 185 through 188 removed outlier: 6.300A pdb=" N LEU 5 193 " --> pdb=" O VAL 5 220 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU 5 222 " --> pdb=" O LEU 5 193 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N THR 5 195 " --> pdb=" O LEU 5 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '5' and resid 228 through 230 Processing sheet with id=AA6, first strand: chain '11' and resid 861 through 864 Processing sheet with id=AA7, first strand: chain '14' and resid 88 through 90 removed outlier: 3.810A pdb=" N VAL14 304 " --> pdb=" O LYS14 182 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR14 176 " --> pdb=" O HIS14 310 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N MET14 312 " --> pdb=" O LEU14 174 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU14 174 " --> pdb=" O MET14 312 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N ALA14 126 " --> pdb=" O GLN14 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '14' and resid 88 through 90 removed outlier: 3.810A pdb=" N VAL14 304 " --> pdb=" O LYS14 182 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TYR14 176 " --> pdb=" O HIS14 310 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N MET14 312 " --> pdb=" O LEU14 174 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N LEU14 174 " --> pdb=" O MET14 312 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL14 172 " --> pdb=" O PHE14 346 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N PHE14 346 " --> pdb=" O VAL14 172 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LEU14 174 " --> pdb=" O VAL14 344 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL14 344 " --> pdb=" O LEU14 174 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '14' and resid 190 through 193 removed outlier: 5.161A pdb=" N THR14 295 " --> pdb=" O PRO14 191 " (cutoff:3.500A) 1703 hydrogen bonds defined for protein. 4989 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 4.75 Time building geometry restraints manager: 3.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 8915 1.34 - 1.46: 4576 1.46 - 1.58: 15607 1.58 - 1.70: 72 1.70 - 1.82: 311 Bond restraints: 29481 Sorted by residual: bond pdb=" N THR14 121 " pdb=" CA THR14 121 " ideal model delta sigma weight residual 1.459 1.487 -0.027 1.23e-02 6.61e+03 4.98e+00 bond pdb=" C3' U g -2 " pdb=" O3' U g -2 " ideal model delta sigma weight residual 1.415 1.446 -0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" CB PRO 6 350 " pdb=" CG PRO 6 350 " ideal model delta sigma weight residual 1.492 1.566 -0.074 5.00e-02 4.00e+02 2.22e+00 bond pdb=" C3' A m 120 " pdb=" O3' A m 120 " ideal model delta sigma weight residual 1.415 1.444 -0.029 2.00e-02 2.50e+03 2.07e+00 bond pdb=" CA ARG13 131 " pdb=" CB ARG13 131 " ideal model delta sigma weight residual 1.531 1.574 -0.043 3.28e-02 9.30e+02 1.76e+00 ... (remaining 29476 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 39567 2.20 - 4.40: 415 4.40 - 6.60: 88 6.60 - 8.79: 5 8.79 - 10.99: 1 Bond angle restraints: 40076 Sorted by residual: angle pdb=" C3' U g -2 " pdb=" O3' U g -2 " pdb=" P U g -1 " ideal model delta sigma weight residual 119.70 125.61 -5.91 1.20e+00 6.94e-01 2.43e+01 angle pdb=" C3' A m 120 " pdb=" O3' A m 120 " pdb=" P G m 121 " ideal model delta sigma weight residual 119.70 125.12 -5.42 1.20e+00 6.94e-01 2.04e+01 angle pdb=" CB MET14 270 " pdb=" CG MET14 270 " pdb=" SD MET14 270 " ideal model delta sigma weight residual 112.70 123.69 -10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CA GLN 9 240 " pdb=" CB GLN 9 240 " pdb=" CG GLN 9 240 " ideal model delta sigma weight residual 114.10 120.59 -6.49 2.00e+00 2.50e-01 1.05e+01 angle pdb=" CA MET 9 295 " pdb=" CB MET 9 295 " pdb=" CG MET 9 295 " ideal model delta sigma weight residual 114.10 120.44 -6.34 2.00e+00 2.50e-01 1.01e+01 ... (remaining 40071 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.26: 17321 33.26 - 66.53: 559 66.53 - 99.79: 61 99.79 - 133.05: 0 133.05 - 166.32: 2 Dihedral angle restraints: 17943 sinusoidal: 7528 harmonic: 10415 Sorted by residual: dihedral pdb=" C4' U g -6 " pdb=" C3' U g -6 " pdb=" C2' U g -6 " pdb=" C1' U g -6 " ideal model delta sinusoidal sigma weight residual 36.34 -36.61 72.96 1 3.10e+00 1.04e-01 7.06e+02 dihedral pdb=" C4' A m 114 " pdb=" C3' A m 114 " pdb=" C2' A m 114 " pdb=" C1' A m 114 " ideal model delta sinusoidal sigma weight residual 36.34 -36.53 72.88 1 3.10e+00 1.04e-01 7.05e+02 dihedral pdb=" C4' A m 115 " pdb=" C3' A m 115 " pdb=" C2' A m 115 " pdb=" C1' A m 115 " ideal model delta sinusoidal sigma weight residual 36.34 -36.41 72.76 1 3.10e+00 1.04e-01 7.03e+02 ... (remaining 17940 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 4222 0.069 - 0.138: 303 0.138 - 0.208: 3 0.208 - 0.277: 80 0.277 - 0.346: 8 Chirality restraints: 4616 Sorted by residual: chirality pdb=" P G m 121 " pdb=" OP1 G m 121 " pdb=" OP2 G m 121 " pdb=" O5' G m 121 " both_signs ideal model delta sigma weight residual True 2.17 -2.52 -0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" P U g -1 " pdb=" OP1 U g -1 " pdb=" OP2 U g -1 " pdb=" O5' U g -1 " both_signs ideal model delta sigma weight residual True 2.17 -2.50 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C2' A m 120 " pdb=" C3' A m 120 " pdb=" O2' A m 120 " pdb=" C1' A m 120 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 4613 not shown) Planarity restraints: 5048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN 6 349 " 0.048 5.00e-02 4.00e+02 7.17e-02 8.22e+00 pdb=" N PRO 6 350 " -0.124 5.00e-02 4.00e+02 pdb=" CA PRO 6 350 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO 6 350 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG 9 344 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.86e+00 pdb=" N PRO 9 345 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO 9 345 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO 9 345 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' U m 105 " 0.022 2.00e-02 2.50e+03 1.20e-02 3.22e+00 pdb=" N1 U m 105 " -0.027 2.00e-02 2.50e+03 pdb=" C2 U m 105 " -0.002 2.00e-02 2.50e+03 pdb=" O2 U m 105 " -0.002 2.00e-02 2.50e+03 pdb=" N3 U m 105 " 0.002 2.00e-02 2.50e+03 pdb=" C4 U m 105 " 0.003 2.00e-02 2.50e+03 pdb=" O4 U m 105 " 0.005 2.00e-02 2.50e+03 pdb=" C5 U m 105 " 0.001 2.00e-02 2.50e+03 pdb=" C6 U m 105 " -0.003 2.00e-02 2.50e+03 ... (remaining 5045 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 5767 2.78 - 3.31: 28569 3.31 - 3.84: 47055 3.84 - 4.37: 54099 4.37 - 4.90: 93593 Nonbonded interactions: 229083 Sorted by model distance: nonbonded pdb=" OG SER11 214 " pdb=" OD1 ASP11 216 " model vdw 2.247 3.040 nonbonded pdb=" OE2 GLU 9 398 " pdb=" NE2 GLN 9 402 " model vdw 2.249 3.120 nonbonded pdb=" O ALA 9 151 " pdb=" NE ARG 9 181 " model vdw 2.256 3.120 nonbonded pdb=" OP1 A m 119 " pdb=" NH2 ARG 6 370 " model vdw 2.264 3.120 nonbonded pdb=" O GLU 9 364 " pdb=" OG SER 9 368 " model vdw 2.265 3.040 ... (remaining 229078 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.470 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 25.450 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 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 : 0.002 0.074 29481 Z= 0.109 Angle : 0.555 10.992 40076 Z= 0.278 Chirality : 0.050 0.346 4616 Planarity : 0.004 0.072 5048 Dihedral : 16.095 166.318 11161 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.03 % Allowed : 8.82 % Favored : 91.15 % 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: 1.46 (0.15), residues: 3527 helix: 1.75 (0.11), residues: 2341 sheet: 0.37 (0.47), residues: 112 loop : -0.69 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG11 765 TYR 0.020 0.001 TYR 5 232 PHE 0.015 0.001 PHE10 161 TRP 0.017 0.001 TRP 9 114 HIS 0.013 0.001 HIS 9 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (29481) covalent geometry : angle 0.55469 / 0.28 (40076) hydrogen bonds : bond 0.13283 / 7.85 ( 1685) hydrogen bonds : angle 4.92103 / 3.20 ( 4989) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 238 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 9 26 MET cc_start: -0.1713 (ttp) cc_final: -0.2609 (mmm) REVERT: 9 106 LEU cc_start: 0.5450 (tt) cc_final: 0.4898 (tp) REVERT: 9 647 TYR cc_start: 0.8414 (m-80) cc_final: 0.8027 (m-80) REVERT: 13 129 ARG cc_start: 0.7875 (mtm180) cc_final: 0.7662 (ptm160) outliers start: 1 outliers final: 1 residues processed: 238 average time/residue: 0.1620 time to fit residues: 63.9381 Evaluate side-chains 215 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 214 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 11 residue 360 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.0070 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 0.6980 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 overall best weight: 1.0802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 283 HIS 14 54 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.144637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.109043 restraints weight = 51620.214| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.11 r_work: 0.3140 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.0770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 29481 Z= 0.146 Angle : 0.770 22.018 40076 Z= 0.337 Chirality : 0.072 1.148 4616 Planarity : 0.004 0.051 5048 Dihedral : 11.104 167.078 4325 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.02 % Allowed : 9.74 % Favored : 89.25 % 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: 1.68 (0.14), residues: 3527 helix: 1.95 (0.11), residues: 2360 sheet: 0.42 (0.49), residues: 107 loop : -0.71 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG11 765 TYR 0.010 0.001 TYR 9 119 PHE 0.011 0.001 PHE 6 308 TRP 0.012 0.001 TRP 9 791 HIS 0.010 0.001 HIS 9 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (29481) covalent geometry : angle 0.76973 / 0.34 (40076) hydrogen bonds : bond 0.03935 / 2.37 ( 1685) hydrogen bonds : angle 3.96748 / 2.58 ( 4989) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 235 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 9 106 LEU cc_start: 0.5532 (tt) cc_final: 0.5182 (tp) REVERT: 9 123 MET cc_start: 0.4898 (mmm) cc_final: 0.4674 (mmm) REVERT: 9 398 GLU cc_start: 0.7624 (tp30) cc_final: 0.7259 (tp30) outliers start: 31 outliers final: 13 residues processed: 253 average time/residue: 0.1526 time to fit residues: 64.0333 Evaluate side-chains 219 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 206 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 91 MET Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 407 MET Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 10 residue 458 THR Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 11 residue 546 MET Chi-restraints excluded: chain 11 residue 694 VAL Chi-restraints excluded: chain 14 residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 236 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 279 optimal weight: 8.9990 chunk 41 optimal weight: 1.9990 chunk 302 optimal weight: 10.0000 chunk 48 optimal weight: 0.9980 chunk 333 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 64 optimal weight: 9.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 6 171 GLN ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 394 HIS ** 11 429 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 14 54 ASN 14 118 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.140927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.105664 restraints weight = 51991.124| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 2.08 r_work: 0.3066 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 29481 Z= 0.226 Angle : 0.695 14.825 40076 Z= 0.329 Chirality : 0.055 0.595 4616 Planarity : 0.004 0.052 5048 Dihedral : 11.845 170.072 4322 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.03 % Allowed : 10.79 % Favored : 87.18 % 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: 1.47 (0.14), residues: 3527 helix: 1.78 (0.11), residues: 2363 sheet: 0.21 (0.46), residues: 113 loop : -0.76 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG 8 363 TYR 0.015 0.002 TYR 5 232 PHE 0.025 0.002 PHE11 257 TRP 0.021 0.002 TRP11 245 HIS 0.018 0.001 HIS 9 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 (29481) covalent geometry : angle 0.69474 / 0.33 (40076) hydrogen bonds : bond 0.04550 / 2.71 ( 1685) hydrogen bonds : angle 4.07249 / 2.64 ( 4989) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 213 time to evaluate : 0.964 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 306 PHE cc_start: 0.8881 (OUTLIER) cc_final: 0.7981 (m-80) REVERT: 8 315 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8794 (mm) REVERT: 9 123 MET cc_start: 0.5119 (mmm) cc_final: 0.4844 (mmm) REVERT: 9 398 GLU cc_start: 0.7677 (tp30) cc_final: 0.7354 (tp30) REVERT: 9 470 GLU cc_start: 0.6219 (OUTLIER) cc_final: 0.5562 (mp0) REVERT: 9 757 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8526 (tt) outliers start: 62 outliers final: 35 residues processed: 262 average time/residue: 0.1410 time to fit residues: 62.3218 Evaluate side-chains 236 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 197 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 6 residue 278 LEU Chi-restraints excluded: chain 6 residue 407 MET Chi-restraints excluded: chain 6 residue 437 VAL Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 7 residue 84 VAL Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 315 LEU Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 354 ASP Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 319 VAL Chi-restraints excluded: chain 9 residue 342 HIS Chi-restraints excluded: chain 9 residue 402 GLN Chi-restraints excluded: chain 9 residue 445 MET Chi-restraints excluded: chain 9 residue 470 GLU Chi-restraints excluded: chain 9 residue 492 LEU Chi-restraints excluded: chain 9 residue 656 VAL Chi-restraints excluded: chain 9 residue 709 ILE Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 9 residue 757 LEU Chi-restraints excluded: chain 9 residue 819 LEU Chi-restraints excluded: chain 10 residue 136 LEU Chi-restraints excluded: chain 10 residue 458 THR Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 11 residue 546 MET Chi-restraints excluded: chain 11 residue 569 THR Chi-restraints excluded: chain 11 residue 630 LEU Chi-restraints excluded: chain 11 residue 737 VAL Chi-restraints excluded: chain 11 residue 919 MET Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 277 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 1 optimal weight: 7.9990 chunk 303 optimal weight: 40.0000 chunk 7 optimal weight: 0.4980 chunk 277 optimal weight: 10.0000 chunk 172 optimal weight: 3.9990 chunk 259 optimal weight: 1.9990 chunk 274 optimal weight: 10.0000 chunk 265 optimal weight: 0.0010 chunk 316 optimal weight: 20.0000 chunk 33 optimal weight: 0.7980 chunk 73 optimal weight: 0.9980 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 14 54 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.143970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.109515 restraints weight = 51637.482| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.19 r_work: 0.3124 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29481 Z= 0.112 Angle : 0.578 12.764 40076 Z= 0.272 Chirality : 0.047 0.416 4616 Planarity : 0.004 0.050 5048 Dihedral : 11.637 177.152 4322 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.38 % Allowed : 11.77 % Favored : 86.85 % 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: 1.71 (0.14), residues: 3527 helix: 1.95 (0.11), residues: 2380 sheet: 0.30 (0.48), residues: 108 loop : -0.70 (0.19), residues: 1039 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG 8 363 TYR 0.015 0.001 TYR 5 232 PHE 0.010 0.001 PHE10 161 TRP 0.009 0.001 TRP 9 114 HIS 0.017 0.001 HIS 9 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (29481) covalent geometry : angle 0.57816 / 0.27 (40076) hydrogen bonds : bond 0.03344 / 2.02 ( 1685) hydrogen bonds : angle 3.76704 / 2.45 ( 4989) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 218 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 306 PHE cc_start: 0.8751 (OUTLIER) cc_final: 0.8315 (m-80) REVERT: 9 26 MET cc_start: 0.1124 (mmm) cc_final: -0.0384 (ttp) REVERT: 9 106 LEU cc_start: 0.5565 (tt) cc_final: 0.5166 (tp) REVERT: 9 398 GLU cc_start: 0.7516 (tp30) cc_final: 0.7259 (tp30) REVERT: 9 470 GLU cc_start: 0.6051 (OUTLIER) cc_final: 0.5536 (mp0) REVERT: 9 510 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7822 (tp30) REVERT: 9 757 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8319 (tt) outliers start: 42 outliers final: 25 residues processed: 250 average time/residue: 0.1447 time to fit residues: 61.5373 Evaluate side-chains 237 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 208 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 91 MET Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 6 residue 278 LEU Chi-restraints excluded: chain 6 residue 407 MET Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 402 GLN Chi-restraints excluded: chain 9 residue 470 GLU Chi-restraints excluded: chain 9 residue 492 LEU Chi-restraints excluded: chain 9 residue 510 GLU Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 9 residue 757 LEU Chi-restraints excluded: chain 9 residue 812 VAL Chi-restraints excluded: chain 9 residue 819 LEU Chi-restraints excluded: chain 10 residue 136 LEU Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 10 residue 536 VAL Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 11 residue 546 MET Chi-restraints excluded: chain 11 residue 919 MET Chi-restraints excluded: chain 14 residue 49 ASP Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 275 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 341 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 chunk 235 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 221 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 242 optimal weight: 0.2980 chunk 346 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 810 GLN 14 252 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.144831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.109418 restraints weight = 51465.206| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 2.19 r_work: 0.3132 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 29481 Z= 0.108 Angle : 0.558 11.235 40076 Z= 0.263 Chirality : 0.046 0.445 4616 Planarity : 0.004 0.050 5048 Dihedral : 11.487 177.900 4322 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.84 % Allowed : 12.03 % Favored : 86.13 % 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: 1.85 (0.14), residues: 3527 helix: 2.07 (0.11), residues: 2378 sheet: 0.29 (0.48), residues: 108 loop : -0.65 (0.19), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG11 765 TYR 0.017 0.001 TYR 5 232 PHE 0.010 0.001 PHE 9 406 TRP 0.007 0.001 TRP10 370 HIS 0.014 0.001 HIS 9 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (29481) covalent geometry : angle 0.55846 / 0.26 (40076) hydrogen bonds : bond 0.03104 / 1.87 ( 1685) hydrogen bonds : angle 3.65011 / 2.37 ( 4989) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 224 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 8 315 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8831 (mm) REVERT: 9 106 LEU cc_start: 0.5507 (tt) cc_final: 0.5129 (tp) REVERT: 9 398 GLU cc_start: 0.7502 (tp30) cc_final: 0.7231 (tp30) REVERT: 9 470 GLU cc_start: 0.5840 (OUTLIER) cc_final: 0.5451 (mp0) REVERT: 9 510 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8115 (tp30) REVERT: 9 757 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8384 (tt) outliers start: 56 outliers final: 39 residues processed: 268 average time/residue: 0.1643 time to fit residues: 74.3500 Evaluate side-chains 254 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 91 MET Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 6 residue 278 LEU Chi-restraints excluded: chain 6 residue 324 VAL Chi-restraints excluded: chain 6 residue 407 MET Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 499 PHE Chi-restraints excluded: chain 7 residue 84 VAL Chi-restraints excluded: chain 8 residue 39 THR Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 295 THR Chi-restraints excluded: chain 8 residue 315 LEU Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 460 THR Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 334 LEU Chi-restraints excluded: chain 9 residue 366 ILE Chi-restraints excluded: chain 9 residue 402 GLN Chi-restraints excluded: chain 9 residue 445 MET Chi-restraints excluded: chain 9 residue 470 GLU Chi-restraints excluded: chain 9 residue 492 LEU Chi-restraints excluded: chain 9 residue 510 GLU Chi-restraints excluded: chain 9 residue 623 THR Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 9 residue 757 LEU Chi-restraints excluded: chain 9 residue 819 LEU Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 10 residue 536 VAL Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 11 residue 546 MET Chi-restraints excluded: chain 11 residue 919 MET Chi-restraints excluded: chain 14 residue 49 ASP Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 243 SER Chi-restraints excluded: chain 14 residue 277 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 80 optimal weight: 0.4980 chunk 325 optimal weight: 8.9990 chunk 115 optimal weight: 4.9990 chunk 334 optimal weight: 4.9990 chunk 295 optimal weight: 8.9990 chunk 323 optimal weight: 0.7980 chunk 281 optimal weight: 10.0000 chunk 252 optimal weight: 3.9990 chunk 133 optimal weight: 0.0980 chunk 103 optimal weight: 7.9990 chunk 277 optimal weight: 8.9990 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 10 485 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.143428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.108024 restraints weight = 51960.692| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 2.05 r_work: 0.3115 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29481 Z= 0.141 Angle : 0.579 11.582 40076 Z= 0.275 Chirality : 0.046 0.469 4616 Planarity : 0.004 0.049 5048 Dihedral : 11.463 176.140 4322 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.93 % Allowed : 12.33 % Favored : 85.74 % 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: 1.83 (0.14), residues: 3527 helix: 2.06 (0.11), residues: 2373 sheet: 0.30 (0.48), residues: 108 loop : -0.67 (0.19), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 8 363 TYR 0.017 0.001 TYR 5 232 PHE 0.015 0.001 PHE 9 649 TRP 0.009 0.001 TRP11 245 HIS 0.012 0.001 HIS 9 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (29481) covalent geometry : angle 0.57882 / 0.28 (40076) hydrogen bonds : bond 0.03413 / 2.05 ( 1685) hydrogen bonds : angle 3.70896 / 2.40 ( 4989) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 216 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 6 407 MET cc_start: 0.8818 (OUTLIER) cc_final: 0.8605 (ttp) REVERT: 7 108 GLU cc_start: 0.7916 (mp0) cc_final: 0.7698 (mp0) REVERT: 8 315 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8844 (mm) REVERT: 9 26 MET cc_start: 0.0766 (mmm) cc_final: -0.1032 (ppp) REVERT: 9 106 LEU cc_start: 0.5627 (tt) cc_final: 0.5243 (tp) REVERT: 9 142 GLU cc_start: 0.7019 (tp30) cc_final: 0.6747 (tp30) REVERT: 9 398 GLU cc_start: 0.7452 (tp30) cc_final: 0.7168 (tp30) REVERT: 9 470 GLU cc_start: 0.6052 (OUTLIER) cc_final: 0.5616 (mp0) REVERT: 9 510 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8040 (tp30) REVERT: 9 757 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8411 (tt) outliers start: 59 outliers final: 41 residues processed: 263 average time/residue: 0.1697 time to fit residues: 76.1777 Evaluate side-chains 257 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 6 residue 278 LEU Chi-restraints excluded: chain 6 residue 324 VAL Chi-restraints excluded: chain 6 residue 407 MET Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 499 PHE Chi-restraints excluded: chain 7 residue 84 VAL Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 243 VAL Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 295 THR Chi-restraints excluded: chain 8 residue 315 LEU Chi-restraints excluded: chain 8 residue 317 ASP Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 354 ASP Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 395 VAL Chi-restraints excluded: chain 8 residue 460 THR Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 366 ILE Chi-restraints excluded: chain 9 residue 402 GLN Chi-restraints excluded: chain 9 residue 445 MET Chi-restraints excluded: chain 9 residue 470 GLU Chi-restraints excluded: chain 9 residue 492 LEU Chi-restraints excluded: chain 9 residue 510 GLU Chi-restraints excluded: chain 9 residue 623 THR Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 9 residue 757 LEU Chi-restraints excluded: chain 9 residue 812 VAL Chi-restraints excluded: chain 9 residue 819 LEU Chi-restraints excluded: chain 10 residue 458 THR Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 10 residue 536 VAL Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 11 residue 546 MET Chi-restraints excluded: chain 11 residue 630 LEU Chi-restraints excluded: chain 14 residue 49 ASP Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 243 SER Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 277 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 131 optimal weight: 6.9990 chunk 285 optimal weight: 4.9990 chunk 178 optimal weight: 5.9990 chunk 108 optimal weight: 5.9990 chunk 229 optimal weight: 0.8980 chunk 189 optimal weight: 0.9990 chunk 16 optimal weight: 6.9990 chunk 76 optimal weight: 0.0980 chunk 203 optimal weight: 0.2980 chunk 100 optimal weight: 0.9980 chunk 284 optimal weight: 5.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 11 699 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.145824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.110770 restraints weight = 51487.166| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.06 r_work: 0.3161 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 29481 Z= 0.098 Angle : 0.542 9.824 40076 Z= 0.256 Chirality : 0.045 0.433 4616 Planarity : 0.004 0.049 5048 Dihedral : 11.492 176.438 4322 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.41 % Allowed : 13.15 % Favored : 85.44 % 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: 1.95 (0.14), residues: 3527 helix: 2.15 (0.11), residues: 2372 sheet: 0.43 (0.49), residues: 107 loop : -0.63 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG14 232 TYR 0.018 0.001 TYR 5 232 PHE 0.009 0.001 PHE 9 297 TRP 0.008 0.001 TRP10 370 HIS 0.012 0.001 HIS 9 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (29481) covalent geometry : angle 0.54188 / 0.26 (40076) hydrogen bonds : bond 0.02858 / 1.72 ( 1685) hydrogen bonds : angle 3.57305 / 2.32 ( 4989) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 228 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 6 407 MET cc_start: 0.8564 (OUTLIER) cc_final: 0.8317 (ttp) REVERT: 8 315 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8823 (mm) REVERT: 9 26 MET cc_start: 0.1198 (mmm) cc_final: -0.0433 (ppp) REVERT: 9 106 LEU cc_start: 0.5521 (tt) cc_final: 0.5220 (tp) REVERT: 9 142 GLU cc_start: 0.6918 (tp30) cc_final: 0.6649 (tp30) REVERT: 9 398 GLU cc_start: 0.7369 (tp30) cc_final: 0.7118 (tp30) REVERT: 9 470 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5468 (mp0) REVERT: 10 161 PHE cc_start: 0.6957 (m-80) cc_final: 0.6741 (m-10) REVERT: 11 226 MET cc_start: 0.3859 (tpp) cc_final: 0.3635 (tpp) REVERT: 13 129 ARG cc_start: 0.7950 (mtm180) cc_final: 0.7709 (ptm160) outliers start: 43 outliers final: 30 residues processed: 262 average time/residue: 0.1557 time to fit residues: 69.1152 Evaluate side-chains 248 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 215 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 91 MET Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 6 residue 278 LEU Chi-restraints excluded: chain 6 residue 319 LEU Chi-restraints excluded: chain 6 residue 407 MET Chi-restraints excluded: chain 6 residue 499 PHE Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 291 VAL Chi-restraints excluded: chain 8 residue 295 THR Chi-restraints excluded: chain 8 residue 315 LEU Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 395 VAL Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 366 ILE Chi-restraints excluded: chain 9 residue 402 GLN Chi-restraints excluded: chain 9 residue 470 GLU Chi-restraints excluded: chain 9 residue 492 LEU Chi-restraints excluded: chain 9 residue 623 THR Chi-restraints excluded: chain 9 residue 819 LEU Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 10 residue 536 VAL Chi-restraints excluded: chain 11 residue 335 THR Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 11 residue 546 MET Chi-restraints excluded: chain 14 residue 49 ASP Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 275 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 165 optimal weight: 6.9990 chunk 342 optimal weight: 5.9990 chunk 4 optimal weight: 0.3980 chunk 187 optimal weight: 9.9990 chunk 47 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 296 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 31 optimal weight: 5.9990 chunk 251 optimal weight: 1.9990 chunk 214 optimal weight: 0.0980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 117 ASN 7 124 ASN ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.143132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.107652 restraints weight = 51914.908| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.10 r_work: 0.3107 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2991 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 29481 Z= 0.163 Angle : 0.599 9.521 40076 Z= 0.285 Chirality : 0.047 0.480 4616 Planarity : 0.004 0.049 5048 Dihedral : 11.473 175.044 4322 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.90 % Allowed : 13.28 % Favored : 84.82 % 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: 1.86 (0.14), residues: 3527 helix: 2.08 (0.11), residues: 2368 sheet: 0.31 (0.48), residues: 108 loop : -0.66 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG11 765 TYR 0.017 0.001 TYR 5 232 PHE 0.018 0.001 PHE 9 649 TRP 0.012 0.001 TRP 9 114 HIS 0.011 0.001 HIS 9 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (29481) covalent geometry : angle 0.59863 / 0.28 (40076) hydrogen bonds : bond 0.03520 / 2.11 ( 1685) hydrogen bonds : angle 3.71901 / 2.41 ( 4989) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 217 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 6 407 MET cc_start: 0.8813 (OUTLIER) cc_final: 0.8596 (ttp) REVERT: 8 306 PHE cc_start: 0.8730 (OUTLIER) cc_final: 0.8239 (m-80) REVERT: 8 315 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8833 (mm) REVERT: 9 142 GLU cc_start: 0.7108 (tp30) cc_final: 0.6794 (tp30) REVERT: 9 398 GLU cc_start: 0.7534 (tp30) cc_final: 0.7282 (tp30) REVERT: 9 470 GLU cc_start: 0.6072 (OUTLIER) cc_final: 0.5633 (mp0) REVERT: 10 161 PHE cc_start: 0.7123 (m-80) cc_final: 0.6842 (m-10) REVERT: 10 381 LEU cc_start: 0.8502 (mp) cc_final: 0.8302 (mp) outliers start: 58 outliers final: 46 residues processed: 264 average time/residue: 0.1509 time to fit residues: 68.5453 Evaluate side-chains 260 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 210 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 6 residue 278 LEU Chi-restraints excluded: chain 6 residue 319 LEU Chi-restraints excluded: chain 6 residue 324 VAL Chi-restraints excluded: chain 6 residue 407 MET Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 499 PHE Chi-restraints excluded: chain 7 residue 84 VAL Chi-restraints excluded: chain 7 residue 117 ASN Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 243 VAL Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 291 VAL Chi-restraints excluded: chain 8 residue 295 THR Chi-restraints excluded: chain 8 residue 306 PHE Chi-restraints excluded: chain 8 residue 315 LEU Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 354 ASP Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 395 VAL Chi-restraints excluded: chain 8 residue 460 THR Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 9 residue 46 ILE Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 334 LEU Chi-restraints excluded: chain 9 residue 342 HIS Chi-restraints excluded: chain 9 residue 366 ILE Chi-restraints excluded: chain 9 residue 402 GLN Chi-restraints excluded: chain 9 residue 470 GLU Chi-restraints excluded: chain 9 residue 492 LEU Chi-restraints excluded: chain 9 residue 623 THR Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 9 residue 812 VAL Chi-restraints excluded: chain 9 residue 819 LEU Chi-restraints excluded: chain 10 residue 140 LEU Chi-restraints excluded: chain 10 residue 321 LEU Chi-restraints excluded: chain 10 residue 400 MET Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 10 residue 536 VAL Chi-restraints excluded: chain 11 residue 335 THR Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 11 residue 546 MET Chi-restraints excluded: chain 14 residue 49 ASP Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 275 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 222 optimal weight: 0.0010 chunk 76 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 198 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 528 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.143880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.108418 restraints weight = 51751.452| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 2.07 r_work: 0.3119 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 29481 Z= 0.131 Angle : 0.583 10.144 40076 Z= 0.275 Chirality : 0.046 0.457 4616 Planarity : 0.004 0.049 5048 Dihedral : 11.526 175.150 4322 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.74 % Allowed : 13.57 % Favored : 84.69 % 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: 1.86 (0.14), residues: 3527 helix: 2.09 (0.11), residues: 2368 sheet: 0.34 (0.48), residues: 108 loop : -0.66 (0.19), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG11 765 TYR 0.018 0.001 TYR 5 232 PHE 0.013 0.001 PHE 9 649 TRP 0.009 0.001 TRP 9 114 HIS 0.012 0.001 HIS 9 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (29481) covalent geometry : angle 0.58252 / 0.28 (40076) hydrogen bonds : bond 0.03293 / 1.98 ( 1685) hydrogen bonds : angle 3.67772 / 2.38 ( 4989) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 6 407 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8335 (ttp) REVERT: 8 315 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8838 (mm) REVERT: 9 26 MET cc_start: 0.0259 (mmm) cc_final: -0.1637 (ppp) REVERT: 9 106 LEU cc_start: 0.5515 (tt) cc_final: 0.5127 (tp) REVERT: 9 142 GLU cc_start: 0.7131 (tp30) cc_final: 0.6812 (tp30) REVERT: 9 398 GLU cc_start: 0.7243 (tp30) cc_final: 0.7027 (tp30) REVERT: 9 470 GLU cc_start: 0.5932 (OUTLIER) cc_final: 0.5595 (mp0) REVERT: 10 161 PHE cc_start: 0.6976 (m-80) cc_final: 0.6753 (m-10) REVERT: 10 381 LEU cc_start: 0.8460 (mp) cc_final: 0.8231 (mp) REVERT: 13 129 ARG cc_start: 0.7943 (mtm180) cc_final: 0.7723 (ptm160) outliers start: 53 outliers final: 47 residues processed: 261 average time/residue: 0.1519 time to fit residues: 67.3257 Evaluate side-chains 265 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 215 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 6 residue 278 LEU Chi-restraints excluded: chain 6 residue 319 LEU Chi-restraints excluded: chain 6 residue 324 VAL Chi-restraints excluded: chain 6 residue 407 MET Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 499 PHE Chi-restraints excluded: chain 7 residue 84 VAL Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 291 VAL Chi-restraints excluded: chain 8 residue 295 THR Chi-restraints excluded: chain 8 residue 315 LEU Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 354 ASP Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 395 VAL Chi-restraints excluded: chain 8 residue 460 THR Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 9 residue 46 ILE Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 334 LEU Chi-restraints excluded: chain 9 residue 342 HIS Chi-restraints excluded: chain 9 residue 366 ILE Chi-restraints excluded: chain 9 residue 402 GLN Chi-restraints excluded: chain 9 residue 445 MET Chi-restraints excluded: chain 9 residue 470 GLU Chi-restraints excluded: chain 9 residue 492 LEU Chi-restraints excluded: chain 9 residue 623 THR Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 9 residue 812 VAL Chi-restraints excluded: chain 9 residue 819 LEU Chi-restraints excluded: chain 10 residue 140 LEU Chi-restraints excluded: chain 10 residue 321 LEU Chi-restraints excluded: chain 10 residue 400 MET Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 10 residue 536 VAL Chi-restraints excluded: chain 11 residue 335 THR Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 11 residue 546 MET Chi-restraints excluded: chain 14 residue 49 ASP Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 243 SER Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 277 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 29 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 297 optimal weight: 0.8980 chunk 210 optimal weight: 1.9990 chunk 257 optimal weight: 9.9990 chunk 339 optimal weight: 4.9990 chunk 72 optimal weight: 0.6980 chunk 338 optimal weight: 1.9990 chunk 303 optimal weight: 5.9990 chunk 225 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.144604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.108919 restraints weight = 51367.854| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.05 r_work: 0.3133 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 29481 Z= 0.114 Angle : 0.568 10.679 40076 Z= 0.268 Chirality : 0.045 0.440 4616 Planarity : 0.004 0.049 5048 Dihedral : 11.537 175.213 4322 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.61 % Allowed : 13.74 % Favored : 84.66 % 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: 1.92 (0.15), residues: 3527 helix: 2.12 (0.11), residues: 2374 sheet: 0.41 (0.49), residues: 108 loop : -0.64 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG14 232 TYR 0.018 0.001 TYR 5 232 PHE 0.011 0.001 PHE 9 649 TRP 0.008 0.001 TRP 9 114 HIS 0.012 0.001 HIS 9 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (29481) covalent geometry : angle 0.56818 / 0.27 (40076) hydrogen bonds : bond 0.03088 / 1.86 ( 1685) hydrogen bonds : angle 3.63073 / 2.35 ( 4989) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7054 Ramachandran restraints generated. 3527 Oldfield, 0 Emsley, 3527 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 225 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 6 293 MET cc_start: 0.8725 (mtm) cc_final: 0.8501 (mtp) REVERT: 6 407 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8562 (ttp) REVERT: 8 315 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8816 (mm) REVERT: 9 26 MET cc_start: 0.0010 (mmm) cc_final: -0.1816 (ppp) REVERT: 9 106 LEU cc_start: 0.5529 (tt) cc_final: 0.5119 (tp) REVERT: 9 398 GLU cc_start: 0.7403 (tp30) cc_final: 0.7161 (tp30) REVERT: 9 470 GLU cc_start: 0.5945 (OUTLIER) cc_final: 0.5615 (mp0) REVERT: 10 161 PHE cc_start: 0.7129 (m-80) cc_final: 0.6822 (m-10) REVERT: 13 129 ARG cc_start: 0.8028 (mtm180) cc_final: 0.7788 (ptm160) outliers start: 49 outliers final: 45 residues processed: 264 average time/residue: 0.1511 time to fit residues: 67.9991 Evaluate side-chains 263 residues out of total 3050 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 215 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 85 GLU Chi-restraints excluded: chain 5 residue 195 THR Chi-restraints excluded: chain 6 residue 185 VAL Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 6 residue 278 LEU Chi-restraints excluded: chain 6 residue 319 LEU Chi-restraints excluded: chain 6 residue 324 VAL Chi-restraints excluded: chain 6 residue 407 MET Chi-restraints excluded: chain 6 residue 440 LEU Chi-restraints excluded: chain 6 residue 499 PHE Chi-restraints excluded: chain 8 residue 95 VAL Chi-restraints excluded: chain 8 residue 243 VAL Chi-restraints excluded: chain 8 residue 252 CYS Chi-restraints excluded: chain 8 residue 291 VAL Chi-restraints excluded: chain 8 residue 295 THR Chi-restraints excluded: chain 8 residue 315 LEU Chi-restraints excluded: chain 8 residue 319 MET Chi-restraints excluded: chain 8 residue 349 VAL Chi-restraints excluded: chain 8 residue 354 ASP Chi-restraints excluded: chain 8 residue 394 LEU Chi-restraints excluded: chain 8 residue 395 VAL Chi-restraints excluded: chain 8 residue 460 THR Chi-restraints excluded: chain 8 residue 468 VAL Chi-restraints excluded: chain 9 residue 46 ILE Chi-restraints excluded: chain 9 residue 102 VAL Chi-restraints excluded: chain 9 residue 183 VAL Chi-restraints excluded: chain 9 residue 366 ILE Chi-restraints excluded: chain 9 residue 402 GLN Chi-restraints excluded: chain 9 residue 445 MET Chi-restraints excluded: chain 9 residue 470 GLU Chi-restraints excluded: chain 9 residue 492 LEU Chi-restraints excluded: chain 9 residue 623 THR Chi-restraints excluded: chain 9 residue 732 LEU Chi-restraints excluded: chain 9 residue 812 VAL Chi-restraints excluded: chain 9 residue 819 LEU Chi-restraints excluded: chain 10 residue 140 LEU Chi-restraints excluded: chain 10 residue 321 LEU Chi-restraints excluded: chain 10 residue 400 MET Chi-restraints excluded: chain 10 residue 483 MET Chi-restraints excluded: chain 10 residue 536 VAL Chi-restraints excluded: chain 11 residue 335 THR Chi-restraints excluded: chain 11 residue 351 LYS Chi-restraints excluded: chain 11 residue 546 MET Chi-restraints excluded: chain 14 residue 49 ASP Chi-restraints excluded: chain 14 residue 242 VAL Chi-restraints excluded: chain 14 residue 243 SER Chi-restraints excluded: chain 14 residue 275 VAL Chi-restraints excluded: chain 14 residue 277 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 355 random chunks: chunk 303 optimal weight: 30.0000 chunk 137 optimal weight: 2.9990 chunk 57 optimal weight: 0.0970 chunk 261 optimal weight: 0.6980 chunk 252 optimal weight: 1.9990 chunk 313 optimal weight: 3.9990 chunk 153 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 270 optimal weight: 6.9990 chunk 274 optimal weight: 7.9990 chunk 205 optimal weight: 3.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 8 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.143747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.108219 restraints weight = 52139.075| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.05 r_work: 0.3114 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29481 Z= 0.137 Angle : 0.587 10.792 40076 Z= 0.278 Chirality : 0.046 0.448 4616 Planarity : 0.004 0.049 5048 Dihedral : 11.564 174.831 4322 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.67 % Allowed : 13.61 % Favored : 84.72 % 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: 1.88 (0.14), residues: 3527 helix: 2.11 (0.11), residues: 2367 sheet: 0.34 (0.49), residues: 108 loop : -0.68 (0.19), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG14 232 TYR 0.018 0.001 TYR 5 232 PHE 0.014 0.001 PHE 9 649 TRP 0.015 0.001 TRP10 370 HIS 0.012 0.001 HIS 9 342 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (29481) covalent geometry : angle 0.58744 / 0.28 (40076) hydrogen bonds : bond 0.03289 / 1.97 ( 1685) hydrogen bonds : angle 3.68288 / 2.38 ( 4989) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6416.28 seconds wall clock time: 110 minutes 29.56 seconds (6629.56 seconds total)