Starting phenix.real_space_refine on Fri Mar 6 09:57:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6vbu_21144/03_2026/6vbu_21144.cif Found real_map, /net/cci-nas-00/data/ceres_data/6vbu_21144/03_2026/6vbu_21144.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6vbu_21144/03_2026/6vbu_21144.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6vbu_21144/03_2026/6vbu_21144.map" model { file = "/net/cci-nas-00/data/ceres_data/6vbu_21144/03_2026/6vbu_21144.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6vbu_21144/03_2026/6vbu_21144.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 Ca 2 9.91 5 S 149 5.16 5 C 19254 2.51 5 N 5162 2.21 5 O 5642 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 262 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 30209 Number of models: 1 Model: "" Number of chains: 9 Chain: "0" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 421 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "1" Number of atoms: 3767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3767 Classifications: {'peptide': 486} Link IDs: {'PTRANS': 29, 'TRANS': 456} Chain breaks: 3 Chain: "2" Number of atoms: 5145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 659, 5145 Classifications: {'peptide': 659} Link IDs: {'PTRANS': 22, 'TRANS': 636} Chain breaks: 4 Chain: "4" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3113 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 9, 'TRANS': 376} Chain breaks: 1 Chain: "5" Number of atoms: 2411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2411 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 9, 'TRANS': 290} Chain breaks: 2 Chain: "7" Number of atoms: 5519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 698, 5519 Classifications: {'peptide': 698} Link IDs: {'PTRANS': 25, 'TRANS': 672} Chain breaks: 2 Chain: "8" Number of atoms: 3797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3797 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 20, 'TRANS': 454} Chain breaks: 2 Chain: "9" Number of atoms: 6034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 764, 6034 Classifications: {'peptide': 764} Link IDs: {'PTRANS': 31, 'TRANS': 732} Chain breaks: 5 Chain: "2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.86, per 1000 atoms: 0.23 Number of scatterers: 30209 At special positions: 0 Unit cell: (152.64, 184.44, 172.78, 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) Ca 2 19.99 S 149 16.00 O 5642 8.00 N 5162 7.00 C 19254 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: 2.58 Conformation dependent library (CDL) restraints added in 1.4 seconds 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7198 Finding SS restraints... Secondary structure from input PDB file: 85 helices and 48 sheets defined 35.7% alpha, 22.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain '0' and resid 38 through 57 Processing helix chain '1' and resid 431 through 444 removed outlier: 3.740A pdb=" N VAL 1 435 " --> pdb=" O THR 1 431 " (cutoff:3.500A) Processing helix chain '1' and resid 444 through 474 removed outlier: 3.714A pdb=" N MET 1 448 " --> pdb=" O ALA 1 444 " (cutoff:3.500A) Processing helix chain '2' and resid 339 through 358 removed outlier: 3.685A pdb=" N ASN 2 358 " --> pdb=" O ASN 2 354 " (cutoff:3.500A) Processing helix chain '2' and resid 490 through 494 removed outlier: 3.970A pdb=" N GLU 2 494 " --> pdb=" O PRO 2 491 " (cutoff:3.500A) Processing helix chain '2' and resid 506 through 517 Processing helix chain '2' and resid 560 through 575 Processing helix chain '2' and resid 586 through 634 removed outlier: 3.547A pdb=" N GLU 2 592 " --> pdb=" O VAL 2 588 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ASP 2 601 " --> pdb=" O LEU 2 597 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU 2 602 " --> pdb=" O VAL 2 598 " (cutoff:3.500A) Processing helix chain '2' and resid 636 through 685 Processing helix chain '2' and resid 689 through 704 removed outlier: 3.525A pdb=" N GLN 2 693 " --> pdb=" O LYS 2 689 " (cutoff:3.500A) Processing helix chain '2' and resid 706 through 716 Processing helix chain '4' and resid 36 through 45 Processing helix chain '4' and resid 49 through 63 removed outlier: 3.745A pdb=" N ALA 4 53 " --> pdb=" O GLU 4 49 " (cutoff:3.500A) Processing helix chain '4' and resid 68 through 80 removed outlier: 3.519A pdb=" N VAL 4 72 " --> pdb=" O TYR 4 68 " (cutoff:3.500A) Processing helix chain '4' and resid 82 through 97 removed outlier: 3.628A pdb=" N SER 4 86 " --> pdb=" O ASN 4 82 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG 4 88 " --> pdb=" O GLN 4 84 " (cutoff:3.500A) Processing helix chain '4' and resid 100 through 113 removed outlier: 3.870A pdb=" N LEU 4 104 " --> pdb=" O CYS 4 100 " (cutoff:3.500A) Processing helix chain '4' and resid 117 through 131 removed outlier: 3.844A pdb=" N GLU 4 126 " --> pdb=" O GLU 4 122 " (cutoff:3.500A) Processing helix chain '4' and resid 134 through 148 removed outlier: 4.097A pdb=" N CYS 4 138 " --> pdb=" O ASP 4 134 " (cutoff:3.500A) Processing helix chain '4' and resid 150 through 165 Processing helix chain '4' and resid 167 through 182 removed outlier: 3.568A pdb=" N TYR 4 171 " --> pdb=" O HIS 4 167 " (cutoff:3.500A) Processing helix chain '4' and resid 183 through 197 removed outlier: 4.174A pdb=" N ALA 4 187 " --> pdb=" O ASP 4 183 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N GLU 4 189 " --> pdb=" O ASP 4 185 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N PHE 4 197 " --> pdb=" O LYS 4 193 " (cutoff:3.500A) Processing helix chain '4' and resid 201 through 215 removed outlier: 3.506A pdb=" N LEU 4 205 " --> pdb=" O ASN 4 201 " (cutoff:3.500A) Processing helix chain '4' and resid 218 through 232 Processing helix chain '4' and resid 235 through 249 Processing helix chain '4' and resid 251 through 263 removed outlier: 3.804A pdb=" N VAL 4 262 " --> pdb=" O LYS 4 258 " (cutoff:3.500A) Processing helix chain '4' and resid 269 through 283 Processing helix chain '4' and resid 285 through 299 removed outlier: 3.559A pdb=" N LEU 4 299 " --> pdb=" O ARG 4 295 " (cutoff:3.500A) Processing helix chain '4' and resid 303 through 317 removed outlier: 3.805A pdb=" N LEU 4 307 " --> pdb=" O ASP 4 303 " (cutoff:3.500A) Processing helix chain '4' and resid 322 through 334 Processing helix chain '4' and resid 337 through 350 removed outlier: 3.927A pdb=" N TYR 4 341 " --> pdb=" O MET 4 337 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN 4 350 " --> pdb=" O VAL 4 346 " (cutoff:3.500A) Processing helix chain '4' and resid 354 through 368 Processing helix chain '4' and resid 372 through 385 Processing helix chain '4' and resid 390 through 400 Processing helix chain '4' and resid 412 through 423 removed outlier: 3.809A pdb=" N GLU 4 416 " --> pdb=" O GLU 4 412 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N MET 4 417 " --> pdb=" O PHE 4 413 " (cutoff:3.500A) Processing helix chain '5' and resid 119 through 134 removed outlier: 3.522A pdb=" N SER 5 123 " --> pdb=" O ARG 5 119 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE 5 125 " --> pdb=" O TYR 5 121 " (cutoff:3.500A) Processing helix chain '5' and resid 226 through 229 removed outlier: 3.723A pdb=" N GLY 5 229 " --> pdb=" O GLN 5 226 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 226 through 229' Processing helix chain '5' and resid 239 through 260 removed outlier: 4.107A pdb=" N ASN 5 260 " --> pdb=" O VAL 5 256 " (cutoff:3.500A) Processing helix chain '5' and resid 298 through 303 removed outlier: 3.693A pdb=" N PHE 5 303 " --> pdb=" O VAL 5 300 " (cutoff:3.500A) Processing helix chain '5' and resid 332 through 338 removed outlier: 3.820A pdb=" N GLU 5 338 " --> pdb=" O GLN 5 334 " (cutoff:3.500A) Processing helix chain '7' and resid 337 through 366 Processing helix chain '7' and resid 367 through 369 No H-bonds generated for 'chain '7' and resid 367 through 369' Processing helix chain '7' and resid 516 through 528 Processing helix chain '7' and resid 570 through 588 Processing helix chain '7' and resid 598 through 637 removed outlier: 4.506A pdb=" N VAL 7 602 " --> pdb=" O ASN 7 598 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS 7 603 " --> pdb=" O GLU 7 599 " (cutoff:3.500A) Proline residue: 7 611 - end of helix removed outlier: 3.983A pdb=" N LEU 7 625 " --> pdb=" O LYS 7 621 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N ASP 7 627 " --> pdb=" O VAL 7 623 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N ALA 7 628 " --> pdb=" O GLN 7 624 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS 7 635 " --> pdb=" O GLU 7 631 " (cutoff:3.500A) Processing helix chain '7' and resid 643 through 661 removed outlier: 3.682A pdb=" N ARG 7 647 " --> pdb=" O ILE 7 643 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ILE 7 649 " --> pdb=" O GLU 7 645 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ASP 7 654 " --> pdb=" O LEU 7 650 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N HIS 7 655 " --> pdb=" O GLU 7 651 " (cutoff:3.500A) Processing helix chain '7' and resid 662 through 686 Processing helix chain '7' and resid 693 through 695 No H-bonds generated for 'chain '7' and resid 693 through 695' Processing helix chain '7' and resid 696 through 703 Processing helix chain '7' and resid 704 through 715 Processing helix chain '8' and resid 2 through 13 Processing helix chain '8' and resid 17 through 30 Processing helix chain '8' and resid 33 through 48 removed outlier: 3.652A pdb=" N TRP 8 37 " --> pdb=" O ASP 8 33 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL 8 48 " --> pdb=" O LEU 8 44 " (cutoff:3.500A) Processing helix chain '8' and resid 59 through 65 Processing helix chain '8' and resid 121 through 126 Processing helix chain '8' and resid 167 through 172 removed outlier: 3.510A pdb=" N TYR 8 171 " --> pdb=" O ASN 8 167 " (cutoff:3.500A) Processing helix chain '8' and resid 174 through 188 removed outlier: 4.163A pdb=" N ALA 8 180 " --> pdb=" O LYS 8 176 " (cutoff:3.500A) Processing helix chain '8' and resid 191 through 206 Processing helix chain '8' and resid 210 through 225 removed outlier: 3.763A pdb=" N LYS 8 214 " --> pdb=" O ASP 8 210 " (cutoff:3.500A) Processing helix chain '8' and resid 226 through 239 removed outlier: 3.790A pdb=" N GLN 8 233 " --> pdb=" O GLU 8 229 " (cutoff:3.500A) Processing helix chain '8' and resid 243 through 257 Processing helix chain '8' and resid 259 through 274 Processing helix chain '8' and resid 277 through 291 Processing helix chain '8' and resid 293 through 308 removed outlier: 3.750A pdb=" N GLU 8 299 " --> pdb=" O SER 8 295 " (cutoff:3.500A) Processing helix chain '8' and resid 311 through 325 Processing helix chain '8' and resid 327 through 341 Processing helix chain '8' and resid 346 through 360 Processing helix chain '8' and resid 364 through 376 removed outlier: 3.805A pdb=" N SER 8 368 " --> pdb=" O MET 8 364 " (cutoff:3.500A) Processing helix chain '8' and resid 379 through 397 Processing helix chain '8' and resid 398 through 413 Processing helix chain '8' and resid 416 through 431 Processing helix chain '8' and resid 432 through 447 Processing helix chain '8' and resid 450 through 463 removed outlier: 4.167A pdb=" N HIS 8 454 " --> pdb=" O MET 8 450 " (cutoff:3.500A) Processing helix chain '8' and resid 466 through 481 removed outlier: 3.668A pdb=" N LYS 8 476 " --> pdb=" O ALA 8 472 " (cutoff:3.500A) Processing helix chain '8' and resid 484 through 499 Processing helix chain '9' and resid 207 through 213 Processing helix chain '9' and resid 377 through 397 removed outlier: 4.042A pdb=" N ASN 9 396 " --> pdb=" O ILE 9 392 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS 9 397 " --> pdb=" O LYS 9 393 " (cutoff:3.500A) Processing helix chain '9' and resid 530 through 533 Processing helix chain '9' and resid 558 through 563 removed outlier: 3.806A pdb=" N LEU 9 562 " --> pdb=" O SER 9 558 " (cutoff:3.500A) Processing helix chain '9' and resid 608 through 628 removed outlier: 4.234A pdb=" N ILE 9 612 " --> pdb=" O ASP 9 608 " (cutoff:3.500A) Processing helix chain '9' and resid 644 through 686 removed outlier: 4.230A pdb=" N LEU 9 648 " --> pdb=" O GLU 9 644 " (cutoff:3.500A) Processing helix chain '9' and resid 692 through 742 removed outlier: 3.757A pdb=" N GLY 9 701 " --> pdb=" O THR 9 697 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER 9 729 " --> pdb=" O THR 9 725 " (cutoff:3.500A) Processing helix chain '9' and resid 745 through 757 removed outlier: 3.579A pdb=" N LEU 9 752 " --> pdb=" O GLN 9 748 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU 9 757 " --> pdb=" O GLU 9 753 " (cutoff:3.500A) Processing helix chain '9' and resid 767 through 784 removed outlier: 3.868A pdb=" N THR 9 771 " --> pdb=" O GLY 9 767 " (cutoff:3.500A) Processing helix chain '9' and resid 787 through 794 Processing helix chain '9' and resid 805 through 821 Processing sheet with id=AA1, first strand: chain '0' and resid 36 through 37 removed outlier: 6.206A pdb=" N LEU 0 36 " --> pdb=" O LEU 8 109 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain '1' and resid 3 through 9 removed outlier: 5.407A pdb=" N ASP 1 5 " --> pdb=" O ILE 1 401 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE 1 401 " --> pdb=" O ASP 1 5 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N GLY 1 396 " --> pdb=" O THR 1 392 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N THR 1 392 " --> pdb=" O GLY 1 396 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASN 1 386 " --> pdb=" O LEU 1 402 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ASP 1 385 " --> pdb=" O TYR 1 381 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N TYR 1 381 " --> pdb=" O ASP 1 385 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '1' and resid 21 through 24 removed outlier: 4.000A pdb=" N ASP 1 38 " --> pdb=" O ARG 1 47 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N SER 1 58 " --> pdb=" O VAL 1 50 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LYS 1 52 " --> pdb=" O LEU 1 56 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU 1 56 " --> pdb=" O LYS 1 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '1' and resid 68 through 71 removed outlier: 4.335A pdb=" N ALA 1 68 " --> pdb=" O ALA 1 87 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N LYS 1 96 " --> pdb=" O PRO 1 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '1' and resid 200 through 207 removed outlier: 3.819A pdb=" N THR 1 202 " --> pdb=" O GLY 1 222 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU 1 227 " --> pdb=" O THR 1 223 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 248 through 256 removed outlier: 4.343A pdb=" N SER 1 271 " --> pdb=" O CYS 1 267 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '1' and resid 292 through 297 removed outlier: 3.957A pdb=" N GLY 1 294 " --> pdb=" O GLY 1 305 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER 1 310 " --> pdb=" O SER 1 306 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR 1 315 " --> pdb=" O ARG 1 320 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ARG 1 320 " --> pdb=" O THR 1 315 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '1' and resid 330 through 335 removed outlier: 3.961A pdb=" N ALA 1 332 " --> pdb=" O ALA 1 349 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET 1 347 " --> pdb=" O ASN 1 334 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '1' and resid 354 through 355 Processing sheet with id=AB1, first strand: chain '1' and resid 486 through 493 Processing sheet with id=AB2, first strand: chain '1' and resid 535 through 536 Processing sheet with id=AB3, first strand: chain '2' and resid 6 through 9 removed outlier: 4.369A pdb=" N GLU 2 313 " --> pdb=" O SER 2 309 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '2' and resid 14 through 23 removed outlier: 6.973A pdb=" N MET 2 18 " --> pdb=" O ALA 2 34 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '2' and resid 75 through 81 Processing sheet with id=AB6, first strand: chain '2' and resid 122 through 123 Processing sheet with id=AB7, first strand: chain '2' and resid 144 through 147 removed outlier: 6.776A pdb=" N LEU 2 144 " --> pdb=" O TRP 2 156 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TRP 2 156 " --> pdb=" O LEU 2 144 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N GLY 2 146 " --> pdb=" O LEU 2 154 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '2' and resid 163 through 167 removed outlier: 3.819A pdb=" N SER 2 165 " --> pdb=" O GLY 2 182 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP 2 187 " --> pdb=" O SER 2 183 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '2' and resid 208 through 213 removed outlier: 6.958A pdb=" N ARG 2 216 " --> pdb=" O MET 2 212 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL 2 226 " --> pdb=" O ARG 2 237 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG 2 237 " --> pdb=" O VAL 2 226 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N VAL 2 228 " --> pdb=" O TYR 2 235 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '2' and resid 246 through 250 removed outlier: 3.599A pdb=" N SER 2 246 " --> pdb=" O GLY 2 263 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG 2 272 " --> pdb=" O LEU 2 260 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N VAL 2 269 " --> pdb=" O LYS 2 282 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS 2 282 " --> pdb=" O VAL 2 269 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA 2 271 " --> pdb=" O ILE 2 280 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '2' and resid 377 through 378 Processing sheet with id=AC3, first strand: chain '2' and resid 383 through 390 Processing sheet with id=AC4, first strand: chain '2' and resid 427 through 430 removed outlier: 4.861A pdb=" N ILE 2 412 " --> pdb=" O GLY 2 462 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLY 2 462 " --> pdb=" O ILE 2 412 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA 2 414 " --> pdb=" O PHE 2 460 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N THR 7 480 " --> pdb=" O PRO 7 474 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN 7 406 " --> pdb=" O THR 7 473 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU 7 441 " --> pdb=" O SER 7 411 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain '2' and resid 485 through 486 Processing sheet with id=AC6, first strand: chain '5' and resid 13 through 15 removed outlier: 3.970A pdb=" N ARG 5 56 " --> pdb=" O THR 5 53 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N GLY 5 48 " --> pdb=" O SER 5 36 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ALA 5 94 " --> pdb=" O THR 5 81 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THR 5 81 " --> pdb=" O ALA 5 94 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N TYR 5 96 " --> pdb=" O ILE 5 79 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ILE 5 79 " --> pdb=" O TYR 5 96 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N LEU 5 98 " --> pdb=" O LEU 5 77 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '5' and resid 141 through 142 removed outlier: 4.190A pdb=" N ARG 5 186 " --> pdb=" O THR 5 183 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLY 5 178 " --> pdb=" O GLY 5 166 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '5' and resid 206 through 210 Processing sheet with id=AC9, first strand: chain '5' and resid 314 through 316 Processing sheet with id=AD1, first strand: chain '7' and resid 6 through 12 removed outlier: 4.811A pdb=" N ILE 7 314 " --> pdb=" O TYR 7 10 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain '7' and resid 21 through 24 removed outlier: 6.786A pdb=" N CYS 7 46 " --> pdb=" O VAL 7 57 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '7' and resid 69 through 72 removed outlier: 6.359A pdb=" N ILE 7 90 " --> pdb=" O SER 7 102 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N SER 7 102 " --> pdb=" O ILE 7 90 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLY 7 92 " --> pdb=" O PHE 7 100 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '7' and resid 114 through 117 removed outlier: 6.407A pdb=" N CYS 7 133 " --> pdb=" O ASP 7 137 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N ASP 7 137 " --> pdb=" O CYS 7 133 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain '7' and resid 147 through 152 removed outlier: 7.016A pdb=" N ALA 7 166 " --> pdb=" O ASN 7 148 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N VAL 7 150 " --> pdb=" O VAL 7 164 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N VAL 7 164 " --> pdb=" O VAL 7 150 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '7' and resid 171 through 176 removed outlier: 6.393A pdb=" N LEU 7 172 " --> pdb=" O GLU 7 183 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLU 7 183 " --> pdb=" O LEU 7 172 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL 7 174 " --> pdb=" O THR 7 181 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain '7' and resid 190 through 193 removed outlier: 4.751A pdb=" N LYS 7 215 " --> pdb=" O THR 7 211 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU 7 216 " --> pdb=" O GLU 7 231 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N GLU 7 231 " --> pdb=" O LEU 7 216 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N LEU 7 218 " --> pdb=" O LYS 7 229 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS 7 229 " --> pdb=" O LEU 7 218 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '7' and resid 243 through 246 removed outlier: 3.755A pdb=" N CYS 7 243 " --> pdb=" O GLY 7 260 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE 7 281 " --> pdb=" O VAL 7 268 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLY 7 270 " --> pdb=" O LEU 7 279 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N LEU 7 279 " --> pdb=" O GLY 7 270 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain '7' and resid 384 through 387 removed outlier: 3.687A pdb=" N THR 7 386 " --> pdb=" O SER 7 395 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain '7' and resid 494 through 497 removed outlier: 4.378A pdb=" N TYR 7 544 " --> pdb=" O THR 7 497 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE 7 545 " --> pdb=" O LEU 7 554 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLU 7 562 " --> pdb=" O ARG 7 559 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain '9' and resid 6 through 13 removed outlier: 5.209A pdb=" N ASP 9 8 " --> pdb=" O TYR 9 358 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N TYR 9 358 " --> pdb=" O ASP 9 8 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N TRP 9 10 " --> pdb=" O CYS 9 356 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain '9' and resid 25 through 28 removed outlier: 3.574A pdb=" N ALA 9 28 " --> pdb=" O LYS 9 39 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '9' and resid 80 through 84 removed outlier: 3.824A pdb=" N LEU 9 95 " --> pdb=" O TYR 9 106 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '9' and resid 108 through 111 Processing sheet with id=AE6, first strand: chain '9' and resid 135 through 141 removed outlier: 3.604A pdb=" N ASN 9 137 " --> pdb=" O GLN 9 155 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N MET 9 160 " --> pdb=" O SER 9 156 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU 9 161 " --> pdb=" O GLY 9 172 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLY 9 172 " --> pdb=" O LEU 9 161 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL 9 163 " --> pdb=" O ALA 9 170 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain '9' and resid 184 through 187 removed outlier: 6.732A pdb=" N LYS 9 206 " --> pdb=" O VAL 9 235 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL 9 235 " --> pdb=" O LYS 9 206 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '9' and resid 245 through 251 removed outlier: 3.603A pdb=" N ASP 9 247 " --> pdb=" O LEU 9 263 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL 9 251 " --> pdb=" O SER 9 259 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N SER 9 259 " --> pdb=" O VAL 9 251 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '9' and resid 287 through 291 removed outlier: 3.751A pdb=" N CYS 9 289 " --> pdb=" O GLY 9 306 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N MET 9 311 " --> pdb=" O ASN 9 307 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU 9 312 " --> pdb=" O ALA 9 323 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ALA 9 323 " --> pdb=" O LEU 9 312 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ILE 9 314 " --> pdb=" O LYS 9 321 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '9' and resid 411 through 417 Processing sheet with id=AF2, first strand: chain '9' and resid 471 through 477 removed outlier: 7.026A pdb=" N GLN 9 471 " --> pdb=" O SER 9 458 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N SER 9 458 " --> pdb=" O GLN 9 471 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N THR 9 473 " --> pdb=" O LYS 9 456 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LYS 9 456 " --> pdb=" O THR 9 473 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU 9 475 " --> pdb=" O LYS 9 454 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU 9 452 " --> pdb=" O MET 9 477 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LYS 9 454 " --> pdb=" O SER 9 509 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N SER 9 509 " --> pdb=" O LYS 9 454 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '9' and resid 535 through 537 1515 hydrogen bonds defined for protein. 4350 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.33 Time building geometry restraints manager: 3.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8441 1.33 - 1.45: 5049 1.45 - 1.57: 17077 1.57 - 1.69: 1 1.69 - 1.81: 223 Bond restraints: 30791 Sorted by residual: bond pdb=" N LEU 0 12 " pdb=" CA LEU 0 12 " ideal model delta sigma weight residual 1.453 1.484 -0.030 8.30e-03 1.45e+04 1.34e+01 bond pdb=" C ALA 9 478 " pdb=" N PRO 9 479 " ideal model delta sigma weight residual 1.332 1.375 -0.043 1.26e-02 6.30e+03 1.17e+01 bond pdb=" N VAL 9 202 " pdb=" CA VAL 9 202 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.08e-02 8.57e+03 1.06e+01 bond pdb=" N GLN 0 17 " pdb=" CA GLN 0 17 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.39e+00 bond pdb=" N LEU 0 18 " pdb=" CA LEU 0 18 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.23e-02 6.61e+03 8.15e+00 ... (remaining 30786 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 39959 1.53 - 3.06: 1450 3.06 - 4.59: 200 4.59 - 6.12: 45 6.12 - 7.65: 17 Bond angle restraints: 41671 Sorted by residual: angle pdb=" N ARG 7 360 " pdb=" CA ARG 7 360 " pdb=" C ARG 7 360 " ideal model delta sigma weight residual 111.14 103.94 7.20 1.08e+00 8.57e-01 4.44e+01 angle pdb=" C ALA 9 478 " pdb=" N PRO 9 479 " pdb=" CA PRO 9 479 " ideal model delta sigma weight residual 119.92 125.34 -5.42 1.07e+00 8.73e-01 2.56e+01 angle pdb=" N LYS 2 192 " pdb=" CA LYS 2 192 " pdb=" C LYS 2 192 " ideal model delta sigma weight residual 110.50 103.95 6.55 1.41e+00 5.03e-01 2.16e+01 angle pdb=" N GLN 5 205 " pdb=" CA GLN 5 205 " pdb=" C GLN 5 205 " ideal model delta sigma weight residual 113.41 108.30 5.11 1.22e+00 6.72e-01 1.75e+01 angle pdb=" C TYR 2 644 " pdb=" CA TYR 2 644 " pdb=" CB TYR 2 644 " ideal model delta sigma weight residual 110.79 117.61 -6.82 1.66e+00 3.63e-01 1.69e+01 ... (remaining 41666 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 16641 17.96 - 35.91: 1640 35.91 - 53.87: 266 53.87 - 71.82: 38 71.82 - 89.78: 38 Dihedral angle restraints: 18623 sinusoidal: 7490 harmonic: 11133 Sorted by residual: dihedral pdb=" CA THR 5 40 " pdb=" C THR 5 40 " pdb=" N LYS 5 41 " pdb=" CA LYS 5 41 " ideal model delta harmonic sigma weight residual -180.00 -155.32 -24.68 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ASN 9 307 " pdb=" C ASN 9 307 " pdb=" N HIS 9 308 " pdb=" CA HIS 9 308 " ideal model delta harmonic sigma weight residual 180.00 156.32 23.68 0 5.00e+00 4.00e-02 2.24e+01 dihedral pdb=" CA GLU 1 224 " pdb=" C GLU 1 224 " pdb=" N ASN 1 225 " pdb=" CA ASN 1 225 " ideal model delta harmonic sigma weight residual 180.00 157.14 22.86 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 18620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 4112 0.066 - 0.132: 582 0.132 - 0.198: 43 0.198 - 0.263: 8 0.263 - 0.329: 4 Chirality restraints: 4749 Sorted by residual: chirality pdb=" CA TYR 9 315 " pdb=" N TYR 9 315 " pdb=" C TYR 9 315 " pdb=" CB TYR 9 315 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CA TYR 2 644 " pdb=" N TYR 2 644 " pdb=" C TYR 2 644 " pdb=" CB TYR 2 644 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" CA ASP 2 194 " pdb=" N ASP 2 194 " pdb=" C ASP 2 194 " pdb=" CB ASP 2 194 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.16e+00 ... (remaining 4746 not shown) Planarity restraints: 5343 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS 2 689 " 0.041 5.00e-02 4.00e+02 6.19e-02 6.12e+00 pdb=" N PRO 2 690 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO 2 690 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO 2 690 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU 5 155 " -0.033 5.00e-02 4.00e+02 4.95e-02 3.92e+00 pdb=" N PRO 5 156 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO 5 156 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO 5 156 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN 9 462 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO 9 463 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO 9 463 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO 9 463 " 0.026 5.00e-02 4.00e+02 ... (remaining 5340 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 465 2.66 - 3.22: 28293 3.22 - 3.78: 46018 3.78 - 4.34: 65529 4.34 - 4.90: 108829 Nonbonded interactions: 249134 Sorted by model distance: nonbonded pdb=" OE2 GLU 2 178 " pdb="CA CA 2 801 " model vdw 2.096 2.510 nonbonded pdb=" OH TYR 4 71 " pdb=" OD1 ASP 4 102 " model vdw 2.208 3.040 nonbonded pdb=" O LYS 2 176 " pdb="CA CA 2 801 " model vdw 2.217 2.510 nonbonded pdb=" OG SER 9 156 " pdb=" OD1 ASP 9 158 " model vdw 2.224 3.040 nonbonded pdb=" O ASP 2 194 " pdb=" ND2 ASN 2 692 " model vdw 2.229 3.120 ... (remaining 249129 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: 2.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.410 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 27.500 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 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 : 0.005 0.043 30791 Z= 0.229 Angle : 0.688 7.652 41671 Z= 0.400 Chirality : 0.047 0.329 4749 Planarity : 0.004 0.062 5343 Dihedral : 14.738 89.780 11425 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 0.24 % Allowed : 5.70 % Favored : 94.06 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.06 (0.12), residues: 3766 helix: -0.78 (0.13), residues: 1309 sheet: -1.83 (0.16), residues: 923 loop : -3.25 (0.13), residues: 1534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 681 TYR 0.017 0.002 TYR 2 229 PHE 0.022 0.002 PHE 9 290 TRP 0.018 0.002 TRP 1 322 HIS 0.008 0.001 HIS 7 131 Details of bonding type rmsd covalent geometry : bond 0.00456 (30791) covalent geometry : angle 0.68802 (41671) hydrogen bonds : bond 0.11749 ( 1515) hydrogen bonds : angle 6.13672 ( 4350) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 686 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 2 LYS cc_start: 0.4607 (tttt) cc_final: 0.4392 (tttt) REVERT: 1 309 ASP cc_start: 0.5970 (m-30) cc_final: 0.5676 (p0) REVERT: 1 368 ARG cc_start: 0.4294 (ptp-170) cc_final: 0.2943 (ttp-170) REVERT: 1 448 MET cc_start: 0.7933 (mtp) cc_final: 0.7685 (mtp) REVERT: 2 229 TYR cc_start: 0.7544 (OUTLIER) cc_final: 0.6553 (m-80) REVERT: 2 255 ASP cc_start: 0.6689 (m-30) cc_final: 0.6347 (t0) REVERT: 2 384 HIS cc_start: 0.6021 (OUTLIER) cc_final: 0.5616 (p-80) REVERT: 2 609 LYS cc_start: 0.7733 (mptt) cc_final: 0.7278 (mmtm) REVERT: 2 616 ASP cc_start: 0.7702 (m-30) cc_final: 0.7414 (m-30) REVERT: 2 713 ILE cc_start: 0.5837 (tp) cc_final: 0.5517 (tp) REVERT: 4 52 LYS cc_start: 0.5807 (mtmt) cc_final: 0.5383 (tptt) REVERT: 4 116 LYS cc_start: 0.8261 (mppt) cc_final: 0.8021 (mptt) REVERT: 4 176 LYS cc_start: 0.7243 (ttmm) cc_final: 0.6967 (tttt) REVERT: 5 177 LEU cc_start: 0.8250 (tt) cc_final: 0.8047 (tt) REVERT: 5 334 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7866 (mm-40) REVERT: 7 171 VAL cc_start: 0.6415 (p) cc_final: 0.6213 (t) REVERT: 7 213 ASP cc_start: 0.7291 (p0) cc_final: 0.7039 (p0) REVERT: 7 358 GLN cc_start: 0.5432 (mt0) cc_final: 0.5212 (tp40) REVERT: 7 546 GLN cc_start: 0.6932 (tt0) cc_final: 0.6517 (tp40) REVERT: 7 558 TYR cc_start: 0.6548 (p90) cc_final: 0.6078 (p90) REVERT: 8 64 ILE cc_start: 0.7916 (mp) cc_final: 0.7702 (mp) REVERT: 8 292 ASN cc_start: 0.7537 (t0) cc_final: 0.6807 (t0) REVERT: 8 379 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7474 (mm-30) REVERT: 8 429 ARG cc_start: 0.8156 (ttt-90) cc_final: 0.7885 (ttt-90) REVERT: 9 122 GLN cc_start: 0.7498 (pm20) cc_final: 0.7202 (pm20) REVERT: 9 542 LYS cc_start: 0.7816 (mmmt) cc_final: 0.7448 (tptt) REVERT: 9 553 ASN cc_start: 0.7817 (p0) cc_final: 0.6772 (t0) REVERT: 9 620 LEU cc_start: 0.8493 (mt) cc_final: 0.8222 (mt) outliers start: 8 outliers final: 3 residues processed: 691 average time/residue: 0.2025 time to fit residues: 216.5070 Evaluate side-chains 404 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 399 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 229 TYR Chi-restraints excluded: chain 2 residue 384 HIS Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 205 GLN Chi-restraints excluded: chain 9 residue 9 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 0.0170 chunk 298 optimal weight: 0.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 386 ASN 2 12 HIS 2 44 ASN ** 2 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 431 HIS 4 325 HIS ** 4 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 20 GLN 7 273 ASN 7 283 HIS 7 293 GLN 7 365 GLN 7 410 GLN 7 437 ASN 7 469 GLN 7 495 GLN 7 633 GLN 8 321 ASN 8 322 HIS 8 454 HIS 8 484 HIS 9 200 HIS 9 276 GLN 9 310 ASN 9 471 GLN 9 576 ASN 9 651 HIS 9 761 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.190509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 98)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.140672 restraints weight = 40838.189| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.87 r_work: 0.3548 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 30791 Z= 0.271 Angle : 0.723 10.428 41671 Z= 0.373 Chirality : 0.048 0.183 4749 Planarity : 0.005 0.058 5343 Dihedral : 5.576 49.501 4116 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.22 % Allowed : 13.83 % Favored : 83.95 % 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: -2.05 (0.13), residues: 3766 helix: 0.19 (0.14), residues: 1317 sheet: -1.41 (0.16), residues: 959 loop : -2.74 (0.14), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG 8 165 TYR 0.022 0.002 TYR 7 141 PHE 0.031 0.002 PHE 9 290 TRP 0.018 0.002 TRP 9 322 HIS 0.010 0.002 HIS 5 128 Details of bonding type rmsd covalent geometry : bond 0.00642 (30791) covalent geometry : angle 0.72278 (41671) hydrogen bonds : bond 0.04994 ( 1515) hydrogen bonds : angle 5.20579 ( 4350) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 413 time to evaluate : 1.069 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 2 LYS cc_start: 0.4576 (tttt) cc_final: 0.4250 (tttp) REVERT: 1 368 ARG cc_start: 0.4424 (ptp-170) cc_final: 0.2986 (ttm110) REVERT: 2 9 LYS cc_start: 0.7746 (tptp) cc_final: 0.7415 (mmmt) REVERT: 2 11 ARG cc_start: 0.8078 (tmt170) cc_final: 0.7628 (ptt-90) REVERT: 2 528 ASN cc_start: 0.6403 (m110) cc_final: 0.5664 (t0) REVERT: 2 579 ASP cc_start: 0.6326 (m-30) cc_final: 0.5905 (m-30) REVERT: 2 609 LYS cc_start: 0.7853 (mptt) cc_final: 0.7572 (mmtt) REVERT: 2 630 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7692 (t70) REVERT: 2 640 MET cc_start: 0.8360 (ttp) cc_final: 0.8118 (ttt) REVERT: 2 713 ILE cc_start: 0.6081 (tp) cc_final: 0.5839 (tp) REVERT: 4 95 PHE cc_start: 0.7278 (t80) cc_final: 0.7029 (t80) REVERT: 4 116 LYS cc_start: 0.8442 (mppt) cc_final: 0.8189 (mptt) REVERT: 4 176 LYS cc_start: 0.7231 (ttmm) cc_final: 0.6860 (tttt) REVERT: 4 369 LYS cc_start: 0.8406 (mptt) cc_final: 0.7902 (mptt) REVERT: 4 417 MET cc_start: 0.5224 (ttp) cc_final: 0.4997 (ttm) REVERT: 5 132 GLU cc_start: 0.7888 (mm-30) cc_final: 0.7646 (mm-30) REVERT: 5 236 LYS cc_start: 0.6892 (tttt) cc_final: 0.6659 (tttm) REVERT: 7 297 VAL cc_start: 0.5143 (p) cc_final: 0.4824 (m) REVERT: 7 364 GLN cc_start: 0.6716 (tp-100) cc_final: 0.6171 (mm110) REVERT: 7 455 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7616 (tp30) REVERT: 7 546 GLN cc_start: 0.6769 (tt0) cc_final: 0.5796 (tp40) REVERT: 8 54 ASP cc_start: 0.7770 (m-30) cc_final: 0.7569 (m-30) REVERT: 8 292 ASN cc_start: 0.7903 (t0) cc_final: 0.7132 (t0) REVERT: 9 122 GLN cc_start: 0.7848 (pm20) cc_final: 0.7520 (pm20) REVERT: 9 247 ASP cc_start: 0.8538 (t0) cc_final: 0.8312 (t70) REVERT: 9 542 LYS cc_start: 0.8204 (mmmt) cc_final: 0.7544 (tptt) REVERT: 9 553 ASN cc_start: 0.8033 (p0) cc_final: 0.6747 (t0) REVERT: 9 620 LEU cc_start: 0.8639 (mt) cc_final: 0.8344 (mt) outliers start: 74 outliers final: 45 residues processed: 466 average time/residue: 0.1807 time to fit residues: 137.0385 Evaluate side-chains 412 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 366 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 VAL Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 225 THR Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 314 ILE Chi-restraints excluded: chain 2 residue 630 ASP Chi-restraints excluded: chain 2 residue 702 ILE Chi-restraints excluded: chain 2 residue 703 ARG Chi-restraints excluded: chain 4 residue 152 ASP Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 173 MET Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 354 SER Chi-restraints excluded: chain 5 residue 29 VAL Chi-restraints excluded: chain 5 residue 151 GLN Chi-restraints excluded: chain 5 residue 205 GLN Chi-restraints excluded: chain 5 residue 224 SER Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 436 SER Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 571 SER Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 7 residue 709 ILE Chi-restraints excluded: chain 8 residue 48 VAL Chi-restraints excluded: chain 8 residue 123 GLN Chi-restraints excluded: chain 8 residue 483 ASP Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 33 THR Chi-restraints excluded: chain 9 residue 104 CYS Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 195 THR Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 290 PHE Chi-restraints excluded: chain 9 residue 296 VAL Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 382 ASP Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 473 THR Chi-restraints excluded: chain 9 residue 501 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 19 optimal weight: 6.9990 chunk 357 optimal weight: 0.8980 chunk 310 optimal weight: 3.9990 chunk 339 optimal weight: 0.0170 chunk 247 optimal weight: 2.9990 chunk 288 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 322 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 320 optimal weight: 0.7980 overall best weight: 1.0820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 489 HIS 2 12 HIS 2 99 ASN 2 656 ASN 4 163 HIS 4 249 HIS 4 319 GLN 4 385 GLN 5 148 GLN 5 205 GLN ** 8 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 811 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.193092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 111)---------------| | r_work = 0.3724 r_free = 0.3724 target = 0.143424 restraints weight = 40722.438| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 1.86 r_work: 0.3588 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 30791 Z= 0.153 Angle : 0.592 8.110 41671 Z= 0.308 Chirality : 0.044 0.193 4749 Planarity : 0.004 0.060 5343 Dihedral : 5.083 47.170 4111 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.61 % Allowed : 15.54 % Favored : 81.85 % 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: -1.38 (0.13), residues: 3766 helix: 0.88 (0.14), residues: 1317 sheet: -1.09 (0.16), residues: 961 loop : -2.46 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 68 TYR 0.018 0.001 TYR 7 703 PHE 0.019 0.002 PHE 2 501 TRP 0.014 0.002 TRP 9 237 HIS 0.011 0.001 HIS 7 131 Details of bonding type rmsd covalent geometry : bond 0.00352 (30791) covalent geometry : angle 0.59179 (41671) hydrogen bonds : bond 0.04260 ( 1515) hydrogen bonds : angle 4.82687 ( 4350) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 400 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8028 (mt-10) REVERT: 1 2 LYS cc_start: 0.4569 (tttt) cc_final: 0.4225 (tttp) REVERT: 1 32 TYR cc_start: 0.5029 (m-80) cc_final: 0.4341 (m-80) REVERT: 1 203 MET cc_start: 0.5845 (mtp) cc_final: 0.5600 (mtm) REVERT: 1 309 ASP cc_start: 0.5865 (OUTLIER) cc_final: 0.5452 (p0) REVERT: 1 368 ARG cc_start: 0.4212 (ptp-170) cc_final: 0.2758 (ttm110) REVERT: 2 9 LYS cc_start: 0.7708 (tptp) cc_final: 0.7256 (mmmt) REVERT: 2 153 ASP cc_start: 0.8006 (t0) cc_final: 0.7803 (t0) REVERT: 2 528 ASN cc_start: 0.6314 (m110) cc_final: 0.5570 (t0) REVERT: 2 579 ASP cc_start: 0.6438 (m-30) cc_final: 0.6055 (m-30) REVERT: 4 116 LYS cc_start: 0.8243 (mppt) cc_final: 0.7978 (mptt) REVERT: 4 176 LYS cc_start: 0.7179 (ttmm) cc_final: 0.6815 (tttt) REVERT: 4 201 ASN cc_start: 0.7157 (t0) cc_final: 0.6925 (t0) REVERT: 4 369 LYS cc_start: 0.8398 (mptt) cc_final: 0.7904 (mptt) REVERT: 4 417 MET cc_start: 0.5564 (ttp) cc_final: 0.5308 (ttm) REVERT: 4 423 LYS cc_start: 0.7103 (mmtt) cc_final: 0.6378 (mttt) REVERT: 5 88 LEU cc_start: 0.4268 (OUTLIER) cc_final: 0.3909 (pt) REVERT: 5 114 VAL cc_start: 0.6991 (t) cc_final: 0.6785 (m) REVERT: 5 132 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7567 (mm-30) REVERT: 5 236 LYS cc_start: 0.6717 (tttt) cc_final: 0.6503 (tttm) REVERT: 5 248 LYS cc_start: 0.8399 (mttt) cc_final: 0.8053 (mmtt) REVERT: 7 134 ASP cc_start: 0.6340 (t0) cc_final: 0.5515 (t70) REVERT: 7 165 LEU cc_start: 0.5699 (OUTLIER) cc_final: 0.5489 (mp) REVERT: 7 281 PHE cc_start: 0.5242 (t80) cc_final: 0.5023 (t80) REVERT: 7 297 VAL cc_start: 0.5532 (p) cc_final: 0.5295 (m) REVERT: 7 358 GLN cc_start: 0.5964 (mt0) cc_final: 0.5715 (tm-30) REVERT: 7 364 GLN cc_start: 0.6583 (tp-100) cc_final: 0.5788 (pt0) REVERT: 7 438 ASP cc_start: 0.5762 (t0) cc_final: 0.5375 (t0) REVERT: 7 546 GLN cc_start: 0.6715 (tt0) cc_final: 0.5923 (tp40) REVERT: 7 558 TYR cc_start: 0.7000 (p90) cc_final: 0.5792 (p90) REVERT: 8 26 MET cc_start: 0.7018 (ptm) cc_final: 0.6810 (ptt) REVERT: 8 292 ASN cc_start: 0.7840 (t0) cc_final: 0.7077 (t0) REVERT: 9 382 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7250 (m-30) REVERT: 9 394 ASN cc_start: 0.7304 (m-40) cc_final: 0.7056 (m-40) REVERT: 9 542 LYS cc_start: 0.8164 (mmmt) cc_final: 0.7536 (tptt) REVERT: 9 553 ASN cc_start: 0.7942 (p0) cc_final: 0.6614 (t0) REVERT: 9 620 LEU cc_start: 0.8685 (mt) cc_final: 0.8431 (mt) outliers start: 87 outliers final: 48 residues processed: 467 average time/residue: 0.1778 time to fit residues: 136.1638 Evaluate side-chains 411 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 359 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 VAL Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 1 residue 309 ASP Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 1 residue 439 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 1 residue 578 LEU Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 196 ILE Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 435 HIS Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 2 residue 630 ASP Chi-restraints excluded: chain 2 residue 702 ILE Chi-restraints excluded: chain 4 residue 152 ASP Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 278 MET Chi-restraints excluded: chain 5 residue 29 VAL Chi-restraints excluded: chain 5 residue 37 VAL Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 5 residue 199 VAL Chi-restraints excluded: chain 5 residue 205 GLN Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 165 LEU Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 266 VAL Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 436 SER Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 571 SER Chi-restraints excluded: chain 7 residue 627 ASP Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 33 THR Chi-restraints excluded: chain 9 residue 104 CYS Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 276 GLN Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 382 ASP Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 473 THR Chi-restraints excluded: chain 9 residue 501 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 230 optimal weight: 7.9990 chunk 370 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 224 optimal weight: 8.9990 chunk 263 optimal weight: 0.2980 chunk 120 optimal weight: 6.9990 chunk 201 optimal weight: 0.0010 chunk 93 optimal weight: 4.9990 chunk 219 optimal weight: 0.9980 chunk 203 optimal weight: 6.9990 chunk 353 optimal weight: 5.9990 overall best weight: 1.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 45 GLN ** 1 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 12 HIS 4 319 GLN ** 7 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.192599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.151314 restraints weight = 40363.568| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.68 r_work: 0.3597 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 30791 Z= 0.167 Angle : 0.590 8.759 41671 Z= 0.306 Chirality : 0.044 0.193 4749 Planarity : 0.004 0.058 5343 Dihedral : 4.969 44.384 4111 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 3.18 % Allowed : 17.31 % Favored : 79.51 % 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: -1.05 (0.14), residues: 3766 helix: 1.16 (0.14), residues: 1319 sheet: -0.88 (0.17), residues: 957 loop : -2.30 (0.15), residues: 1490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG 7 68 TYR 0.018 0.002 TYR 2 213 PHE 0.018 0.002 PHE 2 41 TRP 0.013 0.002 TRP 9 9 HIS 0.006 0.001 HIS 5 128 Details of bonding type rmsd covalent geometry : bond 0.00391 (30791) covalent geometry : angle 0.59008 (41671) hydrogen bonds : bond 0.04162 ( 1515) hydrogen bonds : angle 4.72231 ( 4350) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 375 time to evaluate : 1.199 Fit side-chains revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7978 (mt-10) REVERT: 1 2 LYS cc_start: 0.4604 (tttt) cc_final: 0.4269 (tttp) REVERT: 1 32 TYR cc_start: 0.5358 (m-80) cc_final: 0.4867 (m-80) REVERT: 1 203 MET cc_start: 0.5869 (mtp) cc_final: 0.5643 (mtm) REVERT: 1 309 ASP cc_start: 0.5969 (OUTLIER) cc_final: 0.5529 (p0) REVERT: 1 368 ARG cc_start: 0.4343 (ptp-170) cc_final: 0.2789 (ttm110) REVERT: 1 429 ARG cc_start: 0.7373 (tpp-160) cc_final: 0.7117 (tpp80) REVERT: 2 9 LYS cc_start: 0.7587 (tptp) cc_final: 0.7324 (mmmt) REVERT: 2 153 ASP cc_start: 0.7910 (t0) cc_final: 0.7703 (t0) REVERT: 2 498 TYR cc_start: 0.7816 (p90) cc_final: 0.7506 (p90) REVERT: 2 500 ASN cc_start: 0.7060 (m-40) cc_final: 0.6706 (m-40) REVERT: 2 528 ASN cc_start: 0.6288 (m110) cc_final: 0.5704 (t0) REVERT: 4 52 LYS cc_start: 0.6441 (mtpp) cc_final: 0.5551 (tptt) REVERT: 4 116 LYS cc_start: 0.8161 (mppt) cc_final: 0.7958 (mptt) REVERT: 4 176 LYS cc_start: 0.7275 (ttmm) cc_final: 0.6958 (tttt) REVERT: 4 229 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6913 (mm) REVERT: 4 369 LYS cc_start: 0.8415 (mptt) cc_final: 0.8035 (mptt) REVERT: 4 423 LYS cc_start: 0.7328 (mmtt) cc_final: 0.6527 (mttt) REVERT: 5 88 LEU cc_start: 0.4474 (OUTLIER) cc_final: 0.4096 (pt) REVERT: 5 114 VAL cc_start: 0.7052 (t) cc_final: 0.6835 (m) REVERT: 7 39 ASP cc_start: 0.5794 (t0) cc_final: 0.4879 (t0) REVERT: 7 59 LYS cc_start: 0.6223 (OUTLIER) cc_final: 0.6007 (tttp) REVERT: 7 134 ASP cc_start: 0.6269 (t0) cc_final: 0.5407 (t70) REVERT: 7 173 ARG cc_start: 0.2323 (mtt180) cc_final: 0.2099 (mtm180) REVERT: 7 364 GLN cc_start: 0.6740 (tp-100) cc_final: 0.5894 (pt0) REVERT: 7 438 ASP cc_start: 0.5755 (t0) cc_final: 0.5526 (t0) REVERT: 7 546 GLN cc_start: 0.6888 (tt0) cc_final: 0.6181 (tp40) REVERT: 8 135 ARG cc_start: 0.5573 (OUTLIER) cc_final: 0.5308 (ttp-110) REVERT: 8 204 GLU cc_start: 0.7535 (mt-10) cc_final: 0.7303 (mt-10) REVERT: 8 292 ASN cc_start: 0.7944 (t0) cc_final: 0.7477 (t0) REVERT: 9 247 ASP cc_start: 0.8351 (t0) cc_final: 0.8130 (t70) REVERT: 9 382 ASP cc_start: 0.7681 (OUTLIER) cc_final: 0.7372 (m-30) REVERT: 9 542 LYS cc_start: 0.8071 (mmmt) cc_final: 0.7531 (tptt) REVERT: 9 553 ASN cc_start: 0.7874 (p0) cc_final: 0.6539 (t0) REVERT: 9 620 LEU cc_start: 0.8686 (mt) cc_final: 0.8423 (mt) REVERT: 9 657 ILE cc_start: 0.8852 (mm) cc_final: 0.8642 (mm) outliers start: 106 outliers final: 70 residues processed: 460 average time/residue: 0.1815 time to fit residues: 136.7330 Evaluate side-chains 435 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 359 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 VAL Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 1 residue 232 ASP Chi-restraints excluded: chain 1 residue 309 ASP Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 1 residue 387 THR Chi-restraints excluded: chain 1 residue 439 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 1 residue 578 LEU Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 196 ILE Chi-restraints excluded: chain 2 residue 225 THR Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 311 ASP Chi-restraints excluded: chain 2 residue 435 HIS Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 2 residue 459 THR Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 2 residue 630 ASP Chi-restraints excluded: chain 2 residue 702 ILE Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 229 LEU Chi-restraints excluded: chain 4 residue 278 MET Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 5 residue 22 MET Chi-restraints excluded: chain 5 residue 29 VAL Chi-restraints excluded: chain 5 residue 37 VAL Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 142 LEU Chi-restraints excluded: chain 5 residue 151 GLN Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 5 residue 205 GLN Chi-restraints excluded: chain 5 residue 224 SER Chi-restraints excluded: chain 7 residue 59 LYS Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 127 TYR Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 208 LEU Chi-restraints excluded: chain 7 residue 266 VAL Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 436 SER Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 524 VAL Chi-restraints excluded: chain 7 residue 571 SER Chi-restraints excluded: chain 7 residue 627 ASP Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 8 residue 48 VAL Chi-restraints excluded: chain 8 residue 135 ARG Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 33 THR Chi-restraints excluded: chain 9 residue 104 CYS Chi-restraints excluded: chain 9 residue 111 THR Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 195 THR Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 276 GLN Chi-restraints excluded: chain 9 residue 290 PHE Chi-restraints excluded: chain 9 residue 307 ASN Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 382 ASP Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 473 THR Chi-restraints excluded: chain 9 residue 496 SER Chi-restraints excluded: chain 9 residue 501 GLU Chi-restraints excluded: chain 9 residue 551 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 6 optimal weight: 20.0000 chunk 272 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 356 optimal weight: 2.9990 chunk 150 optimal weight: 4.9990 chunk 314 optimal weight: 2.9990 chunk 212 optimal weight: 8.9990 chunk 367 optimal weight: 0.5980 chunk 254 optimal weight: 3.9990 chunk 317 optimal weight: 0.7980 chunk 76 optimal weight: 0.0370 overall best weight: 1.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 359 HIS 2 656 ASN 4 319 GLN 7 482 GLN ** 7 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.191706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.143844 restraints weight = 40522.378| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 1.91 r_work: 0.3567 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3447 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3447 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 30791 Z= 0.181 Angle : 0.599 9.848 41671 Z= 0.310 Chirality : 0.044 0.207 4749 Planarity : 0.004 0.055 5343 Dihedral : 4.965 45.955 4111 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.69 % Allowed : 18.09 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.14), residues: 3766 helix: 1.23 (0.14), residues: 1320 sheet: -0.85 (0.17), residues: 990 loop : -2.21 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 2 712 TYR 0.016 0.002 TYR 7 703 PHE 0.020 0.002 PHE 4 95 TRP 0.014 0.002 TRP 9 9 HIS 0.005 0.001 HIS 5 128 Details of bonding type rmsd covalent geometry : bond 0.00429 (30791) covalent geometry : angle 0.59935 (41671) hydrogen bonds : bond 0.04198 ( 1515) hydrogen bonds : angle 4.70335 ( 4350) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 373 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.8361 (mt-10) cc_final: 0.8000 (mt-10) REVERT: 1 2 LYS cc_start: 0.4444 (tttt) cc_final: 0.4088 (tttp) REVERT: 1 32 TYR cc_start: 0.5639 (m-80) cc_final: 0.5131 (m-80) REVERT: 1 203 MET cc_start: 0.5725 (mtp) cc_final: 0.5481 (mtm) REVERT: 1 347 MET cc_start: 0.3686 (OUTLIER) cc_final: 0.3014 (mtp) REVERT: 1 368 ARG cc_start: 0.4403 (ptp-170) cc_final: 0.2658 (ttm110) REVERT: 1 429 ARG cc_start: 0.7417 (tpp-160) cc_final: 0.7142 (tpp80) REVERT: 1 488 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8826 (tp) REVERT: 2 9 LYS cc_start: 0.7666 (tptp) cc_final: 0.7463 (mmmt) REVERT: 2 89 TYR cc_start: 0.7170 (p90) cc_final: 0.6722 (p90) REVERT: 2 347 ASN cc_start: 0.8207 (m110) cc_final: 0.7991 (m-40) REVERT: 2 498 TYR cc_start: 0.7938 (p90) cc_final: 0.7624 (p90) REVERT: 2 528 ASN cc_start: 0.6259 (m110) cc_final: 0.5724 (t0) REVERT: 2 544 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7683 (tp) REVERT: 4 52 LYS cc_start: 0.6234 (mtpp) cc_final: 0.5424 (tptt) REVERT: 4 116 LYS cc_start: 0.8199 (mppt) cc_final: 0.7926 (mptt) REVERT: 4 176 LYS cc_start: 0.7188 (ttmm) cc_final: 0.6814 (tttt) REVERT: 4 369 LYS cc_start: 0.8457 (mptt) cc_final: 0.7984 (mptt) REVERT: 4 423 LYS cc_start: 0.7182 (mmtt) cc_final: 0.6340 (mttt) REVERT: 5 39 ASP cc_start: 0.6708 (OUTLIER) cc_final: 0.6389 (t70) REVERT: 5 57 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8200 (mt) REVERT: 5 88 LEU cc_start: 0.4266 (OUTLIER) cc_final: 0.3895 (pt) REVERT: 5 114 VAL cc_start: 0.6889 (t) cc_final: 0.6643 (m) REVERT: 7 59 LYS cc_start: 0.6388 (OUTLIER) cc_final: 0.6182 (tttp) REVERT: 7 134 ASP cc_start: 0.6431 (t0) cc_final: 0.5573 (t70) REVERT: 7 287 GLU cc_start: 0.6560 (mt-10) cc_final: 0.6343 (tt0) REVERT: 7 364 GLN cc_start: 0.6765 (tp-100) cc_final: 0.5893 (pt0) REVERT: 7 438 ASP cc_start: 0.5776 (t0) cc_final: 0.5504 (t0) REVERT: 7 546 GLN cc_start: 0.6752 (tt0) cc_final: 0.5955 (tp40) REVERT: 7 701 ASP cc_start: 0.7647 (m-30) cc_final: 0.7437 (m-30) REVERT: 8 26 MET cc_start: 0.7119 (ptm) cc_final: 0.6893 (ptt) REVERT: 8 135 ARG cc_start: 0.5474 (OUTLIER) cc_final: 0.5204 (ttp-110) REVERT: 8 204 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7435 (mt-10) REVERT: 8 292 ASN cc_start: 0.8090 (t0) cc_final: 0.7614 (t0) REVERT: 9 69 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.8044 (mp) REVERT: 9 382 ASP cc_start: 0.7678 (OUTLIER) cc_final: 0.7365 (m-30) REVERT: 9 542 LYS cc_start: 0.8182 (mmmt) cc_final: 0.7516 (tptt) REVERT: 9 553 ASN cc_start: 0.7963 (p0) cc_final: 0.6664 (t0) REVERT: 9 620 LEU cc_start: 0.8626 (mt) cc_final: 0.8373 (mt) REVERT: 9 704 LYS cc_start: 0.8418 (mmmt) cc_final: 0.8161 (mmtm) outliers start: 123 outliers final: 83 residues processed: 473 average time/residue: 0.1766 time to fit residues: 135.6180 Evaluate side-chains 444 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 351 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 VAL Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 1 residue 216 VAL Chi-restraints excluded: chain 1 residue 232 ASP Chi-restraints excluded: chain 1 residue 309 ASP Chi-restraints excluded: chain 1 residue 347 MET Chi-restraints excluded: chain 1 residue 367 ILE Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 1 residue 387 THR Chi-restraints excluded: chain 1 residue 439 LEU Chi-restraints excluded: chain 1 residue 488 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 1 residue 578 LEU Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 196 ILE Chi-restraints excluded: chain 2 residue 225 THR Chi-restraints excluded: chain 2 residue 262 THR Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 311 ASP Chi-restraints excluded: chain 2 residue 435 HIS Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 2 residue 459 THR Chi-restraints excluded: chain 2 residue 533 VAL Chi-restraints excluded: chain 2 residue 544 LEU Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 2 residue 630 ASP Chi-restraints excluded: chain 4 residue 47 ASP Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 229 LEU Chi-restraints excluded: chain 4 residue 278 MET Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 5 residue 22 MET Chi-restraints excluded: chain 5 residue 29 VAL Chi-restraints excluded: chain 5 residue 37 VAL Chi-restraints excluded: chain 5 residue 39 ASP Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 142 LEU Chi-restraints excluded: chain 5 residue 151 GLN Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 5 residue 199 VAL Chi-restraints excluded: chain 5 residue 205 GLN Chi-restraints excluded: chain 5 residue 224 SER Chi-restraints excluded: chain 7 residue 59 LYS Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 208 LEU Chi-restraints excluded: chain 7 residue 266 VAL Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 427 VAL Chi-restraints excluded: chain 7 residue 436 SER Chi-restraints excluded: chain 7 residue 441 LEU Chi-restraints excluded: chain 7 residue 456 LEU Chi-restraints excluded: chain 7 residue 462 GLU Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 571 SER Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 8 residue 48 VAL Chi-restraints excluded: chain 8 residue 135 ARG Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 166 LEU Chi-restraints excluded: chain 8 residue 367 THR Chi-restraints excluded: chain 8 residue 483 ASP Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 69 LEU Chi-restraints excluded: chain 9 residue 104 CYS Chi-restraints excluded: chain 9 residue 111 THR Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 157 VAL Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 254 ILE Chi-restraints excluded: chain 9 residue 276 GLN Chi-restraints excluded: chain 9 residue 290 PHE Chi-restraints excluded: chain 9 residue 296 VAL Chi-restraints excluded: chain 9 residue 307 ASN Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 382 ASP Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 473 THR Chi-restraints excluded: chain 9 residue 496 SER Chi-restraints excluded: chain 9 residue 501 GLU Chi-restraints excluded: chain 9 residue 551 ASP Chi-restraints excluded: chain 9 residue 706 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 104 optimal weight: 1.9990 chunk 202 optimal weight: 9.9990 chunk 295 optimal weight: 3.9990 chunk 173 optimal weight: 7.9990 chunk 184 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 4 optimal weight: 6.9990 chunk 340 optimal weight: 3.9990 chunk 242 optimal weight: 3.9990 chunk 92 optimal weight: 7.9990 chunk 308 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 12 HIS 4 35 GLN 4 319 GLN ** 7 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 432 HIS ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 310 ASN ** 9 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.189196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.140816 restraints weight = 40384.596| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 1.87 r_work: 0.3535 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 30791 Z= 0.255 Angle : 0.663 10.969 41671 Z= 0.343 Chirality : 0.046 0.185 4749 Planarity : 0.005 0.055 5343 Dihedral : 5.193 48.396 4111 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.93 % Allowed : 18.87 % Favored : 77.20 % 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: -1.09 (0.14), residues: 3766 helix: 0.98 (0.14), residues: 1323 sheet: -0.88 (0.17), residues: 980 loop : -2.21 (0.15), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 2 712 TYR 0.016 0.002 TYR 7 703 PHE 0.024 0.002 PHE 9 290 TRP 0.017 0.002 TRP 9 9 HIS 0.007 0.001 HIS 9 732 Details of bonding type rmsd covalent geometry : bond 0.00614 (30791) covalent geometry : angle 0.66294 (41671) hydrogen bonds : bond 0.04645 ( 1515) hydrogen bonds : angle 4.88242 ( 4350) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 366 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8029 (mt-10) REVERT: 1 2 LYS cc_start: 0.4475 (tttt) cc_final: 0.4120 (tttp) REVERT: 1 32 TYR cc_start: 0.5807 (m-80) cc_final: 0.5306 (m-80) REVERT: 1 59 GLN cc_start: 0.6573 (pm20) cc_final: 0.6361 (pm20) REVERT: 1 203 MET cc_start: 0.5766 (mtp) cc_final: 0.5510 (mtm) REVERT: 1 347 MET cc_start: 0.3584 (OUTLIER) cc_final: 0.2904 (mtp) REVERT: 1 368 ARG cc_start: 0.3957 (ptp-170) cc_final: 0.2041 (ttm110) REVERT: 1 429 ARG cc_start: 0.7454 (tpp-160) cc_final: 0.7162 (tpp80) REVERT: 1 488 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.8855 (tp) REVERT: 2 384 HIS cc_start: 0.6505 (OUTLIER) cc_final: 0.5979 (m-70) REVERT: 2 498 TYR cc_start: 0.8009 (p90) cc_final: 0.7723 (p90) REVERT: 2 528 ASN cc_start: 0.6295 (m110) cc_final: 0.5740 (t0) REVERT: 2 548 ILE cc_start: 0.7466 (mp) cc_final: 0.7226 (mm) REVERT: 2 713 ILE cc_start: 0.6545 (tp) cc_final: 0.5946 (tp) REVERT: 4 52 LYS cc_start: 0.6245 (mtpp) cc_final: 0.5436 (tptt) REVERT: 4 99 GLN cc_start: 0.7374 (pt0) cc_final: 0.7048 (pp30) REVERT: 4 116 LYS cc_start: 0.8443 (mppt) cc_final: 0.8100 (mptt) REVERT: 4 176 LYS cc_start: 0.7267 (ttmm) cc_final: 0.6950 (tttt) REVERT: 4 369 LYS cc_start: 0.8452 (mptt) cc_final: 0.7960 (mptt) REVERT: 4 423 LYS cc_start: 0.7189 (mmtt) cc_final: 0.6183 (mttt) REVERT: 5 57 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8199 (mt) REVERT: 5 88 LEU cc_start: 0.4262 (OUTLIER) cc_final: 0.3897 (pt) REVERT: 5 114 VAL cc_start: 0.7166 (t) cc_final: 0.6897 (m) REVERT: 5 260 ASN cc_start: 0.6599 (t0) cc_final: 0.6244 (t0) REVERT: 7 59 LYS cc_start: 0.6450 (OUTLIER) cc_final: 0.6246 (tttp) REVERT: 7 287 GLU cc_start: 0.6621 (mt-10) cc_final: 0.6352 (tt0) REVERT: 7 364 GLN cc_start: 0.6788 (tp-100) cc_final: 0.5853 (pt0) REVERT: 7 438 ASP cc_start: 0.5939 (t0) cc_final: 0.5666 (t0) REVERT: 7 558 TYR cc_start: 0.6894 (p90) cc_final: 0.5756 (p90) REVERT: 8 135 ARG cc_start: 0.5495 (OUTLIER) cc_final: 0.5244 (ttp-110) REVERT: 8 204 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7606 (mt-10) REVERT: 8 292 ASN cc_start: 0.8059 (t0) cc_final: 0.7596 (t0) REVERT: 9 69 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8122 (mp) REVERT: 9 247 ASP cc_start: 0.8409 (t0) cc_final: 0.8192 (t70) REVERT: 9 542 LYS cc_start: 0.8200 (mmmt) cc_final: 0.7534 (tptt) REVERT: 9 553 ASN cc_start: 0.8010 (p0) cc_final: 0.6719 (t0) REVERT: 9 620 LEU cc_start: 0.8629 (mt) cc_final: 0.8345 (mt) REVERT: 9 657 ILE cc_start: 0.8857 (mm) cc_final: 0.8604 (mm) REVERT: 9 704 LYS cc_start: 0.8453 (mmmt) cc_final: 0.8172 (mmtm) outliers start: 131 outliers final: 92 residues processed: 475 average time/residue: 0.1779 time to fit residues: 138.4958 Evaluate side-chains 447 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 347 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 VAL Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 0 residue 24 THR Chi-restraints excluded: chain 1 residue 216 VAL Chi-restraints excluded: chain 1 residue 309 ASP Chi-restraints excluded: chain 1 residue 347 MET Chi-restraints excluded: chain 1 residue 367 ILE Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 1 residue 387 THR Chi-restraints excluded: chain 1 residue 439 LEU Chi-restraints excluded: chain 1 residue 488 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 1 residue 578 LEU Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 31 LEU Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 225 THR Chi-restraints excluded: chain 2 residue 262 THR Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 311 ASP Chi-restraints excluded: chain 2 residue 352 LEU Chi-restraints excluded: chain 2 residue 384 HIS Chi-restraints excluded: chain 2 residue 435 HIS Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 2 residue 459 THR Chi-restraints excluded: chain 2 residue 533 VAL Chi-restraints excluded: chain 2 residue 544 LEU Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 2 residue 702 ILE Chi-restraints excluded: chain 4 residue 47 ASP Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 173 MET Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 229 LEU Chi-restraints excluded: chain 4 residue 278 MET Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 5 residue 29 VAL Chi-restraints excluded: chain 5 residue 37 VAL Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 142 LEU Chi-restraints excluded: chain 5 residue 151 GLN Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 5 residue 199 VAL Chi-restraints excluded: chain 5 residue 205 GLN Chi-restraints excluded: chain 5 residue 339 VAL Chi-restraints excluded: chain 7 residue 59 LYS Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 208 LEU Chi-restraints excluded: chain 7 residue 266 VAL Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 427 VAL Chi-restraints excluded: chain 7 residue 436 SER Chi-restraints excluded: chain 7 residue 441 LEU Chi-restraints excluded: chain 7 residue 456 LEU Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 571 SER Chi-restraints excluded: chain 7 residue 623 VAL Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 7 residue 709 ILE Chi-restraints excluded: chain 8 residue 48 VAL Chi-restraints excluded: chain 8 residue 135 ARG Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 330 VAL Chi-restraints excluded: chain 8 residue 367 THR Chi-restraints excluded: chain 8 residue 483 ASP Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 69 LEU Chi-restraints excluded: chain 9 residue 104 CYS Chi-restraints excluded: chain 9 residue 111 THR Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 152 ILE Chi-restraints excluded: chain 9 residue 195 THR Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 254 ILE Chi-restraints excluded: chain 9 residue 276 GLN Chi-restraints excluded: chain 9 residue 290 PHE Chi-restraints excluded: chain 9 residue 296 VAL Chi-restraints excluded: chain 9 residue 303 THR Chi-restraints excluded: chain 9 residue 307 ASN Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 382 ASP Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 473 THR Chi-restraints excluded: chain 9 residue 489 VAL Chi-restraints excluded: chain 9 residue 496 SER Chi-restraints excluded: chain 9 residue 501 GLU Chi-restraints excluded: chain 9 residue 551 ASP Chi-restraints excluded: chain 9 residue 706 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 81 optimal weight: 3.9990 chunk 316 optimal weight: 0.9980 chunk 341 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 169 optimal weight: 3.9990 chunk 319 optimal weight: 0.8980 chunk 265 optimal weight: 0.0370 chunk 61 optimal weight: 0.8980 chunk 104 optimal weight: 0.9980 overall best weight: 0.7658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 291 GLN 1 359 HIS ** 2 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 35 GLN 4 319 GLN 7 148 ASN ** 7 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 311 HIS ** 8 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 155 GLN ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.193142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.144614 restraints weight = 40572.251| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 1.86 r_work: 0.3594 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7763 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30791 Z= 0.130 Angle : 0.563 10.426 41671 Z= 0.293 Chirality : 0.043 0.166 4749 Planarity : 0.004 0.055 5343 Dihedral : 4.843 45.746 4111 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.00 % Allowed : 20.13 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.69 (0.14), residues: 3766 helix: 1.47 (0.14), residues: 1314 sheet: -0.70 (0.17), residues: 968 loop : -2.09 (0.15), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 9 483 TYR 0.022 0.001 TYR 2 603 PHE 0.020 0.001 PHE 4 95 TRP 0.014 0.001 TRP 9 237 HIS 0.006 0.001 HIS 7 635 Details of bonding type rmsd covalent geometry : bond 0.00295 (30791) covalent geometry : angle 0.56301 (41671) hydrogen bonds : bond 0.03896 ( 1515) hydrogen bonds : angle 4.57380 ( 4350) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 482 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 382 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.8312 (mt-10) cc_final: 0.8031 (mt-10) REVERT: 1 2 LYS cc_start: 0.4466 (tttt) cc_final: 0.4152 (tttp) REVERT: 1 32 TYR cc_start: 0.5682 (m-80) cc_final: 0.5291 (m-80) REVERT: 1 47 ARG cc_start: 0.6360 (mtm-85) cc_final: 0.5493 (mtp85) REVERT: 1 203 MET cc_start: 0.5692 (mtp) cc_final: 0.5477 (mtm) REVERT: 1 368 ARG cc_start: 0.3673 (ptp-170) cc_final: 0.1953 (ttm110) REVERT: 1 429 ARG cc_start: 0.7427 (tpp-160) cc_final: 0.7161 (tpp80) REVERT: 2 89 TYR cc_start: 0.6955 (p90) cc_final: 0.6613 (p90) REVERT: 2 153 ASP cc_start: 0.8031 (t0) cc_final: 0.7804 (t0) REVERT: 2 458 LYS cc_start: 0.8152 (OUTLIER) cc_final: 0.7815 (mttm) REVERT: 2 498 TYR cc_start: 0.7967 (p90) cc_final: 0.7738 (p90) REVERT: 2 528 ASN cc_start: 0.6239 (m110) cc_final: 0.5712 (t0) REVERT: 4 52 LYS cc_start: 0.6211 (mtpp) cc_final: 0.5376 (tptt) REVERT: 4 116 LYS cc_start: 0.8150 (mppt) cc_final: 0.7874 (mptt) REVERT: 4 176 LYS cc_start: 0.7229 (ttmm) cc_final: 0.6871 (tttt) REVERT: 4 369 LYS cc_start: 0.8397 (mptt) cc_final: 0.7975 (mptt) REVERT: 4 423 LYS cc_start: 0.7323 (mmtt) cc_final: 0.6407 (mttt) REVERT: 5 39 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.6297 (t70) REVERT: 5 57 ILE cc_start: 0.8706 (OUTLIER) cc_final: 0.8177 (mt) REVERT: 5 88 LEU cc_start: 0.4684 (OUTLIER) cc_final: 0.4267 (pt) REVERT: 5 260 ASN cc_start: 0.6767 (t0) cc_final: 0.6420 (t0) REVERT: 7 71 LEU cc_start: 0.3657 (OUTLIER) cc_final: 0.3414 (pp) REVERT: 7 112 LYS cc_start: 0.7755 (mtmm) cc_final: 0.7210 (mppt) REVERT: 7 215 LYS cc_start: 0.6425 (mtmt) cc_final: 0.5971 (tttt) REVERT: 7 287 GLU cc_start: 0.6590 (mt-10) cc_final: 0.5967 (tt0) REVERT: 7 438 ASP cc_start: 0.5738 (t0) cc_final: 0.5490 (t0) REVERT: 7 546 GLN cc_start: 0.6731 (tt0) cc_final: 0.6225 (tp40) REVERT: 7 558 TYR cc_start: 0.6839 (p90) cc_final: 0.5787 (p90) REVERT: 7 706 ASN cc_start: 0.6873 (m-40) cc_final: 0.6037 (t0) REVERT: 8 26 MET cc_start: 0.7013 (ptm) cc_final: 0.6808 (ptt) REVERT: 8 135 ARG cc_start: 0.5373 (OUTLIER) cc_final: 0.5159 (ttp-110) REVERT: 8 292 ASN cc_start: 0.7999 (t0) cc_final: 0.7510 (t0) REVERT: 9 8 ASP cc_start: 0.7999 (t0) cc_final: 0.7697 (t0) REVERT: 9 381 LEU cc_start: 0.7652 (OUTLIER) cc_final: 0.7346 (mt) REVERT: 9 542 LYS cc_start: 0.8166 (mmmt) cc_final: 0.7528 (tptt) REVERT: 9 553 ASN cc_start: 0.7945 (p0) cc_final: 0.6581 (t0) REVERT: 9 620 LEU cc_start: 0.8599 (mt) cc_final: 0.8342 (mt) REVERT: 9 704 LYS cc_start: 0.8418 (mmmt) cc_final: 0.8210 (mmtm) outliers start: 100 outliers final: 69 residues processed: 467 average time/residue: 0.1794 time to fit residues: 136.4087 Evaluate side-chains 431 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 355 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 216 VAL Chi-restraints excluded: chain 1 residue 232 ASP Chi-restraints excluded: chain 1 residue 309 ASP Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 1 residue 439 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 1 residue 578 LEU Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 225 THR Chi-restraints excluded: chain 2 residue 262 THR Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 352 LEU Chi-restraints excluded: chain 2 residue 435 HIS Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 2 residue 458 LYS Chi-restraints excluded: chain 2 residue 459 THR Chi-restraints excluded: chain 2 residue 533 VAL Chi-restraints excluded: chain 4 residue 47 ASP Chi-restraints excluded: chain 4 residue 164 LEU Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 229 LEU Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 5 residue 29 VAL Chi-restraints excluded: chain 5 residue 39 ASP Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 164 ILE Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 5 residue 201 ILE Chi-restraints excluded: chain 5 residue 224 SER Chi-restraints excluded: chain 5 residue 327 LEU Chi-restraints excluded: chain 7 residue 71 LEU Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 127 TYR Chi-restraints excluded: chain 7 residue 180 VAL Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 208 LEU Chi-restraints excluded: chain 7 residue 266 VAL Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 427 VAL Chi-restraints excluded: chain 7 residue 436 SER Chi-restraints excluded: chain 7 residue 441 LEU Chi-restraints excluded: chain 7 residue 456 LEU Chi-restraints excluded: chain 7 residue 462 GLU Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 8 residue 135 ARG Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 367 THR Chi-restraints excluded: chain 8 residue 375 LEU Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 111 THR Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 157 VAL Chi-restraints excluded: chain 9 residue 195 THR Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 254 ILE Chi-restraints excluded: chain 9 residue 276 GLN Chi-restraints excluded: chain 9 residue 290 PHE Chi-restraints excluded: chain 9 residue 296 VAL Chi-restraints excluded: chain 9 residue 307 ASN Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 381 LEU Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 496 SER Chi-restraints excluded: chain 9 residue 501 GLU Chi-restraints excluded: chain 9 residue 551 ASP Chi-restraints excluded: chain 9 residue 706 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 350 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 252 optimal weight: 0.9980 chunk 369 optimal weight: 1.9990 chunk 111 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 122 optimal weight: 0.0370 chunk 335 optimal weight: 4.9990 chunk 177 optimal weight: 0.9980 chunk 375 optimal weight: 1.9990 chunk 212 optimal weight: 9.9990 overall best weight: 0.9260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 557 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 319 GLN ** 5 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 308 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.192917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.144348 restraints weight = 40529.475| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.75 r_work: 0.3593 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3475 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 30791 Z= 0.140 Angle : 0.572 9.595 41671 Z= 0.295 Chirality : 0.043 0.233 4749 Planarity : 0.004 0.054 5343 Dihedral : 4.694 45.967 4108 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.94 % Allowed : 20.43 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.57 (0.14), residues: 3766 helix: 1.57 (0.14), residues: 1320 sheet: -0.61 (0.17), residues: 974 loop : -2.05 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 7 68 TYR 0.029 0.001 TYR 9 623 PHE 0.019 0.001 PHE 4 95 TRP 0.013 0.001 TRP 9 237 HIS 0.011 0.001 HIS 5 128 Details of bonding type rmsd covalent geometry : bond 0.00325 (30791) covalent geometry : angle 0.57174 (41671) hydrogen bonds : bond 0.03914 ( 1515) hydrogen bonds : angle 4.52242 ( 4350) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 365 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.8329 (mt-10) cc_final: 0.7962 (mt-10) REVERT: 1 2 LYS cc_start: 0.4518 (tttt) cc_final: 0.4200 (tttp) REVERT: 1 32 TYR cc_start: 0.5771 (m-80) cc_final: 0.5378 (m-80) REVERT: 1 203 MET cc_start: 0.5748 (mtp) cc_final: 0.5543 (mtm) REVERT: 1 354 GLU cc_start: 0.5117 (tm-30) cc_final: 0.4629 (tm-30) REVERT: 1 368 ARG cc_start: 0.3715 (ptp-170) cc_final: 0.1928 (ttm110) REVERT: 1 429 ARG cc_start: 0.7430 (tpp-160) cc_final: 0.7161 (tpp80) REVERT: 2 89 TYR cc_start: 0.7040 (p90) cc_final: 0.6656 (p90) REVERT: 2 153 ASP cc_start: 0.8028 (t0) cc_final: 0.7805 (t0) REVERT: 2 458 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7871 (mttm) REVERT: 2 528 ASN cc_start: 0.6324 (m110) cc_final: 0.5695 (t0) REVERT: 4 52 LYS cc_start: 0.6183 (mtpp) cc_final: 0.5345 (tptt) REVERT: 4 99 GLN cc_start: 0.7239 (pt0) cc_final: 0.6994 (pp30) REVERT: 4 116 LYS cc_start: 0.8210 (mppt) cc_final: 0.7951 (mptt) REVERT: 4 176 LYS cc_start: 0.7138 (ttmm) cc_final: 0.6786 (tttt) REVERT: 4 369 LYS cc_start: 0.8399 (mptt) cc_final: 0.8010 (mptt) REVERT: 4 423 LYS cc_start: 0.7384 (mmtt) cc_final: 0.6576 (mttt) REVERT: 5 39 ASP cc_start: 0.6573 (OUTLIER) cc_final: 0.6252 (t70) REVERT: 5 57 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8124 (mt) REVERT: 5 88 LEU cc_start: 0.4757 (OUTLIER) cc_final: 0.4357 (pt) REVERT: 5 260 ASN cc_start: 0.6667 (t0) cc_final: 0.6314 (t0) REVERT: 7 71 LEU cc_start: 0.3610 (OUTLIER) cc_final: 0.3390 (pp) REVERT: 7 215 LYS cc_start: 0.6398 (mtmt) cc_final: 0.5946 (tttt) REVERT: 7 287 GLU cc_start: 0.6643 (mt-10) cc_final: 0.6016 (tt0) REVERT: 7 438 ASP cc_start: 0.5789 (t0) cc_final: 0.5535 (t0) REVERT: 7 546 GLN cc_start: 0.6779 (tt0) cc_final: 0.6319 (tp40) REVERT: 7 558 TYR cc_start: 0.6856 (p90) cc_final: 0.5871 (p90) REVERT: 7 706 ASN cc_start: 0.6849 (m-40) cc_final: 0.6022 (t0) REVERT: 8 26 MET cc_start: 0.7015 (ptm) cc_final: 0.6811 (ptt) REVERT: 8 135 ARG cc_start: 0.5461 (OUTLIER) cc_final: 0.5249 (ttp-110) REVERT: 8 292 ASN cc_start: 0.7948 (t0) cc_final: 0.7458 (t0) REVERT: 9 381 LEU cc_start: 0.7684 (OUTLIER) cc_final: 0.7388 (mt) REVERT: 9 542 LYS cc_start: 0.8140 (mmmt) cc_final: 0.7524 (tptt) REVERT: 9 553 ASN cc_start: 0.7922 (p0) cc_final: 0.6594 (t0) REVERT: 9 620 LEU cc_start: 0.8588 (mt) cc_final: 0.8337 (mt) REVERT: 9 657 ILE cc_start: 0.8780 (mm) cc_final: 0.8560 (mm) REVERT: 9 704 LYS cc_start: 0.8428 (mmmt) cc_final: 0.8224 (mmtm) outliers start: 98 outliers final: 73 residues processed: 446 average time/residue: 0.1787 time to fit residues: 130.7219 Evaluate side-chains 438 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 358 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 1 residue 216 VAL Chi-restraints excluded: chain 1 residue 232 ASP Chi-restraints excluded: chain 1 residue 309 ASP Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 1 residue 439 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 161 ASP Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 225 THR Chi-restraints excluded: chain 2 residue 262 THR Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 435 HIS Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 2 residue 458 LYS Chi-restraints excluded: chain 2 residue 459 THR Chi-restraints excluded: chain 2 residue 533 VAL Chi-restraints excluded: chain 2 residue 544 LEU Chi-restraints excluded: chain 4 residue 47 ASP Chi-restraints excluded: chain 4 residue 164 LEU Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 177 ILE Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 229 LEU Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 5 residue 29 VAL Chi-restraints excluded: chain 5 residue 39 ASP Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 164 ILE Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 5 residue 201 ILE Chi-restraints excluded: chain 7 residue 71 LEU Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 127 TYR Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 208 LEU Chi-restraints excluded: chain 7 residue 266 VAL Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 413 VAL Chi-restraints excluded: chain 7 residue 427 VAL Chi-restraints excluded: chain 7 residue 441 LEU Chi-restraints excluded: chain 7 residue 456 LEU Chi-restraints excluded: chain 7 residue 511 LEU Chi-restraints excluded: chain 7 residue 542 THR Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 8 residue 135 ARG Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 367 THR Chi-restraints excluded: chain 8 residue 375 LEU Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 111 THR Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 157 VAL Chi-restraints excluded: chain 9 residue 195 THR Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 254 ILE Chi-restraints excluded: chain 9 residue 276 GLN Chi-restraints excluded: chain 9 residue 290 PHE Chi-restraints excluded: chain 9 residue 296 VAL Chi-restraints excluded: chain 9 residue 307 ASN Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 381 LEU Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 489 VAL Chi-restraints excluded: chain 9 residue 496 SER Chi-restraints excluded: chain 9 residue 501 GLU Chi-restraints excluded: chain 9 residue 551 ASP Chi-restraints excluded: chain 9 residue 692 LEU Chi-restraints excluded: chain 9 residue 706 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 369 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 246 optimal weight: 8.9990 chunk 342 optimal weight: 0.6980 chunk 131 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 371 optimal weight: 0.9980 chunk 372 optimal weight: 0.9980 chunk 358 optimal weight: 0.9990 chunk 170 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 359 HIS 2 557 ASN 2 656 ASN 4 35 GLN 4 319 GLN ** 5 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.193172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.144063 restraints weight = 40441.061| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.82 r_work: 0.3599 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7768 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 30791 Z= 0.139 Angle : 0.574 10.438 41671 Z= 0.296 Chirality : 0.043 0.223 4749 Planarity : 0.004 0.054 5343 Dihedral : 4.651 46.333 4108 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.91 % Allowed : 20.70 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3766 helix: 1.65 (0.14), residues: 1318 sheet: -0.58 (0.17), residues: 981 loop : -1.99 (0.15), residues: 1467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 9 824 TYR 0.028 0.001 TYR 9 623 PHE 0.020 0.001 PHE 9 476 TRP 0.013 0.001 TRP 9 237 HIS 0.011 0.001 HIS 5 128 Details of bonding type rmsd covalent geometry : bond 0.00321 (30791) covalent geometry : angle 0.57352 (41671) hydrogen bonds : bond 0.03860 ( 1515) hydrogen bonds : angle 4.46888 ( 4350) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 467 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 370 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.8311 (mt-10) cc_final: 0.8047 (mt-10) REVERT: 1 2 LYS cc_start: 0.4489 (tttt) cc_final: 0.4173 (tttp) REVERT: 1 32 TYR cc_start: 0.5841 (m-80) cc_final: 0.5577 (m-80) REVERT: 1 203 MET cc_start: 0.5679 (mtp) cc_final: 0.5479 (mtm) REVERT: 1 368 ARG cc_start: 0.3708 (ptp-170) cc_final: 0.1579 (ttp-170) REVERT: 1 429 ARG cc_start: 0.7432 (tpp-160) cc_final: 0.7165 (tpp80) REVERT: 2 89 TYR cc_start: 0.7003 (p90) cc_final: 0.6634 (p90) REVERT: 2 153 ASP cc_start: 0.8016 (t0) cc_final: 0.7791 (t0) REVERT: 2 212 MET cc_start: 0.6600 (mpp) cc_final: 0.5936 (mtm) REVERT: 2 458 LYS cc_start: 0.8170 (OUTLIER) cc_final: 0.7784 (mttm) REVERT: 2 498 TYR cc_start: 0.8109 (p90) cc_final: 0.7734 (p90) REVERT: 2 500 ASN cc_start: 0.7169 (m-40) cc_final: 0.6870 (m110) REVERT: 2 528 ASN cc_start: 0.6318 (m110) cc_final: 0.5677 (t0) REVERT: 2 538 LEU cc_start: 0.7035 (mt) cc_final: 0.6820 (mt) REVERT: 2 713 ILE cc_start: 0.6424 (tp) cc_final: 0.5816 (tp) REVERT: 4 52 LYS cc_start: 0.6106 (mtpp) cc_final: 0.5268 (tptt) REVERT: 4 116 LYS cc_start: 0.8164 (mppt) cc_final: 0.7893 (mptt) REVERT: 4 176 LYS cc_start: 0.7123 (ttmm) cc_final: 0.6781 (tttt) REVERT: 4 369 LYS cc_start: 0.8431 (mptt) cc_final: 0.8021 (mptt) REVERT: 4 423 LYS cc_start: 0.7371 (mmtt) cc_final: 0.6634 (mttt) REVERT: 5 39 ASP cc_start: 0.6472 (OUTLIER) cc_final: 0.6177 (t70) REVERT: 5 57 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8122 (mt) REVERT: 5 88 LEU cc_start: 0.4618 (OUTLIER) cc_final: 0.4211 (pt) REVERT: 5 153 ARG cc_start: 0.7867 (mtp180) cc_final: 0.7568 (mtt90) REVERT: 5 260 ASN cc_start: 0.6653 (t0) cc_final: 0.6287 (t0) REVERT: 7 71 LEU cc_start: 0.3452 (OUTLIER) cc_final: 0.3249 (pp) REVERT: 7 215 LYS cc_start: 0.6420 (mtmt) cc_final: 0.5942 (tttt) REVERT: 7 287 GLU cc_start: 0.6700 (mt-10) cc_final: 0.6125 (tt0) REVERT: 7 438 ASP cc_start: 0.5767 (t0) cc_final: 0.5505 (t0) REVERT: 7 546 GLN cc_start: 0.6683 (tt0) cc_final: 0.6208 (tp40) REVERT: 7 558 TYR cc_start: 0.6900 (p90) cc_final: 0.5912 (p90) REVERT: 7 706 ASN cc_start: 0.6831 (m-40) cc_final: 0.5907 (t0) REVERT: 8 26 MET cc_start: 0.7047 (ptm) cc_final: 0.6818 (ptt) REVERT: 8 123 GLN cc_start: 0.8508 (tt0) cc_final: 0.8094 (tt0) REVERT: 8 135 ARG cc_start: 0.5401 (OUTLIER) cc_final: 0.5196 (ttp-110) REVERT: 8 292 ASN cc_start: 0.7988 (t0) cc_final: 0.7461 (t0) REVERT: 9 8 ASP cc_start: 0.8031 (t0) cc_final: 0.7738 (t0) REVERT: 9 309 ASN cc_start: 0.7477 (t0) cc_final: 0.7234 (t0) REVERT: 9 381 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7438 (mt) REVERT: 9 481 MET cc_start: 0.7174 (tpp) cc_final: 0.6857 (tpp) REVERT: 9 542 LYS cc_start: 0.8180 (mmmt) cc_final: 0.7518 (tptt) REVERT: 9 553 ASN cc_start: 0.7949 (p0) cc_final: 0.6618 (t0) REVERT: 9 620 LEU cc_start: 0.8566 (mt) cc_final: 0.8321 (mt) REVERT: 9 657 ILE cc_start: 0.8763 (mm) cc_final: 0.8542 (mm) REVERT: 9 704 LYS cc_start: 0.8410 (mmmt) cc_final: 0.8199 (mmtm) outliers start: 97 outliers final: 81 residues processed: 450 average time/residue: 0.1770 time to fit residues: 130.3162 Evaluate side-chains 446 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 358 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 VAL Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 1 residue 216 VAL Chi-restraints excluded: chain 1 residue 309 ASP Chi-restraints excluded: chain 1 residue 359 HIS Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 1 residue 439 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 161 ASP Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 225 THR Chi-restraints excluded: chain 2 residue 262 THR Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 352 LEU Chi-restraints excluded: chain 2 residue 435 HIS Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 2 residue 458 LYS Chi-restraints excluded: chain 2 residue 459 THR Chi-restraints excluded: chain 2 residue 533 VAL Chi-restraints excluded: chain 2 residue 544 LEU Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 4 residue 47 ASP Chi-restraints excluded: chain 4 residue 79 LEU Chi-restraints excluded: chain 4 residue 164 LEU Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 177 ILE Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 229 LEU Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 5 residue 29 VAL Chi-restraints excluded: chain 5 residue 39 ASP Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 81 THR Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 164 ILE Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 5 residue 201 ILE Chi-restraints excluded: chain 5 residue 243 LEU Chi-restraints excluded: chain 7 residue 71 LEU Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 127 TYR Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 208 LEU Chi-restraints excluded: chain 7 residue 266 VAL Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 413 VAL Chi-restraints excluded: chain 7 residue 427 VAL Chi-restraints excluded: chain 7 residue 436 SER Chi-restraints excluded: chain 7 residue 441 LEU Chi-restraints excluded: chain 7 residue 456 LEU Chi-restraints excluded: chain 7 residue 542 THR Chi-restraints excluded: chain 7 residue 623 VAL Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 8 residue 135 ARG Chi-restraints excluded: chain 8 residue 161 ILE Chi-restraints excluded: chain 8 residue 367 THR Chi-restraints excluded: chain 8 residue 375 LEU Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 111 THR Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 157 VAL Chi-restraints excluded: chain 9 residue 195 THR Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 254 ILE Chi-restraints excluded: chain 9 residue 276 GLN Chi-restraints excluded: chain 9 residue 290 PHE Chi-restraints excluded: chain 9 residue 296 VAL Chi-restraints excluded: chain 9 residue 307 ASN Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 381 LEU Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 489 VAL Chi-restraints excluded: chain 9 residue 496 SER Chi-restraints excluded: chain 9 residue 501 GLU Chi-restraints excluded: chain 9 residue 551 ASP Chi-restraints excluded: chain 9 residue 692 LEU Chi-restraints excluded: chain 9 residue 706 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 201 optimal weight: 0.0870 chunk 316 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 31 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 160 optimal weight: 4.9990 chunk 315 optimal weight: 0.6980 chunk 180 optimal weight: 4.9990 chunk 353 optimal weight: 6.9990 chunk 141 optimal weight: 3.9990 chunk 354 optimal weight: 8.9990 overall best weight: 2.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 359 HIS ** 2 152 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 319 GLN ** 5 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 547 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 311 HIS ** 8 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 155 GLN ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 651 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.188882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.140050 restraints weight = 40385.002| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.77 r_work: 0.3531 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3412 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 30791 Z= 0.276 Angle : 0.693 10.968 41671 Z= 0.357 Chirality : 0.047 0.219 4749 Planarity : 0.005 0.053 5343 Dihedral : 5.077 46.845 4108 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.13 % Favored : 93.84 % Rotamer: Outliers : 3.00 % Allowed : 20.49 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.14), residues: 3766 helix: 1.12 (0.14), residues: 1320 sheet: -0.74 (0.17), residues: 986 loop : -2.07 (0.15), residues: 1460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG 9 656 TYR 0.028 0.002 TYR 9 623 PHE 0.026 0.002 PHE 9 290 TRP 0.017 0.002 TRP 9 9 HIS 0.016 0.002 HIS 1 359 Details of bonding type rmsd covalent geometry : bond 0.00663 (30791) covalent geometry : angle 0.69316 (41671) hydrogen bonds : bond 0.04679 ( 1515) hydrogen bonds : angle 4.81542 ( 4350) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7532 Ramachandran restraints generated. 3766 Oldfield, 0 Emsley, 3766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 364 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 42 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8046 (mt-10) REVERT: 1 2 LYS cc_start: 0.4444 (tttt) cc_final: 0.4134 (tttp) REVERT: 1 32 TYR cc_start: 0.5826 (m-80) cc_final: 0.5506 (m-80) REVERT: 1 203 MET cc_start: 0.5795 (mtp) cc_final: 0.5569 (mtm) REVERT: 1 368 ARG cc_start: 0.3645 (ptp-170) cc_final: 0.1719 (ttm110) REVERT: 1 429 ARG cc_start: 0.7467 (tpp-160) cc_final: 0.7178 (tpp80) REVERT: 2 458 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7843 (mttm) REVERT: 2 498 TYR cc_start: 0.8158 (p90) cc_final: 0.7937 (p90) REVERT: 2 528 ASN cc_start: 0.6508 (m110) cc_final: 0.5877 (t0) REVERT: 2 548 ILE cc_start: 0.7525 (mp) cc_final: 0.7266 (mm) REVERT: 2 713 ILE cc_start: 0.6514 (tp) cc_final: 0.5928 (tp) REVERT: 4 52 LYS cc_start: 0.6214 (mtpp) cc_final: 0.5417 (tptt) REVERT: 4 116 LYS cc_start: 0.8508 (mppt) cc_final: 0.8176 (mptt) REVERT: 4 176 LYS cc_start: 0.7223 (ttmm) cc_final: 0.6873 (tttt) REVERT: 4 369 LYS cc_start: 0.8491 (mptt) cc_final: 0.7993 (mptt) REVERT: 4 423 LYS cc_start: 0.7472 (mmtt) cc_final: 0.6482 (mttt) REVERT: 5 57 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8168 (mt) REVERT: 5 88 LEU cc_start: 0.4264 (OUTLIER) cc_final: 0.3899 (pt) REVERT: 5 260 ASN cc_start: 0.6651 (t0) cc_final: 0.6276 (t0) REVERT: 7 71 LEU cc_start: 0.3827 (OUTLIER) cc_final: 0.3364 (pp) REVERT: 7 215 LYS cc_start: 0.6406 (mtmt) cc_final: 0.5890 (tttt) REVERT: 7 287 GLU cc_start: 0.6762 (mt-10) cc_final: 0.6212 (tt0) REVERT: 7 438 ASP cc_start: 0.6095 (t0) cc_final: 0.5768 (t0) REVERT: 7 504 ARG cc_start: 0.7306 (mmp-170) cc_final: 0.7024 (mmm160) REVERT: 7 558 TYR cc_start: 0.6912 (p90) cc_final: 0.5739 (p90) REVERT: 8 123 GLN cc_start: 0.8636 (tt0) cc_final: 0.8123 (tt0) REVERT: 8 135 ARG cc_start: 0.5610 (OUTLIER) cc_final: 0.5380 (ttp-110) REVERT: 8 292 ASN cc_start: 0.8088 (t0) cc_final: 0.7632 (t0) REVERT: 8 293 ASN cc_start: 0.7956 (t0) cc_final: 0.7749 (t0) REVERT: 8 306 LYS cc_start: 0.8491 (mtmm) cc_final: 0.8247 (mttp) REVERT: 9 381 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7359 (mt) REVERT: 9 462 GLN cc_start: 0.7574 (OUTLIER) cc_final: 0.7131 (mm-40) REVERT: 9 542 LYS cc_start: 0.8248 (mmmt) cc_final: 0.7544 (tptt) REVERT: 9 553 ASN cc_start: 0.7998 (p0) cc_final: 0.6725 (t0) REVERT: 9 620 LEU cc_start: 0.8622 (mt) cc_final: 0.8362 (mt) REVERT: 9 704 LYS cc_start: 0.8462 (mmmt) cc_final: 0.8231 (mmtm) outliers start: 100 outliers final: 79 residues processed: 452 average time/residue: 0.1819 time to fit residues: 133.6615 Evaluate side-chains 439 residues out of total 3333 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 353 time to evaluate : 0.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 20 VAL Chi-restraints excluded: chain 0 residue 23 ILE Chi-restraints excluded: chain 1 residue 216 VAL Chi-restraints excluded: chain 1 residue 309 ASP Chi-restraints excluded: chain 1 residue 367 ILE Chi-restraints excluded: chain 1 residue 373 VAL Chi-restraints excluded: chain 1 residue 439 LEU Chi-restraints excluded: chain 1 residue 502 THR Chi-restraints excluded: chain 2 residue 19 VAL Chi-restraints excluded: chain 2 residue 27 THR Chi-restraints excluded: chain 2 residue 109 SER Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 138 ILE Chi-restraints excluded: chain 2 residue 161 ASP Chi-restraints excluded: chain 2 residue 183 SER Chi-restraints excluded: chain 2 residue 225 THR Chi-restraints excluded: chain 2 residue 262 THR Chi-restraints excluded: chain 2 residue 308 CYS Chi-restraints excluded: chain 2 residue 352 LEU Chi-restraints excluded: chain 2 residue 435 HIS Chi-restraints excluded: chain 2 residue 443 ILE Chi-restraints excluded: chain 2 residue 458 LYS Chi-restraints excluded: chain 2 residue 459 THR Chi-restraints excluded: chain 2 residue 533 VAL Chi-restraints excluded: chain 2 residue 544 LEU Chi-restraints excluded: chain 2 residue 620 LEU Chi-restraints excluded: chain 4 residue 47 ASP Chi-restraints excluded: chain 4 residue 79 LEU Chi-restraints excluded: chain 4 residue 164 LEU Chi-restraints excluded: chain 4 residue 167 HIS Chi-restraints excluded: chain 4 residue 177 ILE Chi-restraints excluded: chain 4 residue 185 ASP Chi-restraints excluded: chain 4 residue 197 PHE Chi-restraints excluded: chain 4 residue 229 LEU Chi-restraints excluded: chain 4 residue 290 ILE Chi-restraints excluded: chain 5 residue 29 VAL Chi-restraints excluded: chain 5 residue 40 THR Chi-restraints excluded: chain 5 residue 57 ILE Chi-restraints excluded: chain 5 residue 81 THR Chi-restraints excluded: chain 5 residue 88 LEU Chi-restraints excluded: chain 5 residue 99 THR Chi-restraints excluded: chain 5 residue 160 VAL Chi-restraints excluded: chain 5 residue 164 ILE Chi-restraints excluded: chain 5 residue 188 VAL Chi-restraints excluded: chain 7 residue 71 LEU Chi-restraints excluded: chain 7 residue 82 ILE Chi-restraints excluded: chain 7 residue 203 SER Chi-restraints excluded: chain 7 residue 208 LEU Chi-restraints excluded: chain 7 residue 266 VAL Chi-restraints excluded: chain 7 residue 340 ASN Chi-restraints excluded: chain 7 residue 381 VAL Chi-restraints excluded: chain 7 residue 413 VAL Chi-restraints excluded: chain 7 residue 427 VAL Chi-restraints excluded: chain 7 residue 436 SER Chi-restraints excluded: chain 7 residue 441 LEU Chi-restraints excluded: chain 7 residue 456 LEU Chi-restraints excluded: chain 7 residue 542 THR Chi-restraints excluded: chain 7 residue 623 VAL Chi-restraints excluded: chain 7 residue 673 MET Chi-restraints excluded: chain 8 residue 135 ARG Chi-restraints excluded: chain 8 residue 330 VAL Chi-restraints excluded: chain 8 residue 367 THR Chi-restraints excluded: chain 8 residue 375 LEU Chi-restraints excluded: chain 9 residue 9 TRP Chi-restraints excluded: chain 9 residue 104 CYS Chi-restraints excluded: chain 9 residue 111 THR Chi-restraints excluded: chain 9 residue 134 THR Chi-restraints excluded: chain 9 residue 151 LEU Chi-restraints excluded: chain 9 residue 195 THR Chi-restraints excluded: chain 9 residue 238 THR Chi-restraints excluded: chain 9 residue 254 ILE Chi-restraints excluded: chain 9 residue 276 GLN Chi-restraints excluded: chain 9 residue 290 PHE Chi-restraints excluded: chain 9 residue 296 VAL Chi-restraints excluded: chain 9 residue 307 ASN Chi-restraints excluded: chain 9 residue 331 VAL Chi-restraints excluded: chain 9 residue 381 LEU Chi-restraints excluded: chain 9 residue 395 VAL Chi-restraints excluded: chain 9 residue 461 VAL Chi-restraints excluded: chain 9 residue 462 GLN Chi-restraints excluded: chain 9 residue 473 THR Chi-restraints excluded: chain 9 residue 489 VAL Chi-restraints excluded: chain 9 residue 496 SER Chi-restraints excluded: chain 9 residue 501 GLU Chi-restraints excluded: chain 9 residue 551 ASP Chi-restraints excluded: chain 9 residue 706 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 378 random chunks: chunk 129 optimal weight: 0.6980 chunk 143 optimal weight: 0.8980 chunk 115 optimal weight: 5.9990 chunk 372 optimal weight: 0.5980 chunk 301 optimal weight: 0.7980 chunk 241 optimal weight: 6.9990 chunk 344 optimal weight: 0.0970 chunk 1 optimal weight: 1.9990 chunk 365 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 1 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 656 ASN 2 664 ASN ** 4 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 249 HIS 4 319 GLN ** 5 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 410 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 311 HIS ** 8 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 484 HIS 9 155 GLN ** 9 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.193473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.144684 restraints weight = 40654.471| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.81 r_work: 0.3612 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.103 30791 Z= 0.125 Angle : 0.575 10.807 41671 Z= 0.298 Chirality : 0.043 0.211 4749 Planarity : 0.004 0.054 5343 Dihedral : 4.702 46.822 4108 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.62 % Favored : 95.35 % Rotamer: Outliers : 2.70 % Allowed : 20.91 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.14), residues: 3766 helix: 1.60 (0.14), residues: 1319 sheet: -0.59 (0.17), residues: 975 loop : -1.94 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG 5 56 TYR 0.032 0.001 TYR 2 603 PHE 0.019 0.001 PHE 9 476 TRP 0.014 0.001 TRP 9 237 HIS 0.006 0.001 HIS 5 128 Details of bonding type rmsd covalent geometry : bond 0.00285 (30791) covalent geometry : angle 0.57508 (41671) hydrogen bonds : bond 0.03829 ( 1515) hydrogen bonds : angle 4.48355 ( 4350) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10679.52 seconds wall clock time: 182 minutes 40.12 seconds (10960.12 seconds total)