Starting phenix.real_space_refine on Mon May 4 15:21:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lpw_63277/05_2026/9lpw_63277.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lpw_63277/05_2026/9lpw_63277.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lpw_63277/05_2026/9lpw_63277.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lpw_63277/05_2026/9lpw_63277.map" model { file = "/net/cci-nas-00/data/ceres_data/9lpw_63277/05_2026/9lpw_63277.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lpw_63277/05_2026/9lpw_63277.cif" } resolution = 2.78 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.056 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: 4 Type Number sf(0) Gaussians S 88 5.16 5 C 13852 2.51 5 N 3701 2.21 5 O 4042 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21683 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 6675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 837, 6675 Classifications: {'peptide': 837} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 803} Chain breaks: 1 Chain: "D" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4170 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 494} Chain: "A" Number of atoms: 6668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 836, 6668 Classifications: {'peptide': 836} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 33, 'TRANS': 802} Chain breaks: 1 Chain: "C" Number of atoms: 4170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 4170 Classifications: {'peptide': 524} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 29, 'TRANS': 494} Time building chain proxies: 5.31, per 1000 atoms: 0.24 Number of scatterers: 21683 At special positions: 0 Unit cell: (122.64, 136.08, 184.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 88 16.00 O 4042 8.00 N 3701 7.00 C 13852 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 356 " - pdb=" SG CYS B 396 " distance=2.93 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: 2.03 Conformation dependent library (CDL) restraints added in 1.1 seconds 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5074 Finding SS restraints... Secondary structure from input PDB file: 147 helices and 14 sheets defined 56.5% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'B' and resid 77 through 92 Processing helix chain 'B' and resid 101 through 132 Processing helix chain 'B' and resid 148 through 156 Processing helix chain 'B' and resid 158 through 170 Processing helix chain 'B' and resid 172 through 178 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 304 through 308 Processing helix chain 'B' and resid 309 through 315 Processing helix chain 'B' and resid 317 through 322 Processing helix chain 'B' and resid 322 through 330 Processing helix chain 'B' and resid 331 through 333 No H-bonds generated for 'chain 'B' and resid 331 through 333' Processing helix chain 'B' and resid 341 through 372 removed outlier: 3.615A pdb=" N GLY B 372 " --> pdb=" O GLU B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 376 through 382 removed outlier: 3.636A pdb=" N ASP B 379 " --> pdb=" O SER B 376 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N PHE B 380 " --> pdb=" O TRP B 377 " (cutoff:3.500A) Proline residue: B 381 - end of helix No H-bonds generated for 'chain 'B' and resid 376 through 382' Processing helix chain 'B' and resid 391 through 394 Processing helix chain 'B' and resid 395 through 407 Processing helix chain 'B' and resid 411 through 422 Processing helix chain 'B' and resid 431 through 435 removed outlier: 3.794A pdb=" N LEU B 435 " --> pdb=" O PRO B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 447 Processing helix chain 'B' and resid 447 through 470 Processing helix chain 'B' and resid 474 through 484 Processing helix chain 'B' and resid 493 through 498 removed outlier: 3.538A pdb=" N LYS B 498 " --> pdb=" O ASP B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.994A pdb=" N GLU B 505 " --> pdb=" O LYS B 502 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 587 Processing helix chain 'B' and resid 595 through 605 Processing helix chain 'B' and resid 607 through 614 Processing helix chain 'B' and resid 626 through 631 removed outlier: 3.564A pdb=" N TRP B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 635 through 647 Processing helix chain 'B' and resid 649 through 653 Processing helix chain 'B' and resid 654 through 665 removed outlier: 4.205A pdb=" N LYS B 663 " --> pdb=" O GLU B 660 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA B 665 " --> pdb=" O LYS B 662 " (cutoff:3.500A) Processing helix chain 'B' and resid 667 through 694 Processing helix chain 'B' and resid 715 through 733 removed outlier: 3.769A pdb=" N ASN B 719 " --> pdb=" O ARG B 715 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 742 removed outlier: 3.928A pdb=" N ASN B 740 " --> pdb=" O LYS B 736 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 776 removed outlier: 4.001A pdb=" N HIS B 776 " --> pdb=" O ALA B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 782 No H-bonds generated for 'chain 'B' and resid 780 through 782' Processing helix chain 'B' and resid 793 through 801 Processing helix chain 'B' and resid 802 through 804 No H-bonds generated for 'chain 'B' and resid 802 through 804' Processing helix chain 'B' and resid 820 through 828 Processing helix chain 'B' and resid 839 through 848 Processing helix chain 'B' and resid 858 through 871 removed outlier: 3.825A pdb=" N ALA B 863 " --> pdb=" O ALA B 859 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN B 871 " --> pdb=" O LYS B 867 " (cutoff:3.500A) Processing helix chain 'B' and resid 877 through 889 Processing helix chain 'B' and resid 897 through 903 removed outlier: 3.518A pdb=" N SER B 903 " --> pdb=" O ASP B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 921 through 937 Processing helix chain 'B' and resid 938 through 952 Processing helix chain 'B' and resid 953 through 956 Processing helix chain 'B' and resid 957 through 969 removed outlier: 4.109A pdb=" N THR B 961 " --> pdb=" O ASN B 957 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.541A pdb=" N MET D 86 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET D 87 " --> pdb=" O ASP D 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 83 through 87' Processing helix chain 'D' and resid 103 through 107 Processing helix chain 'D' and resid 117 through 130 Processing helix chain 'D' and resid 163 through 167 Processing helix chain 'D' and resid 168 through 175 Processing helix chain 'D' and resid 179 through 183 removed outlier: 3.941A pdb=" N LEU D 183 " --> pdb=" O GLU D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 214 removed outlier: 3.861A pdb=" N ALA D 198 " --> pdb=" O PHE D 194 " (cutoff:3.500A) Proline residue: D 203 - end of helix Processing helix chain 'D' and resid 217 through 227 Processing helix chain 'D' and resid 235 through 250 removed outlier: 3.880A pdb=" N ARG D 247 " --> pdb=" O ALA D 243 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N SER D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASP D 250 " --> pdb=" O ASP D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 253 through 257 Processing helix chain 'D' and resid 258 through 263 Processing helix chain 'D' and resid 269 through 276 Processing helix chain 'D' and resid 277 through 304 Processing helix chain 'D' and resid 320 through 325 Processing helix chain 'D' and resid 326 through 330 removed outlier: 3.589A pdb=" N PHE D 330 " --> pdb=" O ARG D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 362 through 370 Processing helix chain 'D' and resid 371 through 385 Processing helix chain 'D' and resid 392 through 397 Processing helix chain 'D' and resid 419 through 430 removed outlier: 4.264A pdb=" N PHE D 423 " --> pdb=" O ARG D 419 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA D 425 " --> pdb=" O ALA D 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 454 removed outlier: 3.749A pdb=" N VAL D 448 " --> pdb=" O THR D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 465 No H-bonds generated for 'chain 'D' and resid 463 through 465' Processing helix chain 'D' and resid 475 through 479 removed outlier: 3.523A pdb=" N HIS D 479 " --> pdb=" O PRO D 476 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 501 removed outlier: 3.500A pdb=" N THR D 501 " --> pdb=" O GLY D 497 " (cutoff:3.500A) Processing helix chain 'D' and resid 503 through 514 Processing helix chain 'D' and resid 521 through 532 removed outlier: 3.671A pdb=" N THR D 528 " --> pdb=" O TRP D 524 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 547 Processing helix chain 'D' and resid 549 through 553 Processing helix chain 'D' and resid 573 through 576 Processing helix chain 'D' and resid 577 through 591 Processing helix chain 'A' and resid 77 through 80 Processing helix chain 'A' and resid 81 through 91 removed outlier: 3.803A pdb=" N LYS A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 132 removed outlier: 4.007A pdb=" N THR A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 156 Processing helix chain 'A' and resid 158 through 169 Processing helix chain 'A' and resid 172 through 178 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 304 through 308 Processing helix chain 'A' and resid 309 through 315 Processing helix chain 'A' and resid 317 through 322 removed outlier: 3.544A pdb=" N ALA A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR A 322 " --> pdb=" O HIS A 318 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 317 through 322' Processing helix chain 'A' and resid 322 through 330 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 341 through 372 removed outlier: 4.002A pdb=" N GLY A 372 " --> pdb=" O GLU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 382 Proline residue: A 381 - end of helix Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 395 through 407 Processing helix chain 'A' and resid 411 through 421 removed outlier: 3.880A pdb=" N ARG A 421 " --> pdb=" O SER A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 435 removed outlier: 3.623A pdb=" N LEU A 435 " --> pdb=" O PRO A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 447 Processing helix chain 'A' and resid 447 through 470 Processing helix chain 'A' and resid 473 through 484 removed outlier: 3.657A pdb=" N LEU A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 587 Processing helix chain 'A' and resid 595 through 605 Processing helix chain 'A' and resid 607 through 614 removed outlier: 3.759A pdb=" N MET A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 626 through 631 removed outlier: 3.665A pdb=" N TRP A 630 " --> pdb=" O THR A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 635 through 647 Processing helix chain 'A' and resid 649 through 653 Processing helix chain 'A' and resid 654 through 665 removed outlier: 3.771A pdb=" N LYS A 663 " --> pdb=" O GLU A 660 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA A 665 " --> pdb=" O LYS A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 667 through 694 Processing helix chain 'A' and resid 715 through 732 removed outlier: 3.885A pdb=" N ASN A 719 " --> pdb=" O ARG A 715 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 742 Processing helix chain 'A' and resid 757 through 776 Processing helix chain 'A' and resid 793 through 801 Processing helix chain 'A' and resid 802 through 804 No H-bonds generated for 'chain 'A' and resid 802 through 804' Processing helix chain 'A' and resid 820 through 828 removed outlier: 3.748A pdb=" N ASN A 828 " --> pdb=" O LYS A 824 " (cutoff:3.500A) Processing helix chain 'A' and resid 839 through 848 Processing helix chain 'A' and resid 849 through 852 removed outlier: 3.767A pdb=" N PHE A 852 " --> pdb=" O GLU A 849 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 849 through 852' Processing helix chain 'A' and resid 858 through 860 No H-bonds generated for 'chain 'A' and resid 858 through 860' Processing helix chain 'A' and resid 861 through 871 Processing helix chain 'A' and resid 877 through 889 Processing helix chain 'A' and resid 890 through 893 removed outlier: 3.519A pdb=" N GLY A 893 " --> pdb=" O GLY A 890 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 890 through 893' Processing helix chain 'A' and resid 897 through 903 removed outlier: 3.663A pdb=" N SER A 903 " --> pdb=" O ASP A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 936 Processing helix chain 'A' and resid 938 through 952 Processing helix chain 'A' and resid 957 through 969 removed outlier: 3.984A pdb=" N THR A 961 " --> pdb=" O ASN A 957 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 107 removed outlier: 3.557A pdb=" N LEU C 107 " --> pdb=" O PRO C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 117 through 130 Processing helix chain 'C' and resid 163 through 167 Processing helix chain 'C' and resid 168 through 174 Processing helix chain 'C' and resid 175 through 177 No H-bonds generated for 'chain 'C' and resid 175 through 177' Processing helix chain 'C' and resid 193 through 215 Proline residue: C 203 - end of helix Processing helix chain 'C' and resid 217 through 228 removed outlier: 3.629A pdb=" N THR C 221 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 229 through 234 removed outlier: 4.051A pdb=" N GLY C 234 " --> pdb=" O PRO C 230 " (cutoff:3.500A) Processing helix chain 'C' and resid 235 through 249 removed outlier: 3.588A pdb=" N SER C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 257 Processing helix chain 'C' and resid 258 through 263 Processing helix chain 'C' and resid 265 through 276 Processing helix chain 'C' and resid 276 through 305 Processing helix chain 'C' and resid 320 through 326 Processing helix chain 'C' and resid 327 through 330 Processing helix chain 'C' and resid 362 through 369 Processing helix chain 'C' and resid 373 through 385 Processing helix chain 'C' and resid 392 through 396 Processing helix chain 'C' and resid 419 through 431 removed outlier: 3.915A pdb=" N PHE C 423 " --> pdb=" O ARG C 419 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA C 429 " --> pdb=" O ALA C 425 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 454 removed outlier: 3.735A pdb=" N VAL C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 479 removed outlier: 3.749A pdb=" N HIS C 479 " --> pdb=" O PRO C 476 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 502 Processing helix chain 'C' and resid 503 through 514 Processing helix chain 'C' and resid 515 through 519 removed outlier: 3.505A pdb=" N ASN C 518 " --> pdb=" O PRO C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 521 through 532 Processing helix chain 'C' and resid 542 through 546 Processing helix chain 'C' and resid 549 through 553 Processing helix chain 'C' and resid 577 through 591 Processing sheet with id=AA1, first strand: chain 'B' and resid 245 through 255 removed outlier: 4.366A pdb=" N ALA B 280 " --> pdb=" O ARG B 247 " (cutoff:3.500A) removed outlier: 8.529A pdb=" N ASP B 249 " --> pdb=" O VAL B 278 " (cutoff:3.500A) removed outlier: 10.285A pdb=" N VAL B 278 " --> pdb=" O ASP B 249 " (cutoff:3.500A) removed outlier: 9.681A pdb=" N SER B 251 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 10.871A pdb=" N ILE B 276 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA B 208 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 8.486A pdb=" N ARG B 297 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY B 210 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N TRP B 299 " --> pdb=" O GLY B 210 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N GLY B 212 " --> pdb=" O TRP B 299 " (cutoff:3.500A) removed outlier: 8.891A pdb=" N THR B 301 " --> pdb=" O GLY B 212 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N GLN B 135 " --> pdb=" O ALA B 385 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLN B 387 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR B 137 " --> pdb=" O GLN B 387 " (cutoff:3.500A) removed outlier: 9.628A pdb=" N ASN B 592 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N TYR B 425 " --> pdb=" O ASN B 592 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL B 591 " --> pdb=" O GLN B 619 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 221 through 225 Processing sheet with id=AA3, first strand: chain 'B' and resid 259 through 262 Processing sheet with id=AA4, first strand: chain 'B' and resid 437 through 439 Processing sheet with id=AA5, first strand: chain 'B' and resid 784 through 788 removed outlier: 6.421A pdb=" N MET B 702 " --> pdb=" O VAL B 746 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE B 748 " --> pdb=" O MET B 702 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ASP B 704 " --> pdb=" O ILE B 748 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N GLY B 750 " --> pdb=" O ASP B 704 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLN B 706 " --> pdb=" O GLY B 750 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N VAL B 707 " --> pdb=" O GLN B 808 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 435 through 437 removed outlier: 6.268A pdb=" N ILE D 308 " --> pdb=" O GLU D 387 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N ARG D 389 " --> pdb=" O ILE D 308 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY D 310 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ASP D 391 " --> pdb=" O GLY D 310 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N MET D 312 " --> pdb=" O ASP D 391 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TRP D 135 " --> pdb=" O MET D 309 " (cutoff:3.500A) removed outlier: 8.422A pdb=" N ASP D 311 " --> pdb=" O TRP D 135 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU D 134 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ARG D 97 " --> pdb=" O SER D 538 " (cutoff:3.500A) removed outlier: 8.708A pdb=" N VAL D 540 " --> pdb=" O ARG D 97 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N GLY D 99 " --> pdb=" O VAL D 540 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 354 through 359 removed outlier: 3.539A pdb=" N TRP D 356 " --> pdb=" O SER D 342 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N SER D 342 " --> pdb=" O TRP D 356 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N SER D 358 " --> pdb=" O PHE D 340 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N PHE D 340 " --> pdb=" O SER D 358 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N GLY D 343 " --> pdb=" O TRP D 400 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N TRP D 400 " --> pdb=" O GLY D 343 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 245 through 256 removed outlier: 4.373A pdb=" N ALA A 280 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 8.639A pdb=" N ASP A 249 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N VAL A 278 " --> pdb=" O ASP A 249 " (cutoff:3.500A) removed outlier: 9.685A pdb=" N SER A 251 " --> pdb=" O ILE A 276 " (cutoff:3.500A) removed outlier: 10.942A pdb=" N ILE A 276 " --> pdb=" O SER A 251 " (cutoff:3.500A) removed outlier: 10.876A pdb=" N GLU A 274 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ALA A 208 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASN A 295 " --> pdb=" O ALA A 208 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N ALA A 424 " --> pdb=" O VAL A 384 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A 386 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N THR A 426 " --> pdb=" O VAL A 386 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N MET A 388 " --> pdb=" O THR A 426 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N ASN A 592 " --> pdb=" O VAL A 423 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N TYR A 425 " --> pdb=" O ASN A 592 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL A 591 " --> pdb=" O GLN A 619 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 221 through 225 Processing sheet with id=AB1, first strand: chain 'A' and resid 259 through 262 Processing sheet with id=AB2, first strand: chain 'A' and resid 437 through 439 Processing sheet with id=AB3, first strand: chain 'A' and resid 784 through 788 removed outlier: 6.406A pdb=" N MET A 702 " --> pdb=" O VAL A 746 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ILE A 748 " --> pdb=" O MET A 702 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ASP A 704 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 8.421A pdb=" N GLY A 750 " --> pdb=" O ASP A 704 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLN A 706 " --> pdb=" O GLY A 750 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N VAL A 707 " --> pdb=" O GLN A 808 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 435 through 437 removed outlier: 6.415A pdb=" N TRP C 135 " --> pdb=" O MET C 309 " (cutoff:3.500A) removed outlier: 8.480A pdb=" N ASP C 311 " --> pdb=" O TRP C 135 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ALA C 98 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 8.356A pdb=" N GLN C 136 " --> pdb=" O ALA C 98 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VAL C 100 " --> pdb=" O GLN C 136 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLN C 483 " --> pdb=" O THR C 537 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N MET C 539 " --> pdb=" O GLN C 483 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL C 485 " --> pdb=" O MET C 539 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N THR C 541 " --> pdb=" O VAL C 485 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY C 458 " --> pdb=" O VAL C 484 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N TYR C 486 " --> pdb=" O GLY C 458 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ALA C 460 " --> pdb=" O TYR C 486 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 354 through 355 removed outlier: 3.997A pdb=" N GLY C 343 " --> pdb=" O TRP C 400 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP C 400 " --> pdb=" O GLY C 343 " (cutoff:3.500A) 1054 hydrogen bonds defined for protein. 2931 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.92 Time building geometry restraints manager: 2.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7108 1.34 - 1.46: 5187 1.46 - 1.58: 9762 1.58 - 1.71: 0 1.71 - 1.83: 152 Bond restraints: 22209 Sorted by residual: bond pdb=" N LYS B 507 " pdb=" CA LYS B 507 " ideal model delta sigma weight residual 1.453 1.494 -0.041 1.31e-02 5.83e+03 9.84e+00 bond pdb=" N ASP A 494 " pdb=" CA ASP A 494 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.15e-02 7.56e+03 9.57e+00 bond pdb=" N VAL B 501 " pdb=" CA VAL B 501 " ideal model delta sigma weight residual 1.462 1.491 -0.029 1.06e-02 8.90e+03 7.50e+00 bond pdb=" N ILE A 496 " pdb=" CA ILE A 496 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.91e+00 bond pdb=" N ASP A 491 " pdb=" CA ASP A 491 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.27e-02 6.20e+03 6.76e+00 ... (remaining 22204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 29441 1.88 - 3.76: 585 3.76 - 5.64: 70 5.64 - 7.52: 7 7.52 - 9.40: 3 Bond angle restraints: 30106 Sorted by residual: angle pdb=" N SER A 495 " pdb=" CA SER A 495 " pdb=" C SER A 495 " ideal model delta sigma weight residual 113.20 105.04 8.16 1.21e+00 6.83e-01 4.55e+01 angle pdb=" C PRO A 493 " pdb=" CA PRO A 493 " pdb=" CB PRO A 493 " ideal model delta sigma weight residual 112.97 105.83 7.14 1.43e+00 4.89e-01 2.49e+01 angle pdb=" N VAL B 501 " pdb=" CA VAL B 501 " pdb=" C VAL B 501 " ideal model delta sigma weight residual 112.98 106.74 6.24 1.25e+00 6.40e-01 2.49e+01 angle pdb=" N PRO B 503 " pdb=" CA PRO B 503 " pdb=" C PRO B 503 " ideal model delta sigma weight residual 114.35 108.72 5.63 1.25e+00 6.40e-01 2.03e+01 angle pdb=" N ASP A 494 " pdb=" CA ASP A 494 " pdb=" C ASP A 494 " ideal model delta sigma weight residual 113.38 108.90 4.48 1.17e+00 7.31e-01 1.47e+01 ... (remaining 30101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 11341 17.50 - 35.00: 1433 35.00 - 52.50: 356 52.50 - 70.00: 99 70.00 - 87.50: 25 Dihedral angle restraints: 13254 sinusoidal: 5373 harmonic: 7881 Sorted by residual: dihedral pdb=" CA SER D 233 " pdb=" C SER D 233 " pdb=" N GLY D 234 " pdb=" CA GLY D 234 " ideal model delta harmonic sigma weight residual 180.00 159.18 20.82 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" CA ILE B 631 " pdb=" C ILE B 631 " pdb=" N ARG B 632 " pdb=" CA ARG B 632 " ideal model delta harmonic sigma weight residual -180.00 -160.76 -19.24 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA THR B 92 " pdb=" C THR B 92 " pdb=" N PRO B 93 " pdb=" CA PRO B 93 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 ... (remaining 13251 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 2342 0.045 - 0.091: 727 0.091 - 0.136: 167 0.136 - 0.181: 11 0.181 - 0.227: 3 Chirality restraints: 3250 Sorted by residual: chirality pdb=" CA VAL B 501 " pdb=" N VAL B 501 " pdb=" C VAL B 501 " pdb=" CB VAL B 501 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA LYS A 506 " pdb=" N LYS A 506 " pdb=" C LYS A 506 " pdb=" CB LYS A 506 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA ARG C 419 " pdb=" N ARG C 419 " pdb=" C ARG C 419 " pdb=" CB ARG C 419 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.90e-01 ... (remaining 3247 not shown) Planarity restraints: 3889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 419 " 0.283 9.50e-02 1.11e+02 1.27e-01 9.86e+00 pdb=" NE ARG C 419 " -0.016 2.00e-02 2.50e+03 pdb=" CZ ARG C 419 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 419 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 419 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET D 87 " 0.038 5.00e-02 4.00e+02 5.70e-02 5.20e+00 pdb=" N PRO D 88 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 88 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 88 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 499 " 0.011 2.00e-02 2.50e+03 2.24e-02 5.03e+00 pdb=" C LEU B 499 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU B 499 " 0.015 2.00e-02 2.50e+03 pdb=" N PHE B 500 " 0.013 2.00e-02 2.50e+03 ... (remaining 3886 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 7519 2.86 - 3.37: 19467 3.37 - 3.88: 35893 3.88 - 4.39: 42782 4.39 - 4.90: 72307 Nonbonded interactions: 177968 Sorted by model distance: nonbonded pdb=" O GLN B 929 " pdb=" OD1 ASP B 933 " model vdw 2.351 3.040 nonbonded pdb=" N GLY B 814 " pdb=" OD1 ASP B 837 " model vdw 2.352 3.120 nonbonded pdb=" CD2 LEU D 178 " pdb=" OE1 GLU D 182 " model vdw 2.480 3.460 nonbonded pdb=" O GLU D 77 " pdb=" O ALA C 416 " model vdw 2.484 3.040 nonbonded pdb=" N SER A 495 " pdb=" N ILE A 496 " model vdw 2.522 2.560 ... (remaining 177963 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 77 through 507 or resid 575 through 978)) selection = (chain 'B' and (resid 77 through 507 or resid 575 through 978)) } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 6.820 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: 0.590 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.040 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 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 : 0.008 0.900 22210 Z= 0.378 Angle : 0.654 27.676 30108 Z= 0.366 Chirality : 0.045 0.227 3250 Planarity : 0.005 0.127 3889 Dihedral : 16.963 87.504 8177 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.35 % Allowed : 21.94 % Favored : 77.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.16), residues: 2709 helix: 0.71 (0.14), residues: 1356 sheet: 0.18 (0.31), residues: 279 loop : -0.80 (0.18), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 267 TYR 0.026 0.002 TYR A 257 PHE 0.020 0.002 PHE B 220 TRP 0.013 0.002 TRP B 121 HIS 0.005 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00481 (22209) covalent geometry : angle 0.63257 (30106) SS BOND : bond 0.89963 ( 1) SS BOND : angle 20.36724 ( 2) hydrogen bonds : bond 0.16825 ( 1054) hydrogen bonds : angle 5.80539 ( 2931) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 252 time to evaluate : 0.856 Fit side-chains REVERT: B 115 ASP cc_start: 0.7674 (t0) cc_final: 0.7092 (m-30) REVERT: B 129 ASP cc_start: 0.6849 (m-30) cc_final: 0.6645 (m-30) REVERT: B 388 MET cc_start: 0.8671 (mtp) cc_final: 0.8354 (mtm) REVERT: B 444 GLN cc_start: 0.8187 (tt0) cc_final: 0.7947 (tt0) REVERT: B 462 MET cc_start: 0.7882 (mtp) cc_final: 0.7594 (mmp) REVERT: B 498 LYS cc_start: 0.7312 (pttp) cc_final: 0.6923 (ptmm) REVERT: B 507 LYS cc_start: 0.7244 (mtmt) cc_final: 0.6162 (mttt) REVERT: B 673 GLU cc_start: 0.7879 (pt0) cc_final: 0.7307 (mm-30) REVERT: B 967 LYS cc_start: 0.7867 (tttt) cc_final: 0.7121 (mmtt) REVERT: D 83 TYR cc_start: 0.3070 (p90) cc_final: 0.1680 (p90) REVERT: D 278 ASP cc_start: 0.6177 (p0) cc_final: 0.5717 (m-30) REVERT: D 445 GLU cc_start: 0.6399 (mt-10) cc_final: 0.6018 (mt-10) REVERT: D 459 MET cc_start: 0.8772 (ttm) cc_final: 0.8326 (ttt) REVERT: D 521 GLU cc_start: 0.7188 (mt-10) cc_final: 0.6475 (tt0) REVERT: A 141 MET cc_start: 0.8556 (tpp) cc_final: 0.8338 (tpp) REVERT: A 268 MET cc_start: 0.8874 (mmt) cc_final: 0.8629 (mmp) REVERT: A 311 GLU cc_start: 0.8113 (tt0) cc_final: 0.7810 (tt0) REVERT: A 378 GLU cc_start: 0.8115 (tt0) cc_final: 0.7800 (tp30) REVERT: A 637 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6534 (mp0) REVERT: A 660 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7070 (mm-30) REVERT: A 934 LYS cc_start: 0.8410 (ttmm) cc_final: 0.8017 (ttpt) REVERT: C 86 MET cc_start: 0.6835 (ptt) cc_final: 0.6527 (mpp) REVERT: C 394 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.6377 (ptm160) outliers start: 8 outliers final: 6 residues processed: 258 average time/residue: 0.7310 time to fit residues: 211.5175 Evaluate side-chains 221 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 214 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 434 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN C 231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.121734 restraints weight = 28702.415| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.44 r_work: 0.3227 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.0691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22210 Z= 0.121 Angle : 0.503 7.015 30108 Z= 0.270 Chirality : 0.040 0.148 3250 Planarity : 0.004 0.043 3889 Dihedral : 5.451 166.505 2964 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.33 % Allowed : 20.21 % Favored : 76.46 % 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: 0.44 (0.16), residues: 2709 helix: 1.11 (0.14), residues: 1357 sheet: 0.08 (0.29), residues: 330 loop : -0.67 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 267 TYR 0.016 0.001 TYR C 191 PHE 0.014 0.001 PHE B 220 TRP 0.013 0.001 TRP B 121 HIS 0.003 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00260 (22209) covalent geometry : angle 0.50243 (30106) SS BOND : bond 0.00719 ( 1) SS BOND : angle 2.48833 ( 2) hydrogen bonds : bond 0.05461 ( 1054) hydrogen bonds : angle 4.55911 ( 2931) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 229 time to evaluate : 0.675 Fit side-chains revert: symmetry clash REVERT: B 115 ASP cc_start: 0.7713 (t0) cc_final: 0.7094 (m-30) REVERT: B 239 MET cc_start: 0.7317 (mmm) cc_final: 0.6993 (tpt) REVERT: B 259 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.7702 (ptpt) REVERT: B 388 MET cc_start: 0.8753 (mtp) cc_final: 0.8468 (mtm) REVERT: B 444 GLN cc_start: 0.8232 (tt0) cc_final: 0.8026 (tt0) REVERT: B 462 MET cc_start: 0.8041 (mtp) cc_final: 0.7776 (mmp) REVERT: B 498 LYS cc_start: 0.7249 (pttp) cc_final: 0.6896 (ptmm) REVERT: B 604 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.6761 (mp0) REVERT: B 673 GLU cc_start: 0.7931 (OUTLIER) cc_final: 0.7424 (mm-30) REVERT: B 967 LYS cc_start: 0.7907 (tttt) cc_final: 0.7320 (mptp) REVERT: D 83 TYR cc_start: 0.3151 (p90) cc_final: 0.1738 (p90) REVERT: D 179 MET cc_start: 0.6916 (mmm) cc_final: 0.5531 (mmt) REVERT: D 182 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6152 (mt-10) REVERT: D 278 ASP cc_start: 0.6099 (p0) cc_final: 0.5574 (m-30) REVERT: D 349 PHE cc_start: 0.5296 (m-10) cc_final: 0.4898 (m-10) REVERT: D 445 GLU cc_start: 0.6467 (mt-10) cc_final: 0.6073 (mt-10) REVERT: D 459 MET cc_start: 0.8775 (ttm) cc_final: 0.8368 (ttt) REVERT: D 521 GLU cc_start: 0.7181 (mt-10) cc_final: 0.6407 (tt0) REVERT: A 161 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.7093 (mp10) REVERT: A 311 GLU cc_start: 0.8428 (tt0) cc_final: 0.8137 (tt0) REVERT: A 340 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: A 378 GLU cc_start: 0.8261 (tt0) cc_final: 0.7968 (tp30) REVERT: A 637 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6703 (mp0) REVERT: A 660 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7380 (mm-30) REVERT: A 846 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.6729 (mp0) REVERT: A 934 LYS cc_start: 0.8508 (ttmm) cc_final: 0.8142 (ttpt) REVERT: C 84 ASP cc_start: 0.7154 (OUTLIER) cc_final: 0.6804 (m-30) REVERT: C 87 MET cc_start: 0.6797 (mmm) cc_final: 0.6390 (mtt) REVERT: C 190 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7103 (mp0) REVERT: C 228 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8099 (mtpt) REVERT: C 428 LYS cc_start: 0.7677 (ttmm) cc_final: 0.7077 (mtpp) REVERT: C 500 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7869 (mt0) outliers start: 77 outliers final: 27 residues processed: 288 average time/residue: 0.7117 time to fit residues: 230.6526 Evaluate side-chains 253 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 215 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 506 GLU Chi-restraints excluded: chain D residue 520 THR Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 736 LYS Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain C residue 572 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 125 optimal weight: 0.0980 chunk 75 optimal weight: 7.9990 chunk 265 optimal weight: 0.6980 chunk 162 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 71 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.120176 restraints weight = 28783.378| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.46 r_work: 0.3206 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 22210 Z= 0.159 Angle : 0.534 5.904 30108 Z= 0.285 Chirality : 0.042 0.156 3250 Planarity : 0.004 0.042 3889 Dihedral : 4.488 37.231 2955 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.72 % Allowed : 19.90 % Favored : 76.37 % 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: 0.40 (0.16), residues: 2709 helix: 1.08 (0.14), residues: 1358 sheet: 0.11 (0.30), residues: 301 loop : -0.70 (0.18), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 267 TYR 0.019 0.002 TYR A 257 PHE 0.019 0.002 PHE B 220 TRP 0.015 0.002 TRP A 121 HIS 0.005 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00373 (22209) covalent geometry : angle 0.53348 (30106) SS BOND : bond 0.01026 ( 1) SS BOND : angle 2.02170 ( 2) hydrogen bonds : bond 0.05614 ( 1054) hydrogen bonds : angle 4.43990 ( 2931) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 228 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: B 115 ASP cc_start: 0.7786 (t0) cc_final: 0.7099 (m-30) REVERT: B 259 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.7814 (ptpt) REVERT: B 388 MET cc_start: 0.8786 (mtp) cc_final: 0.8487 (mtm) REVERT: B 462 MET cc_start: 0.8089 (mtp) cc_final: 0.7806 (mmp) REVERT: B 604 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.6768 (mp0) REVERT: B 656 ASP cc_start: 0.8077 (m-30) cc_final: 0.7876 (m-30) REVERT: B 673 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7460 (mm-30) REVERT: B 967 LYS cc_start: 0.7980 (tttt) cc_final: 0.7387 (mptp) REVERT: D 83 TYR cc_start: 0.3088 (p90) cc_final: 0.1618 (p90) REVERT: D 179 MET cc_start: 0.7069 (mmm) cc_final: 0.5630 (mmt) REVERT: D 182 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6060 (mt-10) REVERT: D 278 ASP cc_start: 0.6183 (p0) cc_final: 0.5630 (m-30) REVERT: D 445 GLU cc_start: 0.6450 (mt-10) cc_final: 0.6097 (mt-10) REVERT: D 459 MET cc_start: 0.8789 (ttm) cc_final: 0.8362 (ttt) REVERT: D 521 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6455 (tt0) REVERT: A 92 THR cc_start: 0.7284 (p) cc_final: 0.6840 (t) REVERT: A 311 GLU cc_start: 0.8455 (tt0) cc_final: 0.8169 (tt0) REVERT: A 340 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: A 378 GLU cc_start: 0.8280 (tt0) cc_final: 0.7952 (tp30) REVERT: A 455 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7449 (tt0) REVERT: A 637 GLU cc_start: 0.7308 (mm-30) cc_final: 0.6704 (mp0) REVERT: A 660 GLU cc_start: 0.7632 (mt-10) cc_final: 0.7367 (mm-30) REVERT: A 736 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7586 (ptmt) REVERT: A 846 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.6707 (mp0) REVERT: A 934 LYS cc_start: 0.8530 (ttmm) cc_final: 0.8152 (ttpt) REVERT: C 86 MET cc_start: 0.7241 (ptp) cc_final: 0.6810 (ptp) REVERT: C 171 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6909 (mt-10) REVERT: C 228 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.8157 (mtpt) REVERT: C 394 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.5996 (ptm160) REVERT: C 428 LYS cc_start: 0.7735 (ttmm) cc_final: 0.7372 (tmtm) REVERT: C 500 GLN cc_start: 0.8485 (OUTLIER) cc_final: 0.7939 (mt0) outliers start: 86 outliers final: 38 residues processed: 294 average time/residue: 0.7230 time to fit residues: 239.2499 Evaluate side-chains 269 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 219 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain D residue 145 ARG Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 195 ASP Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain A residue 167 GLN Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 736 LYS Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 171 GLU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 228 LYS Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain C residue 572 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 127 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 chunk 201 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 164 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 202 optimal weight: 9.9990 chunk 7 optimal weight: 2.9990 chunk 200 optimal weight: 1.9990 chunk 141 optimal weight: 0.9980 chunk 148 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 444 GLN A 161 GLN C 85 GLN C 231 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.142884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.123974 restraints weight = 27129.797| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.31 r_work: 0.3316 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.0923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22210 Z= 0.135 Angle : 0.503 7.645 30108 Z= 0.268 Chirality : 0.041 0.151 3250 Planarity : 0.004 0.040 3889 Dihedral : 4.389 37.874 2955 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 3.68 % Allowed : 20.29 % Favored : 76.03 % 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: 0.54 (0.16), residues: 2709 helix: 1.23 (0.14), residues: 1349 sheet: 0.10 (0.30), residues: 303 loop : -0.64 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 267 TYR 0.015 0.002 TYR A 257 PHE 0.016 0.001 PHE B 220 TRP 0.014 0.001 TRP A 121 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00312 (22209) covalent geometry : angle 0.50239 (30106) SS BOND : bond 0.00781 ( 1) SS BOND : angle 1.47976 ( 2) hydrogen bonds : bond 0.05116 ( 1054) hydrogen bonds : angle 4.31259 ( 2931) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 235 time to evaluate : 0.941 Fit side-chains revert: symmetry clash REVERT: B 115 ASP cc_start: 0.7776 (t0) cc_final: 0.7154 (m-30) REVERT: B 239 MET cc_start: 0.7428 (mmm) cc_final: 0.7129 (tpt) REVERT: B 259 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.7893 (ptpt) REVERT: B 261 VAL cc_start: 0.8581 (m) cc_final: 0.8197 (t) REVERT: B 388 MET cc_start: 0.8794 (mtp) cc_final: 0.8530 (mtm) REVERT: B 394 THR cc_start: 0.8852 (t) cc_final: 0.8433 (m) REVERT: B 673 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7471 (mm-30) REVERT: B 967 LYS cc_start: 0.7995 (tttt) cc_final: 0.7535 (mptp) REVERT: D 83 TYR cc_start: 0.3106 (p90) cc_final: 0.1686 (p90) REVERT: D 179 MET cc_start: 0.7270 (mmm) cc_final: 0.5996 (mpm) REVERT: D 180 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7542 (tp30) REVERT: D 182 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.6302 (mt-10) REVERT: D 278 ASP cc_start: 0.6219 (p0) cc_final: 0.5665 (m-30) REVERT: D 349 PHE cc_start: 0.5385 (m-10) cc_final: 0.5089 (m-10) REVERT: D 521 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6515 (tt0) REVERT: A 311 GLU cc_start: 0.8509 (tt0) cc_final: 0.8249 (tt0) REVERT: A 340 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7226 (mp0) REVERT: A 378 GLU cc_start: 0.8170 (tt0) cc_final: 0.7964 (tp30) REVERT: A 483 GLU cc_start: 0.7414 (tt0) cc_final: 0.7134 (pt0) REVERT: A 637 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6874 (mp0) REVERT: A 736 LYS cc_start: 0.8027 (OUTLIER) cc_final: 0.7699 (ptmt) REVERT: A 846 GLU cc_start: 0.8014 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: A 934 LYS cc_start: 0.8589 (ttmm) cc_final: 0.8298 (ttpt) REVERT: C 84 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7113 (t70) REVERT: C 86 MET cc_start: 0.7580 (ptp) cc_final: 0.7193 (ptp) REVERT: C 87 MET cc_start: 0.6709 (mmm) cc_final: 0.6288 (mtt) REVERT: C 150 ASP cc_start: 0.7007 (OUTLIER) cc_final: 0.6543 (p0) REVERT: C 190 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7168 (mt-10) REVERT: C 394 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.6178 (ptm160) REVERT: C 500 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8219 (mp10) outliers start: 85 outliers final: 39 residues processed: 301 average time/residue: 0.7177 time to fit residues: 242.3947 Evaluate side-chains 272 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 221 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain D residue 145 ARG Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 506 GLU Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 736 LYS Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 190 GLU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain C residue 501 THR Chi-restraints excluded: chain C residue 572 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 250 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 181 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 173 optimal weight: 0.6980 chunk 72 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 166 optimal weight: 0.0670 overall best weight: 1.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 444 GLN D 483 GLN A 161 GLN A 808 GLN C 222 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.144056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.125000 restraints weight = 26932.816| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.29 r_work: 0.3335 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22210 Z= 0.114 Angle : 0.475 6.139 30108 Z= 0.254 Chirality : 0.040 0.145 3250 Planarity : 0.004 0.037 3889 Dihedral : 4.245 38.204 2955 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 3.68 % Allowed : 20.34 % Favored : 75.98 % 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: 0.64 (0.16), residues: 2709 helix: 1.37 (0.14), residues: 1349 sheet: 0.02 (0.29), residues: 323 loop : -0.63 (0.19), residues: 1037 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 267 TYR 0.016 0.001 TYR B 469 PHE 0.014 0.001 PHE B 220 TRP 0.013 0.001 TRP B 121 HIS 0.003 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00254 (22209) covalent geometry : angle 0.47446 (30106) SS BOND : bond 0.01290 ( 1) SS BOND : angle 2.17759 ( 2) hydrogen bonds : bond 0.04636 ( 1054) hydrogen bonds : angle 4.20142 ( 2931) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 239 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 115 ASP cc_start: 0.7776 (t0) cc_final: 0.7089 (m-30) REVERT: B 175 ASP cc_start: 0.7748 (OUTLIER) cc_final: 0.7503 (p0) REVERT: B 239 MET cc_start: 0.7390 (mmm) cc_final: 0.7109 (tpt) REVERT: B 259 LYS cc_start: 0.8656 (OUTLIER) cc_final: 0.7822 (ptpt) REVERT: B 261 VAL cc_start: 0.8543 (m) cc_final: 0.8161 (t) REVERT: B 388 MET cc_start: 0.8779 (mtp) cc_final: 0.8509 (mtm) REVERT: B 394 THR cc_start: 0.8766 (t) cc_final: 0.8383 (m) REVERT: B 604 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.6805 (mp0) REVERT: B 673 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7428 (mm-30) REVERT: B 967 LYS cc_start: 0.7950 (tttt) cc_final: 0.7513 (mptp) REVERT: D 83 TYR cc_start: 0.3059 (p90) cc_final: 0.1663 (p90) REVERT: D 179 MET cc_start: 0.7286 (mmm) cc_final: 0.5993 (mpm) REVERT: D 180 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7599 (tp30) REVERT: D 182 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6431 (mt-10) REVERT: D 278 ASP cc_start: 0.6162 (p0) cc_final: 0.5592 (m-30) REVERT: D 349 PHE cc_start: 0.5322 (m-10) cc_final: 0.5047 (m-10) REVERT: D 521 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6487 (tt0) REVERT: A 311 GLU cc_start: 0.8492 (tt0) cc_final: 0.8227 (tt0) REVERT: A 340 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7262 (mp0) REVERT: A 378 GLU cc_start: 0.8128 (tt0) cc_final: 0.7909 (tp30) REVERT: A 464 ILE cc_start: 0.7821 (tt) cc_final: 0.7560 (tp) REVERT: A 637 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6862 (mp0) REVERT: A 846 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.6800 (mp0) REVERT: A 934 LYS cc_start: 0.8577 (ttmm) cc_final: 0.8300 (ttpt) REVERT: C 84 ASP cc_start: 0.7507 (OUTLIER) cc_final: 0.7192 (t70) REVERT: C 86 MET cc_start: 0.7570 (ptp) cc_final: 0.7193 (ptp) REVERT: C 150 ASP cc_start: 0.6978 (OUTLIER) cc_final: 0.6500 (p0) REVERT: C 394 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.6032 (ptm160) outliers start: 85 outliers final: 39 residues processed: 304 average time/residue: 0.7199 time to fit residues: 245.5319 Evaluate side-chains 275 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 225 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain D residue 506 GLU Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 406 SER Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 572 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 56 optimal weight: 0.7980 chunk 93 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 267 optimal weight: 0.0570 chunk 160 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 196 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 chunk 262 optimal weight: 0.0670 overall best weight: 0.7238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN B 719 ASN A 161 GLN C 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.127028 restraints weight = 26970.913| |-----------------------------------------------------------------------------| r_work (start): 0.3460 rms_B_bonded: 1.42 r_work: 0.3354 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 22210 Z= 0.098 Angle : 0.455 8.514 30108 Z= 0.241 Chirality : 0.040 0.140 3250 Planarity : 0.003 0.052 3889 Dihedral : 4.081 37.972 2955 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.12 % Allowed : 21.25 % Favored : 75.64 % 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: 0.81 (0.16), residues: 2709 helix: 1.50 (0.15), residues: 1349 sheet: 0.05 (0.30), residues: 301 loop : -0.52 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 267 TYR 0.013 0.001 TYR A 469 PHE 0.013 0.001 PHE A 220 TRP 0.012 0.001 TRP B 121 HIS 0.002 0.000 HIS D 477 Details of bonding type rmsd covalent geometry : bond 0.00213 (22209) covalent geometry : angle 0.45467 (30106) SS BOND : bond 0.00896 ( 1) SS BOND : angle 2.33127 ( 2) hydrogen bonds : bond 0.04142 ( 1054) hydrogen bonds : angle 4.07413 ( 2931) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 239 time to evaluate : 0.860 Fit side-chains revert: symmetry clash REVERT: B 115 ASP cc_start: 0.7800 (t0) cc_final: 0.7054 (m-30) REVERT: B 175 ASP cc_start: 0.7777 (OUTLIER) cc_final: 0.7530 (p0) REVERT: B 259 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.7825 (ptpt) REVERT: B 261 VAL cc_start: 0.8534 (m) cc_final: 0.8154 (t) REVERT: B 388 MET cc_start: 0.8755 (mtp) cc_final: 0.8534 (mtm) REVERT: B 394 THR cc_start: 0.8648 (t) cc_final: 0.8325 (m) REVERT: B 600 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7329 (mm-30) REVERT: B 604 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: B 613 MET cc_start: 0.8715 (mtm) cc_final: 0.8514 (ttm) REVERT: B 673 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7404 (mm-30) REVERT: B 967 LYS cc_start: 0.7972 (tttt) cc_final: 0.7563 (mptp) REVERT: D 83 TYR cc_start: 0.2918 (p90) cc_final: 0.1581 (p90) REVERT: D 179 MET cc_start: 0.7344 (mmm) cc_final: 0.6052 (mpm) REVERT: D 180 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7599 (tp30) REVERT: D 182 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.6513 (mt-10) REVERT: D 278 ASP cc_start: 0.6108 (p0) cc_final: 0.5549 (m-30) REVERT: D 349 PHE cc_start: 0.5230 (m-10) cc_final: 0.4896 (m-10) REVERT: A 161 GLN cc_start: 0.7394 (OUTLIER) cc_final: 0.7120 (mp10) REVERT: A 311 GLU cc_start: 0.8487 (tt0) cc_final: 0.8237 (tt0) REVERT: A 340 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: A 378 GLU cc_start: 0.8106 (tt0) cc_final: 0.7895 (tp30) REVERT: A 464 ILE cc_start: 0.7701 (tt) cc_final: 0.7469 (tp) REVERT: A 637 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6903 (mp0) REVERT: A 736 LYS cc_start: 0.7962 (ptpt) cc_final: 0.7678 (ptmt) REVERT: A 846 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.6860 (mp0) REVERT: A 934 LYS cc_start: 0.8549 (ttmm) cc_final: 0.8260 (ttpt) REVERT: C 86 MET cc_start: 0.7539 (ptp) cc_final: 0.7228 (ptp) REVERT: C 87 MET cc_start: 0.6693 (mmm) cc_final: 0.6347 (mtt) REVERT: C 150 ASP cc_start: 0.7028 (OUTLIER) cc_final: 0.6513 (p0) REVERT: C 284 MET cc_start: 0.8287 (mtt) cc_final: 0.8024 (mtt) REVERT: C 394 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.6092 (ptm160) outliers start: 72 outliers final: 34 residues processed: 293 average time/residue: 0.7117 time to fit residues: 234.4418 Evaluate side-chains 274 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 229 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 314 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 554 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 72 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 117 optimal weight: 7.9990 chunk 207 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 197 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN A 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.146536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.127549 restraints weight = 26993.078| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.31 r_work: 0.3344 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3243 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 22210 Z= 0.105 Angle : 0.464 7.943 30108 Z= 0.246 Chirality : 0.040 0.142 3250 Planarity : 0.003 0.053 3889 Dihedral : 4.044 38.351 2953 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.77 % Allowed : 21.90 % Favored : 75.34 % 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: 0.84 (0.16), residues: 2709 helix: 1.52 (0.14), residues: 1349 sheet: 0.03 (0.30), residues: 302 loop : -0.48 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 267 TYR 0.020 0.001 TYR B 469 PHE 0.014 0.001 PHE B 220 TRP 0.012 0.001 TRP B 121 HIS 0.002 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00232 (22209) covalent geometry : angle 0.46365 (30106) SS BOND : bond 0.00796 ( 1) SS BOND : angle 1.89503 ( 2) hydrogen bonds : bond 0.04220 ( 1054) hydrogen bonds : angle 4.06070 ( 2931) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 238 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 115 ASP cc_start: 0.7788 (t0) cc_final: 0.7038 (m-30) REVERT: B 175 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7448 (p0) REVERT: B 259 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.7831 (ptpt) REVERT: B 261 VAL cc_start: 0.8515 (m) cc_final: 0.8131 (t) REVERT: B 388 MET cc_start: 0.8755 (mtp) cc_final: 0.8539 (mtm) REVERT: B 394 THR cc_start: 0.8670 (t) cc_final: 0.8341 (m) REVERT: B 505 GLU cc_start: 0.7844 (OUTLIER) cc_final: 0.7053 (pm20) REVERT: B 600 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7308 (mm-30) REVERT: B 604 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.6789 (mp0) REVERT: B 613 MET cc_start: 0.8719 (mtm) cc_final: 0.8514 (ttm) REVERT: B 673 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7401 (mm-30) REVERT: B 736 LYS cc_start: 0.8154 (tptt) cc_final: 0.7728 (mmtm) REVERT: B 967 LYS cc_start: 0.7977 (tttt) cc_final: 0.7555 (mptp) REVERT: D 83 TYR cc_start: 0.2922 (p90) cc_final: 0.1568 (p90) REVERT: D 179 MET cc_start: 0.7291 (mmm) cc_final: 0.5977 (mpm) REVERT: D 180 GLU cc_start: 0.8129 (OUTLIER) cc_final: 0.7558 (tp30) REVERT: D 182 GLU cc_start: 0.7417 (OUTLIER) cc_final: 0.6511 (mt-10) REVERT: D 278 ASP cc_start: 0.6125 (p0) cc_final: 0.5523 (m-30) REVERT: D 349 PHE cc_start: 0.5214 (m-10) cc_final: 0.4857 (m-10) REVERT: A 174 GLU cc_start: 0.7314 (mp0) cc_final: 0.7052 (mm-30) REVERT: A 311 GLU cc_start: 0.8498 (tt0) cc_final: 0.8239 (tt0) REVERT: A 340 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: A 378 GLU cc_start: 0.8092 (tt0) cc_final: 0.7864 (tp30) REVERT: A 441 ASP cc_start: 0.8099 (m-30) cc_final: 0.7681 (m-30) REVERT: A 464 ILE cc_start: 0.7712 (tt) cc_final: 0.7471 (tp) REVERT: A 637 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6887 (mp0) REVERT: A 846 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.6829 (mp0) REVERT: A 934 LYS cc_start: 0.8546 (ttmm) cc_final: 0.8247 (ttpt) REVERT: C 86 MET cc_start: 0.7493 (ptp) cc_final: 0.7189 (ptp) REVERT: C 87 MET cc_start: 0.6743 (mmm) cc_final: 0.6336 (mtt) REVERT: C 150 ASP cc_start: 0.7021 (OUTLIER) cc_final: 0.6493 (p0) REVERT: C 394 ARG cc_start: 0.8242 (OUTLIER) cc_final: 0.6029 (ptm160) REVERT: C 424 ASP cc_start: 0.8277 (t0) cc_final: 0.7776 (m-30) REVERT: C 500 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7721 (mt0) outliers start: 64 outliers final: 40 residues processed: 288 average time/residue: 0.7359 time to fit residues: 237.8646 Evaluate side-chains 280 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 228 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 500 GLN Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 572 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 266 optimal weight: 2.9990 chunk 173 optimal weight: 0.6980 chunk 161 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 207 optimal weight: 3.9990 chunk 202 optimal weight: 9.9990 chunk 168 optimal weight: 0.9990 chunk 213 optimal weight: 2.9990 chunk 216 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN B 444 GLN B 719 ASN A 161 GLN A 428 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.144133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124773 restraints weight = 27040.266| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 1.32 r_work: 0.3317 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 22210 Z= 0.145 Angle : 0.513 8.149 30108 Z= 0.272 Chirality : 0.042 0.152 3250 Planarity : 0.004 0.057 3889 Dihedral : 4.258 39.263 2953 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 3.03 % Allowed : 21.81 % Favored : 75.16 % 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: 0.67 (0.16), residues: 2709 helix: 1.37 (0.14), residues: 1351 sheet: 0.00 (0.29), residues: 323 loop : -0.57 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 267 TYR 0.017 0.002 TYR B 469 PHE 0.018 0.001 PHE B 220 TRP 0.013 0.001 TRP A 121 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00340 (22209) covalent geometry : angle 0.51311 (30106) SS BOND : bond 0.01075 ( 1) SS BOND : angle 2.09244 ( 2) hydrogen bonds : bond 0.05029 ( 1054) hydrogen bonds : angle 4.19423 ( 2931) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 232 time to evaluate : 0.813 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 115 ASP cc_start: 0.7815 (t0) cc_final: 0.7109 (m-30) REVERT: B 175 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7559 (p0) REVERT: B 239 MET cc_start: 0.7335 (mmm) cc_final: 0.7042 (tpt) REVERT: B 259 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.7843 (ptpt) REVERT: B 261 VAL cc_start: 0.8560 (m) cc_final: 0.8181 (t) REVERT: B 388 MET cc_start: 0.8772 (mtp) cc_final: 0.8504 (mtm) REVERT: B 394 THR cc_start: 0.8785 (t) cc_final: 0.8430 (m) REVERT: B 505 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7042 (pm20) REVERT: B 600 GLU cc_start: 0.7642 (mm-30) cc_final: 0.7363 (mm-30) REVERT: B 604 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6766 (mp0) REVERT: B 673 GLU cc_start: 0.7780 (OUTLIER) cc_final: 0.7456 (mm-30) REVERT: B 736 LYS cc_start: 0.8088 (tptt) cc_final: 0.7667 (mmtm) REVERT: B 842 GLU cc_start: 0.7915 (mt-10) cc_final: 0.7673 (mp0) REVERT: B 967 LYS cc_start: 0.7999 (tttt) cc_final: 0.7574 (mptp) REVERT: D 83 TYR cc_start: 0.3019 (p90) cc_final: 0.1567 (p90) REVERT: D 179 MET cc_start: 0.7279 (mmm) cc_final: 0.5975 (mpm) REVERT: D 180 GLU cc_start: 0.8127 (OUTLIER) cc_final: 0.7574 (tp30) REVERT: D 182 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.6492 (mt-10) REVERT: D 278 ASP cc_start: 0.6252 (p0) cc_final: 0.5702 (m-30) REVERT: D 349 PHE cc_start: 0.5304 (m-10) cc_final: 0.4985 (m-10) REVERT: D 521 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6264 (tt0) REVERT: A 161 GLN cc_start: 0.7391 (OUTLIER) cc_final: 0.7112 (mp10) REVERT: A 174 GLU cc_start: 0.7320 (mp0) cc_final: 0.7061 (mm-30) REVERT: A 311 GLU cc_start: 0.8498 (tt0) cc_final: 0.8220 (tt0) REVERT: A 340 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7269 (mp0) REVERT: A 378 GLU cc_start: 0.8142 (tt0) cc_final: 0.7915 (tp30) REVERT: A 464 ILE cc_start: 0.7832 (tt) cc_final: 0.7562 (tp) REVERT: A 637 GLU cc_start: 0.7417 (mm-30) cc_final: 0.6888 (mp0) REVERT: A 934 LYS cc_start: 0.8586 (ttmm) cc_final: 0.8283 (ttpt) REVERT: C 84 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.7199 (t70) REVERT: C 86 MET cc_start: 0.7468 (ptp) cc_final: 0.7230 (ptp) REVERT: C 87 MET cc_start: 0.6794 (mmm) cc_final: 0.6321 (mtt) REVERT: C 108 ARG cc_start: 0.7795 (OUTLIER) cc_final: 0.7565 (mtm180) REVERT: C 150 ASP cc_start: 0.7083 (OUTLIER) cc_final: 0.6516 (p0) REVERT: C 394 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.6075 (ptm160) REVERT: C 424 ASP cc_start: 0.8267 (t0) cc_final: 0.7870 (m-30) outliers start: 70 outliers final: 41 residues processed: 285 average time/residue: 0.7127 time to fit residues: 227.6812 Evaluate side-chains 277 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 223 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain B residue 962 ILE Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 108 ARG Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 572 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 2 optimal weight: 0.9980 chunk 137 optimal weight: 0.5980 chunk 254 optimal weight: 4.9990 chunk 242 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.144644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.125610 restraints weight = 27050.147| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.30 r_work: 0.3338 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 22210 Z= 0.105 Angle : 0.471 7.798 30108 Z= 0.251 Chirality : 0.040 0.141 3250 Planarity : 0.003 0.051 3889 Dihedral : 4.103 38.660 2953 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.68 % Allowed : 22.24 % Favored : 75.08 % 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: 0.80 (0.16), residues: 2709 helix: 1.50 (0.14), residues: 1347 sheet: -0.03 (0.30), residues: 302 loop : -0.49 (0.19), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 267 TYR 0.014 0.001 TYR B 469 PHE 0.013 0.001 PHE B 220 TRP 0.013 0.001 TRP B 121 HIS 0.002 0.001 HIS D 477 Details of bonding type rmsd covalent geometry : bond 0.00233 (22209) covalent geometry : angle 0.47103 (30106) SS BOND : bond 0.00765 ( 1) SS BOND : angle 1.71775 ( 2) hydrogen bonds : bond 0.04334 ( 1054) hydrogen bonds : angle 4.10105 ( 2931) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 231 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 115 ASP cc_start: 0.7771 (t0) cc_final: 0.7041 (m-30) REVERT: B 175 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7512 (p0) REVERT: B 259 LYS cc_start: 0.8652 (OUTLIER) cc_final: 0.7813 (ptpt) REVERT: B 388 MET cc_start: 0.8739 (mtp) cc_final: 0.8480 (mtm) REVERT: B 394 THR cc_start: 0.8695 (t) cc_final: 0.8383 (m) REVERT: B 505 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7006 (pm20) REVERT: B 600 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7285 (mm-30) REVERT: B 604 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.6760 (mp0) REVERT: B 673 GLU cc_start: 0.7750 (OUTLIER) cc_final: 0.7400 (mm-30) REVERT: B 736 LYS cc_start: 0.8060 (tptt) cc_final: 0.7682 (mmtm) REVERT: B 967 LYS cc_start: 0.7986 (tttt) cc_final: 0.7553 (mptp) REVERT: D 83 TYR cc_start: 0.2928 (p90) cc_final: 0.1518 (p90) REVERT: D 179 MET cc_start: 0.7332 (mmm) cc_final: 0.5960 (mpm) REVERT: D 180 GLU cc_start: 0.8145 (OUTLIER) cc_final: 0.7620 (tp30) REVERT: D 182 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6547 (mt-10) REVERT: D 278 ASP cc_start: 0.6198 (p0) cc_final: 0.5601 (m-30) REVERT: D 349 PHE cc_start: 0.5239 (m-10) cc_final: 0.4918 (m-10) REVERT: D 521 GLU cc_start: 0.6898 (mt-10) cc_final: 0.6314 (tt0) REVERT: A 174 GLU cc_start: 0.7292 (mp0) cc_final: 0.7050 (mm-30) REVERT: A 311 GLU cc_start: 0.8491 (tt0) cc_final: 0.8222 (tt0) REVERT: A 340 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7295 (mp0) REVERT: A 378 GLU cc_start: 0.8087 (tt0) cc_final: 0.7853 (tp30) REVERT: A 462 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7145 (mpp) REVERT: A 464 ILE cc_start: 0.7717 (tt) cc_final: 0.7480 (tp) REVERT: A 637 GLU cc_start: 0.7372 (mm-30) cc_final: 0.6863 (mp0) REVERT: A 934 LYS cc_start: 0.8556 (ttmm) cc_final: 0.8253 (ttpt) REVERT: C 87 MET cc_start: 0.6800 (mmm) cc_final: 0.6336 (mtt) REVERT: C 150 ASP cc_start: 0.7045 (OUTLIER) cc_final: 0.6462 (p0) REVERT: C 267 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.8128 (ptm-80) REVERT: C 394 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.5946 (ptm160) REVERT: C 424 ASP cc_start: 0.8268 (t0) cc_final: 0.7840 (m-30) outliers start: 62 outliers final: 42 residues processed: 278 average time/residue: 0.7160 time to fit residues: 223.3659 Evaluate side-chains 283 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 229 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 420 GLU Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 868 GLU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 267 ARG Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 572 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 44 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 chunk 265 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 269 optimal weight: 0.5980 chunk 77 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 GLN A 161 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.144466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.124618 restraints weight = 27019.777| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.38 r_work: 0.3323 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22210 Z= 0.134 Angle : 0.508 8.933 30108 Z= 0.268 Chirality : 0.041 0.150 3250 Planarity : 0.004 0.053 3889 Dihedral : 4.219 39.209 2953 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.64 % Allowed : 22.33 % Favored : 75.03 % 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 (0.16), residues: 2709 helix: 1.39 (0.14), residues: 1351 sheet: -0.07 (0.30), residues: 301 loop : -0.53 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 267 TYR 0.016 0.002 TYR B 469 PHE 0.017 0.001 PHE B 220 TRP 0.013 0.001 TRP B 121 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00313 (22209) covalent geometry : angle 0.50741 (30106) SS BOND : bond 0.01008 ( 1) SS BOND : angle 1.92248 ( 2) hydrogen bonds : bond 0.04862 ( 1054) hydrogen bonds : angle 4.16833 ( 2931) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 230 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 115 ASP cc_start: 0.7812 (t0) cc_final: 0.7097 (m-30) REVERT: B 175 ASP cc_start: 0.7726 (OUTLIER) cc_final: 0.7475 (p0) REVERT: B 239 MET cc_start: 0.7305 (mmm) cc_final: 0.6770 (tpp) REVERT: B 259 LYS cc_start: 0.8662 (OUTLIER) cc_final: 0.7835 (ptpt) REVERT: B 388 MET cc_start: 0.8761 (mtp) cc_final: 0.8495 (mtm) REVERT: B 394 THR cc_start: 0.8781 (t) cc_final: 0.8426 (m) REVERT: B 505 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7020 (pm20) REVERT: B 600 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7302 (mm-30) REVERT: B 604 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.6765 (mp0) REVERT: B 673 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7431 (mm-30) REVERT: B 736 LYS cc_start: 0.8088 (tptt) cc_final: 0.7635 (mmtm) REVERT: B 842 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7669 (mp0) REVERT: B 967 LYS cc_start: 0.7999 (tttt) cc_final: 0.7549 (mptp) REVERT: D 83 TYR cc_start: 0.3032 (p90) cc_final: 0.1549 (p90) REVERT: D 179 MET cc_start: 0.7283 (mmm) cc_final: 0.5941 (mpm) REVERT: D 180 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7622 (tp30) REVERT: D 182 GLU cc_start: 0.7398 (OUTLIER) cc_final: 0.6486 (mt-10) REVERT: D 278 ASP cc_start: 0.6260 (p0) cc_final: 0.5677 (m-30) REVERT: D 349 PHE cc_start: 0.5252 (m-10) cc_final: 0.4912 (m-10) REVERT: D 521 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6264 (tt0) REVERT: A 161 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.7186 (mp10) REVERT: A 174 GLU cc_start: 0.7295 (mp0) cc_final: 0.7067 (mm-30) REVERT: A 311 GLU cc_start: 0.8494 (tt0) cc_final: 0.8224 (tt0) REVERT: A 340 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7276 (mp0) REVERT: A 378 GLU cc_start: 0.8133 (tt0) cc_final: 0.7894 (tp30) REVERT: A 462 MET cc_start: 0.7668 (OUTLIER) cc_final: 0.7120 (mpp) REVERT: A 464 ILE cc_start: 0.7808 (tt) cc_final: 0.7546 (tp) REVERT: A 637 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6853 (mp0) REVERT: A 934 LYS cc_start: 0.8580 (ttmm) cc_final: 0.8270 (ttpt) REVERT: C 86 MET cc_start: 0.7234 (ptp) cc_final: 0.6961 (ptp) REVERT: C 87 MET cc_start: 0.6851 (mmm) cc_final: 0.6356 (mtt) REVERT: C 150 ASP cc_start: 0.7141 (OUTLIER) cc_final: 0.6504 (p0) REVERT: C 394 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.6083 (ptm160) outliers start: 61 outliers final: 41 residues processed: 275 average time/residue: 0.7393 time to fit residues: 228.0848 Evaluate side-chains 275 residues out of total 2311 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 222 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 175 ASP Chi-restraints excluded: chain B residue 259 LYS Chi-restraints excluded: chain B residue 391 THR Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 467 SER Chi-restraints excluded: chain B residue 505 GLU Chi-restraints excluded: chain B residue 604 GLU Chi-restraints excluded: chain B residue 673 GLU Chi-restraints excluded: chain B residue 691 GLU Chi-restraints excluded: chain B residue 787 VAL Chi-restraints excluded: chain B residue 812 THR Chi-restraints excluded: chain B residue 837 ASP Chi-restraints excluded: chain B residue 849 GLU Chi-restraints excluded: chain B residue 883 VAL Chi-restraints excluded: chain B residue 894 THR Chi-restraints excluded: chain B residue 927 GLU Chi-restraints excluded: chain D residue 108 ARG Chi-restraints excluded: chain D residue 180 GLU Chi-restraints excluded: chain D residue 182 GLU Chi-restraints excluded: chain D residue 214 LEU Chi-restraints excluded: chain D residue 241 LEU Chi-restraints excluded: chain D residue 248 SER Chi-restraints excluded: chain D residue 249 ILE Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 501 THR Chi-restraints excluded: chain A residue 161 GLN Chi-restraints excluded: chain A residue 192 ARG Chi-restraints excluded: chain A residue 246 VAL Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 455 GLU Chi-restraints excluded: chain A residue 462 MET Chi-restraints excluded: chain A residue 499 LEU Chi-restraints excluded: chain A residue 501 VAL Chi-restraints excluded: chain A residue 613 MET Chi-restraints excluded: chain A residue 655 THR Chi-restraints excluded: chain A residue 820 THR Chi-restraints excluded: chain A residue 846 GLU Chi-restraints excluded: chain A residue 850 GLU Chi-restraints excluded: chain A residue 867 LYS Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 976 ILE Chi-restraints excluded: chain C residue 150 ASP Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 299 LYS Chi-restraints excluded: chain C residue 394 ARG Chi-restraints excluded: chain C residue 411 VAL Chi-restraints excluded: chain C residue 554 MET Chi-restraints excluded: chain C residue 572 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 270 random chunks: chunk 45 optimal weight: 0.6980 chunk 199 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 191 optimal weight: 1.9990 chunk 70 optimal weight: 0.1980 chunk 114 optimal weight: 2.9990 chunk 236 optimal weight: 0.3980 chunk 37 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.144458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.124628 restraints weight = 27036.155| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.41 r_work: 0.3323 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.428 22210 Z= 0.205 Angle : 0.675 65.897 30108 Z= 0.397 Chirality : 0.041 0.150 3250 Planarity : 0.006 0.272 3889 Dihedral : 4.222 39.198 2953 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.60 % Allowed : 22.46 % Favored : 74.95 % 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: 0.69 (0.16), residues: 2709 helix: 1.39 (0.14), residues: 1351 sheet: -0.07 (0.30), residues: 301 loop : -0.53 (0.19), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 267 TYR 0.013 0.001 TYR A 353 PHE 0.017 0.001 PHE B 220 TRP 0.013 0.001 TRP B 121 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00457 (22209) covalent geometry : angle 0.67451 (30106) SS BOND : bond 0.00774 ( 1) SS BOND : angle 1.87110 ( 2) hydrogen bonds : bond 0.04827 ( 1054) hydrogen bonds : angle 4.16914 ( 2931) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7943.75 seconds wall clock time: 135 minutes 47.41 seconds (8147.41 seconds total)