Starting phenix.real_space_refine on Sat Jul 4 16:01:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpm_37719/07_2026/8wpm_37719.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpm_37719/07_2026/8wpm_37719.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8wpm_37719/07_2026/8wpm_37719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpm_37719/07_2026/8wpm_37719.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wpm_37719/07_2026/8wpm_37719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpm_37719/07_2026/8wpm_37719.map" } resolution = 3.43 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= 0.002 sd= 0.020 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: 8 Type Number sf(0) Gaussians Ca 3 9.91 5 Zn 4 6.06 5 S 116 5.16 5 Cl 4 4.86 5 C 14317 2.51 5 N 3654 2.21 5 O 3924 1.98 5 F 12 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 80 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 22034 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 669, 5421 Classifications: {'peptide': 669} Link IDs: {'PTRANS': 15, 'TRANS': 653} Chain breaks: 4 Chain: "B" Number of atoms: 5435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 666, 5435 Classifications: {'peptide': 666} Link IDs: {'PTRANS': 23, 'TRANS': 642} Chain breaks: 5 Chain: "C" Number of atoms: 5501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5501 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 24, 'TRANS': 648} Chain breaks: 5 Chain: "D" Number of atoms: 5526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 677, 5526 Classifications: {'peptide': 677} Link IDs: {'PTRANS': 24, 'TRANS': 652} Chain breaks: 4 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 37 Unusual residues: {' ZN': 1, 'PJQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'PJQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'PJQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 37 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'PJQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain breaks: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1081 SG CYS A 193 13.039 79.737 61.796 1.00142.89 S ATOM 1096 SG CYS A 195 10.262 78.095 63.896 1.00134.50 S ATOM 1117 SG CYS A 198 13.850 76.668 63.963 1.00139.79 S ATOM 6570 SG CYS B 176 57.664 55.160 96.833 1.00131.20 S ATOM 6584 SG CYS B 178 56.901 52.372 99.333 1.00126.35 S ATOM 6606 SG CYS B 181 60.216 52.352 97.327 1.00125.25 S ATOM 12015 SG CYS C 176 97.090 56.851 52.193 1.00131.66 S ATOM 12029 SG CYS C 178 98.496 55.112 49.064 1.00131.62 S ATOM 12051 SG CYS C 181 94.881 56.374 49.043 1.00129.92 S ATOM 17505 SG CYS D 176 54.190 81.838 17.088 1.00118.12 S ATOM 17519 SG CYS D 178 52.071 81.300 13.888 1.00119.31 S ATOM 17541 SG CYS D 181 50.857 79.917 17.221 1.00117.98 S Time building chain proxies: 5.15, per 1000 atoms: 0.23 Number of scatterers: 22034 At special positions: 0 Unit cell: (118.9, 150.06, 122.18, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 Ca 3 19.99 Cl 4 17.00 S 116 16.00 F 12 9.00 O 3924 8.00 N 3654 7.00 C 14317 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 571 " - pdb=" SG CYS A 576 " distance=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 554 " distance=2.03 Simple disulfide: pdb=" SG CYS C 549 " - pdb=" SG CYS C 554 " distance=2.03 Simple disulfide: pdb=" SG CYS D 549 " - pdb=" SG CYS D 554 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 882.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 802 " pdb="ZN ZN A 802 " - pdb=" ND1 HIS A 189 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 193 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 195 " pdb="ZN ZN A 802 " - pdb=" SG CYS A 198 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 178 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 176 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 181 " pdb=" ZN C1002 " pdb="ZN ZN C1002 " - pdb=" ND1 HIS C 172 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 178 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 181 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 176 " pdb=" ZN D1002 " pdb="ZN ZN D1002 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 181 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 178 " pdb="ZN ZN D1002 " - pdb=" SG CYS D 176 " Number of angles added : 12 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5168 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 3 sheets defined 77.2% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 removed outlier: 4.043A pdb=" N LYS A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 73 Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.564A pdb=" N ASN A 94 " --> pdb=" O ILE A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 107 Processing helix chain 'A' and resid 113 through 120 Processing helix chain 'A' and resid 123 through 130 Processing helix chain 'A' and resid 161 through 170 Processing helix chain 'A' and resid 171 through 179 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 197 through 205 removed outlier: 3.586A pdb=" N ASN A 202 " --> pdb=" O CYS A 198 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N LYS A 203 " --> pdb=" O SER A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 221 Processing helix chain 'A' and resid 222 through 229 Processing helix chain 'A' and resid 232 through 251 Processing helix chain 'A' and resid 254 through 275 Processing helix chain 'A' and resid 278 through 287 Processing helix chain 'A' and resid 307 through 316 Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.758A pdb=" N VAL A 322 " --> pdb=" O GLN A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 337 removed outlier: 3.637A pdb=" N GLY A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 343 removed outlier: 3.978A pdb=" N ARG A 343 " --> pdb=" O SER A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 360 removed outlier: 4.143A pdb=" N PHE A 360 " --> pdb=" O THR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 371 Processing helix chain 'A' and resid 382 through 407 removed outlier: 3.729A pdb=" N SER A 405 " --> pdb=" O LEU A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 445 Processing helix chain 'A' and resid 447 through 453 removed outlier: 3.666A pdb=" N GLU A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 480 Processing helix chain 'A' and resid 485 through 489 Processing helix chain 'A' and resid 493 through 512 Processing helix chain 'A' and resid 513 through 520 removed outlier: 4.091A pdb=" N THR A 518 " --> pdb=" O PHE A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 559 removed outlier: 5.000A pdb=" N GLN A 535 " --> pdb=" O GLY A 531 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ASP A 536 " --> pdb=" O GLN A 532 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N PHE A 537 " --> pdb=" O MET A 533 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LEU A 546 " --> pdb=" O GLY A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 584 removed outlier: 4.021A pdb=" N THR A 583 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE A 584 " --> pdb=" O ASN A 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 580 through 584' Processing helix chain 'A' and resid 586 through 596 removed outlier: 3.516A pdb=" N TRP A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 removed outlier: 3.510A pdb=" N VAL A 608 " --> pdb=" O ALA A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 633 Processing helix chain 'A' and resid 636 through 653 Processing helix chain 'A' and resid 656 through 671 Processing helix chain 'A' and resid 722 through 754 Processing helix chain 'A' and resid 757 through 779 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 45 through 57 removed outlier: 3.848A pdb=" N ILE B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 72 through 81 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.611A pdb=" N PHE B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 107 Processing helix chain 'B' and resid 110 through 117 removed outlier: 4.064A pdb=" N LEU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 165 Processing helix chain 'B' and resid 178 through 188 Processing helix chain 'B' and resid 188 through 204 Processing helix chain 'B' and resid 205 through 213 Processing helix chain 'B' and resid 215 through 234 Processing helix chain 'B' and resid 237 through 258 Processing helix chain 'B' and resid 261 through 270 Processing helix chain 'B' and resid 286 through 295 Processing helix chain 'B' and resid 297 through 302 Processing helix chain 'B' and resid 303 through 315 Processing helix chain 'B' and resid 325 through 339 Processing helix chain 'B' and resid 339 through 346 removed outlier: 3.734A pdb=" N PHE B 343 " --> pdb=" O LEU B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 360 removed outlier: 3.652A pdb=" N ILE B 359 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 385 Processing helix chain 'B' and resid 399 through 404 removed outlier: 4.181A pdb=" N TRP B 404 " --> pdb=" O THR B 400 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 423 removed outlier: 3.826A pdb=" N TRP B 409 " --> pdb=" O MET B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 432 removed outlier: 3.700A pdb=" N ASP B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 458 Processing helix chain 'B' and resid 472 through 491 Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.660A pdb=" N PHE B 496 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N THR B 497 " --> pdb=" O SER B 494 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA B 498 " --> pdb=" O LEU B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 539 removed outlier: 4.715A pdb=" N LEU B 514 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 5.130A pdb=" N ASP B 515 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE B 522 " --> pdb=" O LYS B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 574 Processing helix chain 'B' and resid 580 through 585 removed outlier: 3.667A pdb=" N VAL B 583 " --> pdb=" O ASN B 580 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR B 584 " --> pdb=" O LEU B 581 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 610 Processing helix chain 'B' and resid 611 through 630 removed outlier: 4.451A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 646 Processing helix chain 'B' and resid 696 through 726 Processing helix chain 'B' and resid 731 through 754 removed outlier: 3.627A pdb=" N ASN B 735 " --> pdb=" O LEU B 731 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N PHE B 736 " --> pdb=" O THR B 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 58 removed outlier: 3.517A pdb=" N VAL C 48 " --> pdb=" O ASP C 44 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 57 " --> pdb=" O GLU C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 83 through 92 removed outlier: 3.634A pdb=" N PHE C 92 " --> pdb=" O LEU C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 106 Processing helix chain 'C' and resid 110 through 117 removed outlier: 3.527A pdb=" N ASN C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 165 Processing helix chain 'C' and resid 178 through 188 Processing helix chain 'C' and resid 188 through 204 Processing helix chain 'C' and resid 205 through 213 Processing helix chain 'C' and resid 215 through 234 Processing helix chain 'C' and resid 237 through 258 removed outlier: 3.513A pdb=" N TYR C 241 " --> pdb=" O PHE C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 261 through 270 Processing helix chain 'C' and resid 286 through 295 Processing helix chain 'C' and resid 297 through 302 Processing helix chain 'C' and resid 303 through 315 Processing helix chain 'C' and resid 325 through 339 removed outlier: 3.752A pdb=" N LEU C 339 " --> pdb=" O ILE C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 350 Processing helix chain 'C' and resid 353 through 359 removed outlier: 3.788A pdb=" N ILE C 359 " --> pdb=" O LEU C 355 " (cutoff:3.500A) Processing helix chain 'C' and resid 361 through 386 Processing helix chain 'C' and resid 402 through 423 Proline residue: C 408 - end of helix Processing helix chain 'C' and resid 426 through 432 removed outlier: 3.527A pdb=" N ASP C 432 " --> pdb=" O ASP C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 458 Processing helix chain 'C' and resid 464 through 468 Processing helix chain 'C' and resid 472 through 491 Processing helix chain 'C' and resid 492 through 497 removed outlier: 3.739A pdb=" N THR C 497 " --> pdb=" O SER C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 539 removed outlier: 4.487A pdb=" N LEU C 505 " --> pdb=" O HIS C 501 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET C 512 " --> pdb=" O SER C 508 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LEU C 514 " --> pdb=" O GLY C 510 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ASP C 515 " --> pdb=" O ARG C 511 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE C 522 " --> pdb=" O LYS C 518 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 574 Processing helix chain 'C' and resid 580 through 585 removed outlier: 3.635A pdb=" N VAL C 583 " --> pdb=" O ASN C 580 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN C 585 " --> pdb=" O TYR C 582 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 610 Processing helix chain 'C' and resid 611 through 628 removed outlier: 3.832A pdb=" N ILE C 617 " --> pdb=" O LEU C 613 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 645 Processing helix chain 'C' and resid 695 through 728 Processing helix chain 'C' and resid 732 through 754 removed outlier: 4.150A pdb=" N PHE C 736 " --> pdb=" O THR C 732 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 56 removed outlier: 3.650A pdb=" N VAL D 48 " --> pdb=" O ASP D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 91 removed outlier: 3.557A pdb=" N ILE D 86 " --> pdb=" O ASN D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 108 through 110 No H-bonds generated for 'chain 'D' and resid 108 through 110' Processing helix chain 'D' and resid 111 through 117 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 165 Processing helix chain 'D' and resid 178 through 188 Processing helix chain 'D' and resid 188 through 204 Processing helix chain 'D' and resid 205 through 213 Processing helix chain 'D' and resid 215 through 234 Processing helix chain 'D' and resid 237 through 258 Processing helix chain 'D' and resid 261 through 270 removed outlier: 3.571A pdb=" N LEU D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 295 Processing helix chain 'D' and resid 297 through 302 Processing helix chain 'D' and resid 303 through 315 Processing helix chain 'D' and resid 325 through 339 Processing helix chain 'D' and resid 339 through 350 Processing helix chain 'D' and resid 361 through 386 removed outlier: 3.536A pdb=" N GLN D 385 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 405 through 423 removed outlier: 4.025A pdb=" N TRP D 409 " --> pdb=" O MET D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 424 through 432 removed outlier: 4.197A pdb=" N ASP D 428 " --> pdb=" O GLY D 424 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP D 432 " --> pdb=" O ASP D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 458 removed outlier: 3.520A pdb=" N LEU D 436 " --> pdb=" O ASP D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 468 Processing helix chain 'D' and resid 472 through 489 Processing helix chain 'D' and resid 490 through 498 removed outlier: 3.974A pdb=" N THR D 497 " --> pdb=" O SER D 494 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA D 498 " --> pdb=" O LEU D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 502 through 539 removed outlier: 4.450A pdb=" N LEU D 514 " --> pdb=" O GLY D 510 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP D 515 " --> pdb=" O ARG D 511 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ILE D 522 " --> pdb=" O LYS D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 540 through 542 No H-bonds generated for 'chain 'D' and resid 540 through 542' Processing helix chain 'D' and resid 563 through 574 Processing helix chain 'D' and resid 575 through 577 No H-bonds generated for 'chain 'D' and resid 575 through 577' Processing helix chain 'D' and resid 580 through 584 removed outlier: 3.777A pdb=" N VAL D 583 " --> pdb=" O ASN D 580 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR D 584 " --> pdb=" O LEU D 581 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 580 through 584' Processing helix chain 'D' and resid 590 through 628 removed outlier: 5.384A pdb=" N LEU D 612 " --> pdb=" O SER D 608 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LEU D 613 " --> pdb=" O LEU D 609 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN D 614 " --> pdb=" O VAL D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 646 removed outlier: 3.692A pdb=" N TYR D 646 " --> pdb=" O LEU D 642 " (cutoff:3.500A) Processing helix chain 'D' and resid 654 through 658 removed outlier: 3.817A pdb=" N ASN D 658 " --> pdb=" O THR D 655 " (cutoff:3.500A) Processing helix chain 'D' and resid 696 through 726 Processing helix chain 'D' and resid 732 through 754 removed outlier: 4.088A pdb=" N PHE D 736 " --> pdb=" O THR D 732 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 186 removed outlier: 3.582A pdb=" N LEU A 185 " --> pdb=" O ILE D 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 17 through 19 Processing sheet with id=AA3, first strand: chain 'C' and resid 17 through 18 1441 hydrogen bonds defined for protein. 4248 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: 3.84 Time building geometry restraints manager: 2.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 3523 1.31 - 1.43: 6210 1.43 - 1.56: 12614 1.56 - 1.69: 2 1.69 - 1.82: 183 Bond restraints: 22532 Sorted by residual: bond pdb=" C02 PJQ C1001 " pdb=" O01 PJQ C1001 " ideal model delta sigma weight residual 1.222 1.399 -0.177 2.00e-02 2.50e+03 7.87e+01 bond pdb=" C02 PJQ B1001 " pdb=" O01 PJQ B1001 " ideal model delta sigma weight residual 1.222 1.399 -0.177 2.00e-02 2.50e+03 7.85e+01 bond pdb=" C02 PJQ D1001 " pdb=" O01 PJQ D1001 " ideal model delta sigma weight residual 1.222 1.399 -0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" C02 PJQ A 801 " pdb=" O01 PJQ A 801 " ideal model delta sigma weight residual 1.222 1.397 -0.175 2.00e-02 2.50e+03 7.66e+01 bond pdb=" C06 PJQ C1001 " pdb=" O07 PJQ C1001 " ideal model delta sigma weight residual 1.324 1.410 -0.086 2.00e-02 2.50e+03 1.84e+01 ... (remaining 22527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 29954 2.51 - 5.02: 455 5.02 - 7.54: 84 7.54 - 10.05: 18 10.05 - 12.56: 6 Bond angle restraints: 30517 Sorted by residual: angle pdb=" CA PRO C 397 " pdb=" N PRO C 397 " pdb=" CD PRO C 397 " ideal model delta sigma weight residual 112.00 105.38 6.62 1.40e+00 5.10e-01 2.24e+01 angle pdb=" C GLU D 403 " pdb=" N TRP D 404 " pdb=" CA TRP D 404 " ideal model delta sigma weight residual 121.54 130.51 -8.97 1.91e+00 2.74e-01 2.21e+01 angle pdb=" CA TYR B 36 " pdb=" CB TYR B 36 " pdb=" CG TYR B 36 " ideal model delta sigma weight residual 113.90 122.28 -8.38 1.80e+00 3.09e-01 2.17e+01 angle pdb=" N GLU A 410 " pdb=" CA GLU A 410 " pdb=" C GLU A 410 " ideal model delta sigma weight residual 112.97 108.24 4.73 1.06e+00 8.90e-01 1.99e+01 angle pdb=" N LEU D 392 " pdb=" CA LEU D 392 " pdb=" C LEU D 392 " ideal model delta sigma weight residual 114.31 108.56 5.75 1.29e+00 6.01e-01 1.98e+01 ... (remaining 30512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 11564 17.89 - 35.78: 1404 35.78 - 53.67: 373 53.67 - 71.56: 50 71.56 - 89.44: 21 Dihedral angle restraints: 13412 sinusoidal: 5483 harmonic: 7929 Sorted by residual: dihedral pdb=" CA PHE D 59 " pdb=" C PHE D 59 " pdb=" N LYS D 60 " pdb=" CA LYS D 60 " ideal model delta harmonic sigma weight residual 180.00 -158.77 -21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" CB CYS C 549 " pdb=" SG CYS C 549 " pdb=" SG CYS C 554 " pdb=" CB CYS C 554 " ideal model delta sinusoidal sigma weight residual -86.00 -51.62 -34.38 1 1.00e+01 1.00e-02 1.68e+01 dihedral pdb=" CA MET B 710 " pdb=" C MET B 710 " pdb=" N ARG B 711 " pdb=" CA ARG B 711 " ideal model delta harmonic sigma weight residual 180.00 160.14 19.86 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 13409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 2895 0.060 - 0.121: 472 0.121 - 0.181: 50 0.181 - 0.241: 2 0.241 - 0.302: 2 Chirality restraints: 3421 Sorted by residual: chirality pdb=" CB ILE A 432 " pdb=" CA ILE A 432 " pdb=" CG1 ILE A 432 " pdb=" CG2 ILE A 432 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CA PRO C 68 " pdb=" N PRO C 68 " pdb=" C PRO C 68 " pdb=" CB PRO C 68 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA TRP A 361 " pdb=" N TRP A 361 " pdb=" C TRP A 361 " pdb=" CB TRP A 361 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.53e-01 ... (remaining 3418 not shown) Planarity restraints: 3805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 396 " 0.067 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO C 397 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 397 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 397 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 397 " 0.065 5.00e-02 4.00e+02 9.46e-02 1.43e+01 pdb=" N PRO B 398 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO B 398 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 398 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 655 " 0.059 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO B 656 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO B 656 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 656 " 0.049 5.00e-02 4.00e+02 ... (remaining 3802 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 3919 2.77 - 3.30: 21409 3.30 - 3.83: 37706 3.83 - 4.37: 42231 4.37 - 4.90: 73704 Nonbonded interactions: 178969 Sorted by model distance: nonbonded pdb=" O ILE C 209 " pdb=" OG SER C 213 " model vdw 2.233 3.040 nonbonded pdb=" O LYS A 749 " pdb=" OG1 THR A 753 " model vdw 2.254 3.040 nonbonded pdb=" OG1 THR C 140 " pdb=" OD1 ASP C 142 " model vdw 2.256 3.040 nonbonded pdb=" OG SER B 213 " pdb=" OG1 THR B 219 " model vdw 2.280 3.040 nonbonded pdb=" OD1 ASP C 257 " pdb=" NE2 GLN C 303 " model vdw 2.292 3.120 ... (remaining 178964 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 'B' and resid 16 through 1003) selection = (chain 'C' and (resid 16 through 117 or resid 135 through 385 or resid 391 throu \ gh 458 or resid 465 through 659 or resid 695 through 1003)) selection = (chain 'D' and (resid 16 through 117 or resid 135 through 274 or resid 286 throu \ gh 385 or resid 391 through 458 or resid 465 through 1003)) } 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: 3.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.350 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.177 22552 Z= 0.278 Angle : 0.801 12.562 30537 Z= 0.438 Chirality : 0.044 0.302 3421 Planarity : 0.006 0.098 3805 Dihedral : 16.530 89.444 8232 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.46 % Allowed : 22.29 % Favored : 77.26 % 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: -0.26 (0.15), residues: 2641 helix: 0.26 (0.11), residues: 1965 sheet: None (None), residues: 0 loop : -1.19 (0.23), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 511 TYR 0.029 0.002 TYR A 510 PHE 0.046 0.002 PHE D 746 TRP 0.034 0.002 TRP D 468 HIS 0.015 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00545 / 0.28 (22532) covalent geometry : angle 0.80079 / 0.44 (30517) SS BOND : bond 0.00215 / 0.11 ( 4) SS BOND : angle 0.58259 / 0.28 ( 8) hydrogen bonds : bond 0.13239 / 9.06 ( 1441) hydrogen bonds : angle 5.17368 / 3.64 ( 4248) metal coordination : bond 0.00618 / 0.42 ( 16) metal coordination : angle 0.93367 / 0.51 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 329 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 675 LYS cc_start: 0.7263 (mtmm) cc_final: 0.6719 (ttmm) REVERT: B 421 MET cc_start: 0.6615 (tpp) cc_final: 0.6287 (tpp) REVERT: B 427 GLN cc_start: 0.7227 (mm-40) cc_final: 0.6980 (pm20) REVERT: C 397 PRO cc_start: 0.6919 (Cg_exo) cc_final: 0.6614 (Cg_endo) REVERT: C 470 MET cc_start: 0.7482 (tmm) cc_final: 0.7193 (ttp) REVERT: C 538 TYR cc_start: 0.8673 (m-10) cc_final: 0.8427 (m-80) outliers start: 11 outliers final: 5 residues processed: 333 average time/residue: 0.1495 time to fit residues: 80.0019 Evaluate side-chains 310 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 305 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 550 SER Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain D residue 109 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.0060 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.5980 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 5.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 328 GLN A 329 GLN A 457 GLN A 581 ASN A 646 HIS A 650 GLN A 722 ASN A 732 GLN A 760 ASN B 62 ASN B 102 HIS B 163 GLN B 605 ASN B 614 ASN B 621 ASN B 622 ASN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN C 250 GLN C 442 ASN C 472 HIS C 485 ASN C 559 ASN C 569 GLN C 621 ASN C 630 HIS C 703 HIS D 64 ASN D 135 GLN D 250 GLN D 305 ASN D 308 GLN D 427 GLN D 532 ASN D 569 GLN D 589 GLN D 605 ASN D 614 ASN D 658 ASN D 735 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.207092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.170152 restraints weight = 29565.413| |-----------------------------------------------------------------------------| r_work (start): 0.4064 rms_B_bonded: 2.24 r_work: 0.3901 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 22552 Z= 0.128 Angle : 0.494 7.485 30537 Z= 0.261 Chirality : 0.037 0.155 3421 Planarity : 0.004 0.058 3805 Dihedral : 4.994 59.872 2941 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.20 % Allowed : 20.79 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.16), residues: 2641 helix: 1.38 (0.11), residues: 1993 sheet: None (None), residues: 0 loop : -0.90 (0.25), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 105 TYR 0.026 0.001 TYR A 510 PHE 0.021 0.001 PHE D 539 TRP 0.017 0.001 TRP D 409 HIS 0.006 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (22532) covalent geometry : angle 0.49285 / 0.26 (30517) SS BOND : bond 0.00136 / 0.07 ( 4) SS BOND : angle 0.54981 / 0.27 ( 8) hydrogen bonds : bond 0.04186 / 2.75 ( 1441) hydrogen bonds : angle 3.81475 / 2.69 ( 4248) metal coordination : bond 0.00499 / 0.36 ( 16) metal coordination : angle 1.47906 / 0.67 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 326 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.5344 (ptp) cc_final: 0.5116 (ptp) REVERT: A 652 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7994 (mp) REVERT: B 378 PHE cc_start: 0.6300 (t80) cc_final: 0.6089 (t80) REVERT: B 421 MET cc_start: 0.6547 (tpp) cc_final: 0.6154 (tpp) outliers start: 53 outliers final: 27 residues processed: 360 average time/residue: 0.1452 time to fit residues: 84.4522 Evaluate side-chains 328 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 300 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 340 PHE Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 518 LYS Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 215 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 106 optimal weight: 0.9990 chunk 81 optimal weight: 0.9990 chunk 61 optimal weight: 9.9990 chunk 28 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 214 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 181 GLN A 288 HIS ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 HIS A 683 ASN B 569 GLN B 735 ASN ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN D 532 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.196240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.158977 restraints weight = 29469.084| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.21 r_work: 0.3770 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22552 Z= 0.128 Angle : 0.478 6.881 30537 Z= 0.251 Chirality : 0.037 0.158 3421 Planarity : 0.004 0.061 3805 Dihedral : 4.701 58.222 2936 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.54 % Allowed : 21.16 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.76 (0.17), residues: 2641 helix: 1.80 (0.12), residues: 1989 sheet: None (None), residues: 0 loop : -0.81 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 511 TYR 0.022 0.001 TYR A 408 PHE 0.016 0.001 PHE D 59 TRP 0.012 0.001 TRP D 409 HIS 0.004 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (22532) covalent geometry : angle 0.47759 / 0.25 (30517) SS BOND : bond 0.00121 / 0.06 ( 4) SS BOND : angle 0.80640 / 0.45 ( 8) hydrogen bonds : bond 0.04041 / 2.66 ( 1441) hydrogen bonds : angle 3.67786 / 2.61 ( 4248) metal coordination : bond 0.00353 / 0.21 ( 16) metal coordination : angle 1.06242 / 0.49 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 327 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.5188 (ptp) cc_final: 0.4892 (ptp) REVERT: A 652 ILE cc_start: 0.8100 (OUTLIER) cc_final: 0.7739 (mp) REVERT: A 678 LEU cc_start: 0.7074 (mt) cc_final: 0.6298 (pt) REVERT: A 746 MET cc_start: 0.7207 (tmm) cc_final: 0.6767 (tpp) REVERT: B 378 PHE cc_start: 0.6289 (t80) cc_final: 0.6065 (t80) REVERT: B 421 MET cc_start: 0.6543 (tpp) cc_final: 0.6070 (tpp) REVERT: B 437 MET cc_start: 0.6268 (mmt) cc_final: 0.6009 (ttt) REVERT: B 710 MET cc_start: 0.8496 (tpt) cc_final: 0.7843 (tpt) REVERT: C 88 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8675 (tp) REVERT: C 509 LEU cc_start: 0.7297 (OUTLIER) cc_final: 0.6705 (mp) REVERT: D 67 ASP cc_start: 0.7364 (t0) cc_final: 0.7126 (t0) REVERT: D 256 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8720 (mm) REVERT: D 563 THR cc_start: 0.8100 (t) cc_final: 0.7792 (p) REVERT: D 723 ARG cc_start: 0.7136 (ttm110) cc_final: 0.6869 (ttm110) outliers start: 61 outliers final: 33 residues processed: 365 average time/residue: 0.1438 time to fit residues: 84.5702 Evaluate side-chains 339 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 302 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 472 HIS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 518 LYS Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 15 optimal weight: 5.9990 chunk 108 optimal weight: 1.9990 chunk 138 optimal weight: 0.8980 chunk 250 optimal weight: 3.9990 chunk 170 optimal weight: 20.0000 chunk 171 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 34 optimal weight: 20.0000 chunk 66 optimal weight: 2.9990 chunk 224 optimal weight: 1.9990 chunk 157 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 GLN A 170 ASN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 GLN D 369 HIS D 442 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.194739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.157050 restraints weight = 29429.169| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.23 r_work: 0.3745 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22552 Z= 0.143 Angle : 0.494 7.217 30537 Z= 0.256 Chirality : 0.037 0.161 3421 Planarity : 0.004 0.060 3805 Dihedral : 4.613 57.376 2936 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.24 % Allowed : 20.87 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.93 (0.17), residues: 2641 helix: 1.94 (0.12), residues: 1989 sheet: None (None), residues: 0 loop : -0.81 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 246 TYR 0.020 0.001 TYR A 408 PHE 0.017 0.001 PHE D 59 TRP 0.012 0.001 TRP B 314 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (22532) covalent geometry : angle 0.49419 / 0.26 (30517) SS BOND : bond 0.00212 / 0.11 ( 4) SS BOND : angle 0.42059 / 0.20 ( 8) hydrogen bonds : bond 0.04073 / 2.67 ( 1441) hydrogen bonds : angle 3.66103 / 2.60 ( 4248) metal coordination : bond 0.00449 / 0.26 ( 16) metal coordination : angle 0.92113 / 0.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 328 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.5089 (ptp) cc_final: 0.4834 (ptp) REVERT: A 652 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7788 (mp) REVERT: A 746 MET cc_start: 0.7005 (tmm) cc_final: 0.6769 (tpp) REVERT: B 421 MET cc_start: 0.6559 (tpp) cc_final: 0.6062 (tpp) REVERT: B 437 MET cc_start: 0.6207 (mmt) cc_final: 0.5917 (ttp) REVERT: B 710 MET cc_start: 0.8602 (tpt) cc_final: 0.8095 (tpp) REVERT: C 509 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6662 (mp) REVERT: C 587 LYS cc_start: 0.7426 (OUTLIER) cc_final: 0.6865 (pttm) REVERT: C 740 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7874 (mtmt) REVERT: D 67 ASP cc_start: 0.7436 (t0) cc_final: 0.7218 (t0) REVERT: D 250 GLN cc_start: 0.8527 (tp-100) cc_final: 0.8077 (tp40) REVERT: D 253 LYS cc_start: 0.9045 (ttpp) cc_final: 0.8806 (tttm) REVERT: D 256 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8778 (mm) REVERT: D 563 THR cc_start: 0.8141 (t) cc_final: 0.7853 (p) REVERT: D 723 ARG cc_start: 0.7056 (ttm110) cc_final: 0.6781 (ttm110) outliers start: 78 outliers final: 52 residues processed: 377 average time/residue: 0.1510 time to fit residues: 90.6665 Evaluate side-chains 369 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 312 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 740 LYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 496 PHE Chi-restraints excluded: chain D residue 518 LYS Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 26 optimal weight: 5.9990 chunk 155 optimal weight: 3.9990 chunk 6 optimal weight: 9.9990 chunk 250 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 172 optimal weight: 2.9990 chunk 71 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 205 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 101 GLN A 170 ASN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 HIS ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS C 532 ASN C 707 GLN D 442 ASN D 590 HIS D 605 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.191225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.152654 restraints weight = 29346.437| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.24 r_work: 0.3699 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 22552 Z= 0.195 Angle : 0.555 9.382 30537 Z= 0.285 Chirality : 0.039 0.173 3421 Planarity : 0.004 0.060 3805 Dihedral : 4.619 55.798 2933 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.49 % Allowed : 21.33 % Favored : 75.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.17), residues: 2641 helix: 1.92 (0.12), residues: 1983 sheet: None (None), residues: 0 loop : -0.84 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 246 TYR 0.023 0.002 TYR A 217 PHE 0.017 0.002 PHE D 59 TRP 0.015 0.001 TRP D 409 HIS 0.004 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (22532) covalent geometry : angle 0.55478 / 0.28 (30517) SS BOND : bond 0.00158 / 0.08 ( 4) SS BOND : angle 0.54927 / 0.28 ( 8) hydrogen bonds : bond 0.04425 / 2.89 ( 1441) hydrogen bonds : angle 3.77678 / 2.68 ( 4248) metal coordination : bond 0.00616 / 0.37 ( 16) metal coordination : angle 0.92750 / 0.44 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 298 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.5190 (ptp) cc_final: 0.4969 (ptp) REVERT: A 652 ILE cc_start: 0.8089 (OUTLIER) cc_final: 0.7794 (mp) REVERT: A 746 MET cc_start: 0.7056 (tmm) cc_final: 0.6803 (tpp) REVERT: B 79 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.6359 (mp0) REVERT: B 421 MET cc_start: 0.6547 (tpp) cc_final: 0.6048 (tpp) REVERT: B 437 MET cc_start: 0.6293 (mmt) cc_final: 0.5941 (ttp) REVERT: B 634 GLU cc_start: 0.7692 (OUTLIER) cc_final: 0.7471 (mt-10) REVERT: B 710 MET cc_start: 0.8726 (tpt) cc_final: 0.8271 (tpp) REVERT: C 243 GLU cc_start: 0.7400 (tp30) cc_final: 0.7196 (tp30) REVERT: C 470 MET cc_start: 0.7664 (tmm) cc_final: 0.7449 (ttt) REVERT: C 509 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6706 (mp) REVERT: C 587 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7030 (pttm) REVERT: D 67 ASP cc_start: 0.7514 (t0) cc_final: 0.7297 (t0) REVERT: D 250 GLN cc_start: 0.8553 (tp-100) cc_final: 0.8043 (tp40) REVERT: D 253 LYS cc_start: 0.9063 (ttpp) cc_final: 0.8797 (tttm) REVERT: D 256 LEU cc_start: 0.9118 (OUTLIER) cc_final: 0.8873 (mm) REVERT: D 309 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8205 (tp) REVERT: D 557 GLN cc_start: 0.8470 (OUTLIER) cc_final: 0.6652 (mt0) REVERT: D 723 ARG cc_start: 0.7147 (ttm110) cc_final: 0.6852 (ttm110) outliers start: 84 outliers final: 62 residues processed: 354 average time/residue: 0.1497 time to fit residues: 85.0628 Evaluate side-chains 360 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 290 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 652 THR Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 309 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 442 ASN Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 496 PHE Chi-restraints excluded: chain D residue 535 ASN Chi-restraints excluded: chain D residue 557 GLN Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 750 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 107 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 203 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 204 optimal weight: 4.9990 chunk 215 optimal weight: 0.7980 chunk 197 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 chunk 241 optimal weight: 7.9990 chunk 226 optimal weight: 0.9980 chunk 59 optimal weight: 0.6980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 170 ASN A 264 GLN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 GLN D 308 GLN D 442 ASN D 605 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.194116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.155821 restraints weight = 29266.710| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 2.25 r_work: 0.3738 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22552 Z= 0.119 Angle : 0.494 13.610 30537 Z= 0.253 Chirality : 0.037 0.183 3421 Planarity : 0.004 0.061 3805 Dihedral : 4.531 56.722 2933 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.95 % Allowed : 22.08 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.17), residues: 2641 helix: 2.09 (0.12), residues: 1985 sheet: None (None), residues: 0 loop : -0.86 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 246 TYR 0.019 0.001 TYR A 217 PHE 0.019 0.001 PHE D 59 TRP 0.013 0.001 TRP C 314 HIS 0.004 0.000 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (22532) covalent geometry : angle 0.49365 / 0.25 (30517) SS BOND : bond 0.00126 / 0.07 ( 4) SS BOND : angle 0.44351 / 0.21 ( 8) hydrogen bonds : bond 0.03989 / 2.61 ( 1441) hydrogen bonds : angle 3.62998 / 2.58 ( 4248) metal coordination : bond 0.00413 / 0.27 ( 16) metal coordination : angle 0.95118 / 0.45 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 323 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.5124 (ptp) cc_final: 0.4809 (ptp) REVERT: A 652 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7726 (mp) REVERT: A 746 MET cc_start: 0.6997 (tmm) cc_final: 0.6760 (tpp) REVERT: B 88 LEU cc_start: 0.7333 (OUTLIER) cc_final: 0.7091 (mp) REVERT: B 421 MET cc_start: 0.6556 (tpp) cc_final: 0.6025 (tpp) REVERT: B 437 MET cc_start: 0.6283 (mmt) cc_final: 0.5944 (ttt) REVERT: B 634 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7358 (mm-30) REVERT: C 470 MET cc_start: 0.7656 (tmm) cc_final: 0.7328 (ttp) REVERT: C 509 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6653 (mp) REVERT: C 587 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6952 (pttm) REVERT: C 740 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8013 (mtmt) REVERT: D 67 ASP cc_start: 0.7511 (t0) cc_final: 0.7310 (t0) REVERT: D 256 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8848 (mm) REVERT: D 511 ARG cc_start: 0.8096 (mmm-85) cc_final: 0.7847 (mmm-85) REVERT: D 557 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.6541 (mt0) REVERT: D 563 THR cc_start: 0.8131 (t) cc_final: 0.7848 (p) REVERT: D 582 TYR cc_start: 0.9100 (p90) cc_final: 0.8780 (p90) REVERT: D 723 ARG cc_start: 0.7054 (ttm110) cc_final: 0.6782 (ttm110) outliers start: 71 outliers final: 48 residues processed: 372 average time/residue: 0.1456 time to fit residues: 85.9861 Evaluate side-chains 354 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 298 time to evaluate : 0.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 740 LYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 442 ASN Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 496 PHE Chi-restraints excluded: chain D residue 557 GLN Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 186 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 222 optimal weight: 2.9990 chunk 264 optimal weight: 8.9990 chunk 172 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 232 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 chunk 243 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 GLN D 442 ASN D 605 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.188252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.151524 restraints weight = 28920.519| |-----------------------------------------------------------------------------| r_work (start): 0.3895 rms_B_bonded: 2.19 r_work: 0.3733 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22552 Z= 0.145 Angle : 0.516 12.407 30537 Z= 0.263 Chirality : 0.038 0.188 3421 Planarity : 0.004 0.063 3805 Dihedral : 4.522 56.187 2933 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.16 % Allowed : 22.04 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.17), residues: 2641 helix: 2.08 (0.12), residues: 1986 sheet: None (None), residues: 0 loop : -0.86 (0.25), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 105 TYR 0.019 0.001 TYR D 523 PHE 0.025 0.001 PHE B 343 TRP 0.013 0.001 TRP C 314 HIS 0.004 0.001 HIS A 646 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (22532) covalent geometry : angle 0.51596 / 0.26 (30517) SS BOND : bond 0.00129 / 0.07 ( 4) SS BOND : angle 0.45986 / 0.23 ( 8) hydrogen bonds : bond 0.04049 / 2.65 ( 1441) hydrogen bonds : angle 3.64760 / 2.59 ( 4248) metal coordination : bond 0.00468 / 0.29 ( 16) metal coordination : angle 0.89049 / 0.43 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 302 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.5105 (ptp) cc_final: 0.4761 (ptp) REVERT: A 427 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6993 (mp) REVERT: A 652 ILE cc_start: 0.8018 (OUTLIER) cc_final: 0.7709 (mp) REVERT: A 746 MET cc_start: 0.7009 (tmm) cc_final: 0.6745 (tpp) REVERT: B 79 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.6309 (mp0) REVERT: B 421 MET cc_start: 0.6545 (tpp) cc_final: 0.6003 (tpp) REVERT: B 437 MET cc_start: 0.6370 (mmt) cc_final: 0.6028 (ttt) REVERT: B 634 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7354 (mm-30) REVERT: B 710 MET cc_start: 0.8535 (tpp) cc_final: 0.8189 (tpp) REVERT: C 509 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.6797 (mp) REVERT: C 587 LYS cc_start: 0.7459 (OUTLIER) cc_final: 0.6886 (pttm) REVERT: C 723 ARG cc_start: 0.7549 (tpt170) cc_final: 0.7093 (tmt-80) REVERT: C 740 LYS cc_start: 0.8317 (OUTLIER) cc_final: 0.8012 (mtmt) REVERT: D 256 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8836 (mm) REVERT: D 415 TRP cc_start: 0.8275 (t-100) cc_final: 0.8054 (t-100) REVERT: D 511 ARG cc_start: 0.8054 (mmm-85) cc_final: 0.7826 (mmm-85) REVERT: D 557 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.6650 (mt0) REVERT: D 563 THR cc_start: 0.8152 (t) cc_final: 0.7877 (p) REVERT: D 723 ARG cc_start: 0.7058 (ttm110) cc_final: 0.6752 (ttm110) outliers start: 76 outliers final: 52 residues processed: 357 average time/residue: 0.1476 time to fit residues: 84.1317 Evaluate side-chains 356 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 295 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 740 LYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 496 PHE Chi-restraints excluded: chain D residue 535 ASN Chi-restraints excluded: chain D residue 557 GLN Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 750 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 89 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 130 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 170 optimal weight: 10.0000 chunk 57 optimal weight: 0.8980 chunk 246 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN B 605 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 250 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.203380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.166747 restraints weight = 29467.741| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.36 r_work: 0.3818 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22552 Z= 0.215 Angle : 0.587 11.351 30537 Z= 0.300 Chirality : 0.040 0.196 3421 Planarity : 0.004 0.058 3805 Dihedral : 4.666 56.178 2933 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.24 % Allowed : 22.20 % Favored : 74.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.17), residues: 2641 helix: 1.91 (0.12), residues: 1985 sheet: None (None), residues: 0 loop : -0.91 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 105 TYR 0.022 0.002 TYR D 523 PHE 0.025 0.002 PHE B 343 TRP 0.016 0.001 TRP B 409 HIS 0.004 0.001 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.21 (22532) covalent geometry : angle 0.58707 / 0.30 (30517) SS BOND : bond 0.00173 / 0.09 ( 4) SS BOND : angle 0.57594 / 0.30 ( 8) hydrogen bonds : bond 0.04581 / 2.99 ( 1441) hydrogen bonds : angle 3.82626 / 2.72 ( 4248) metal coordination : bond 0.00691 / 0.42 ( 16) metal coordination : angle 1.06783 / 0.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 296 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.5147 (ptp) cc_final: 0.4866 (ptp) REVERT: A 652 ILE cc_start: 0.8159 (OUTLIER) cc_final: 0.7846 (mp) REVERT: A 746 MET cc_start: 0.7148 (tmm) cc_final: 0.6798 (tpp) REVERT: B 79 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6330 (mp0) REVERT: B 235 ASN cc_start: 0.7102 (m110) cc_final: 0.6828 (m110) REVERT: B 437 MET cc_start: 0.6478 (mmt) cc_final: 0.6111 (ttt) REVERT: B 634 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7409 (mm-30) REVERT: B 710 MET cc_start: 0.8591 (tpp) cc_final: 0.8337 (tpp) REVERT: C 88 LEU cc_start: 0.8578 (tp) cc_final: 0.8377 (tp) REVERT: C 404 TRP cc_start: 0.6025 (OUTLIER) cc_final: 0.4281 (m-90) REVERT: C 509 LEU cc_start: 0.7668 (OUTLIER) cc_final: 0.6835 (mp) REVERT: C 587 LYS cc_start: 0.7536 (OUTLIER) cc_final: 0.7089 (pttm) REVERT: C 723 ARG cc_start: 0.7664 (tpt170) cc_final: 0.7199 (tmt-80) REVERT: C 740 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8123 (mtmt) REVERT: D 557 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.6731 (mt0) REVERT: D 563 THR cc_start: 0.8072 (t) cc_final: 0.7852 (p) outliers start: 78 outliers final: 59 residues processed: 352 average time/residue: 0.1386 time to fit residues: 77.7371 Evaluate side-chains 348 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 281 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 404 TRP Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 740 LYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 496 PHE Chi-restraints excluded: chain D residue 535 ASN Chi-restraints excluded: chain D residue 557 GLN Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 750 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 148 optimal weight: 0.9980 chunk 228 optimal weight: 9.9990 chunk 181 optimal weight: 4.9990 chunk 227 optimal weight: 7.9990 chunk 174 optimal weight: 0.8980 chunk 168 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 60 optimal weight: 0.0370 chunk 86 optimal weight: 6.9990 chunk 220 optimal weight: 1.9990 overall best weight: 0.7862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN B 605 ASN ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 GLN D 442 ASN D 605 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.188995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.152526 restraints weight = 28951.459| |-----------------------------------------------------------------------------| r_work (start): 0.3912 rms_B_bonded: 2.20 r_work: 0.3748 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 22552 Z= 0.121 Angle : 0.512 13.539 30537 Z= 0.264 Chirality : 0.037 0.204 3421 Planarity : 0.004 0.060 3805 Dihedral : 4.531 56.074 2933 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.70 % Allowed : 22.87 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.09 (0.17), residues: 2641 helix: 2.12 (0.12), residues: 1982 sheet: None (None), residues: 0 loop : -0.93 (0.25), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 246 TYR 0.017 0.001 TYR D 523 PHE 0.026 0.001 PHE D 746 TRP 0.016 0.001 TRP B 409 HIS 0.003 0.000 HIS A 493 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (22532) covalent geometry : angle 0.51188 / 0.26 (30517) SS BOND : bond 0.00101 / 0.05 ( 4) SS BOND : angle 0.47728 / 0.23 ( 8) hydrogen bonds : bond 0.03947 / 2.59 ( 1441) hydrogen bonds : angle 3.63479 / 2.58 ( 4248) metal coordination : bond 0.00462 / 0.32 ( 16) metal coordination : angle 1.04128 / 0.50 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 297 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7902 (mm) REVERT: A 339 MET cc_start: 0.5048 (ptp) cc_final: 0.4709 (ptp) REVERT: A 652 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7651 (mp) REVERT: A 746 MET cc_start: 0.7067 (tmm) cc_final: 0.6755 (tpp) REVERT: B 421 MET cc_start: 0.6527 (tpp) cc_final: 0.5973 (tpp) REVERT: B 437 MET cc_start: 0.6403 (mmt) cc_final: 0.6033 (ttt) REVERT: B 634 GLU cc_start: 0.7581 (OUTLIER) cc_final: 0.7366 (mm-30) REVERT: C 404 TRP cc_start: 0.6075 (OUTLIER) cc_final: 0.4691 (m-90) REVERT: C 509 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.6721 (mp) REVERT: C 541 TYR cc_start: 0.7774 (m-10) cc_final: 0.7570 (m-80) REVERT: C 587 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6847 (pttm) REVERT: C 723 ARG cc_start: 0.7629 (tpt170) cc_final: 0.7236 (tmt-80) REVERT: C 740 LYS cc_start: 0.8335 (OUTLIER) cc_final: 0.8061 (mtmt) REVERT: D 557 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.6681 (mt0) REVERT: D 563 THR cc_start: 0.8109 (t) cc_final: 0.7816 (p) REVERT: D 604 TYR cc_start: 0.8856 (t80) cc_final: 0.8209 (t80) REVERT: D 723 ARG cc_start: 0.7131 (ttm110) cc_final: 0.6822 (ttm110) REVERT: D 733 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7390 (mm-30) outliers start: 65 outliers final: 48 residues processed: 345 average time/residue: 0.1393 time to fit residues: 76.3939 Evaluate side-chains 338 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 282 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 404 TRP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 740 LYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 442 ASN Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 496 PHE Chi-restraints excluded: chain D residue 507 ILE Chi-restraints excluded: chain D residue 535 ASN Chi-restraints excluded: chain D residue 557 GLN Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 150 optimal weight: 2.9990 chunk 167 optimal weight: 7.9990 chunk 137 optimal weight: 0.9980 chunk 245 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 197 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 104 optimal weight: 0.0270 chunk 212 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 250 optimal weight: 3.9990 overall best weight: 1.3842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 GLN D 442 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.193238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.155925 restraints weight = 29329.653| |-----------------------------------------------------------------------------| r_work (start): 0.3894 rms_B_bonded: 2.19 r_work: 0.3729 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3729 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22552 Z= 0.149 Angle : 0.543 13.993 30537 Z= 0.278 Chirality : 0.038 0.208 3421 Planarity : 0.004 0.059 3805 Dihedral : 4.548 55.793 2933 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.58 % Allowed : 22.95 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.17), residues: 2641 helix: 2.09 (0.12), residues: 1984 sheet: None (None), residues: 0 loop : -0.93 (0.25), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 511 TYR 0.019 0.001 TYR D 523 PHE 0.021 0.001 PHE B 343 TRP 0.019 0.001 TRP B 409 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.15 (22532) covalent geometry : angle 0.54265 / 0.28 (30517) SS BOND : bond 0.00110 / 0.06 ( 4) SS BOND : angle 0.46122 / 0.23 ( 8) hydrogen bonds : bond 0.04099 / 2.69 ( 1441) hydrogen bonds : angle 3.66622 / 2.59 ( 4248) metal coordination : bond 0.00541 / 0.35 ( 16) metal coordination : angle 0.94913 / 0.47 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5282 Ramachandran restraints generated. 2641 Oldfield, 0 Emsley, 2641 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 289 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8215 (OUTLIER) cc_final: 0.7916 (mm) REVERT: A 339 MET cc_start: 0.5153 (ptp) cc_final: 0.4812 (ptp) REVERT: A 652 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7692 (mp) REVERT: A 746 MET cc_start: 0.7031 (tmm) cc_final: 0.6761 (tpp) REVERT: B 79 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6273 (mp0) REVERT: B 378 PHE cc_start: 0.6304 (t80) cc_final: 0.5975 (t80) REVERT: B 421 MET cc_start: 0.6503 (tpp) cc_final: 0.5947 (tpp) REVERT: B 437 MET cc_start: 0.6426 (mmt) cc_final: 0.6063 (ttt) REVERT: B 634 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7358 (mm-30) REVERT: C 404 TRP cc_start: 0.6099 (OUTLIER) cc_final: 0.4906 (m-10) REVERT: C 509 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.6709 (mp) REVERT: C 587 LYS cc_start: 0.7433 (OUTLIER) cc_final: 0.6923 (pttm) REVERT: C 723 ARG cc_start: 0.7607 (tpt170) cc_final: 0.7214 (tmt-80) REVERT: C 740 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.8066 (mtmt) REVERT: D 557 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.6734 (mt0) REVERT: D 563 THR cc_start: 0.8101 (t) cc_final: 0.7828 (p) REVERT: D 723 ARG cc_start: 0.7119 (ttm110) cc_final: 0.6815 (ttm110) REVERT: D 733 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7379 (mm-30) outliers start: 62 outliers final: 51 residues processed: 336 average time/residue: 0.1334 time to fit residues: 72.0125 Evaluate side-chains 343 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 283 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 572 VAL Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 108 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 525 LEU Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain B residue 753 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 404 TRP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 740 LYS Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 496 PHE Chi-restraints excluded: chain D residue 535 ASN Chi-restraints excluded: chain D residue 557 GLN Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 721 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 104 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 191 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 258 optimal weight: 0.8980 chunk 232 optimal weight: 3.9990 chunk 181 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 133 optimal weight: 0.0020 chunk 53 optimal weight: 6.9990 overall best weight: 0.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN B 308 GLN ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 GLN D 177 ASN ** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.194873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.156861 restraints weight = 29130.601| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.24 r_work: 0.3755 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 22552 Z= 0.119 Angle : 0.515 13.587 30537 Z= 0.265 Chirality : 0.037 0.207 3421 Planarity : 0.004 0.059 3805 Dihedral : 4.481 56.096 2933 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.58 % Allowed : 22.99 % Favored : 74.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.18 (0.17), residues: 2641 helix: 2.18 (0.12), residues: 1985 sheet: None (None), residues: 0 loop : -0.89 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 723 TYR 0.028 0.001 TYR B 706 PHE 0.031 0.001 PHE D 746 TRP 0.019 0.001 TRP B 409 HIS 0.003 0.000 HIS B 472 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (22532) covalent geometry : angle 0.51501 / 0.26 (30517) SS BOND : bond 0.00097 / 0.05 ( 4) SS BOND : angle 0.43692 / 0.21 ( 8) hydrogen bonds : bond 0.03831 / 2.51 ( 1441) hydrogen bonds : angle 3.59334 / 2.54 ( 4248) metal coordination : bond 0.00483 / 0.35 ( 16) metal coordination : angle 1.26616 / 0.59 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4594.22 seconds wall clock time: 79 minutes 52.48 seconds (4792.48 seconds total)