Starting phenix.real_space_refine on Sun Oct 12 06:32:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpm_37719/10_2025/8wpm_37719.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpm_37719/10_2025/8wpm_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8wpm_37719/10_2025/8wpm_37719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpm_37719/10_2025/8wpm_37719.map" model { file = "/net/cci-nas-00/data/ceres_data/8wpm_37719/10_2025/8wpm_37719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpm_37719/10_2025/8wpm_37719.cif" } 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-2.0-5842/lib/python3.9/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, 38 Unusual residues: {' CA': 1, ' ZN': 1, 'PJQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {' CA': 1, ' ZN': 1, 'PJQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {' CA': 1, ' ZN': 1, 'PJQ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 5.05, 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: 2.24 Conformation dependent library (CDL) restraints added in 866.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.72 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: 3.80 Time building geometry restraints manager: 2.90 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: 3.330 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 22.850 Find NCS groups from input model: 0.500 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 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 aren 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 covalent geometry : bond 0.00545 (22532) covalent geometry : angle 0.80079 (30517) SS BOND : bond 0.00215 ( 4) SS BOND : angle 0.58259 ( 8) hydrogen bonds : bond 0.13239 ( 1441) hydrogen bonds : angle 5.17368 ( 4248) metal coordination : bond 0.00618 ( 16) metal coordination : angle 0.93367 ( 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 : 0.823 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: 0.1493 time to fit residues: 79.4261 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 : 0.868 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** 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 ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN C 250 GLN C 258 GLN C 442 ASN C 472 HIS C 485 ASN C 559 ASN C 569 GLN C 621 ASN C 630 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: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.207075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.170112 restraints weight = 29563.396| |-----------------------------------------------------------------------------| r_work (start): 0.4069 rms_B_bonded: 2.25 r_work: 0.3901 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22552 Z= 0.128 Angle : 0.497 7.599 30537 Z= 0.262 Chirality : 0.037 0.183 3421 Planarity : 0.004 0.058 3805 Dihedral : 5.019 59.660 2941 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.08 % Allowed : 20.87 % Favored : 77.05 % 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 aren not related in a simple way. whole: 1.17 (0.16), residues: 2641 helix: 1.35 (0.11), residues: 1989 sheet: None (None), residues: 0 loop : -0.92 (0.25), residues: 652 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 511 TYR 0.023 0.001 TYR A 510 PHE 0.020 0.001 PHE D 539 TRP 0.016 0.001 TRP D 409 HIS 0.007 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00281 (22532) covalent geometry : angle 0.49647 (30517) SS BOND : bond 0.00131 ( 4) SS BOND : angle 0.58468 ( 8) hydrogen bonds : bond 0.04360 ( 1441) hydrogen bonds : angle 3.86131 ( 4248) metal coordination : bond 0.00473 ( 16) metal coordination : angle 1.33704 ( 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 370 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 320 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.5323 (ptp) cc_final: 0.5106 (ptp) REVERT: A 652 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7985 (mp) REVERT: B 378 PHE cc_start: 0.6286 (t80) cc_final: 0.6079 (t80) REVERT: B 421 MET cc_start: 0.6536 (tpp) cc_final: 0.6152 (tpp) REVERT: B 427 GLN cc_start: 0.7056 (mm-40) cc_final: 0.6844 (pm20) REVERT: B 437 MET cc_start: 0.6401 (mmt) cc_final: 0.6061 (ttt) outliers start: 50 outliers final: 26 residues processed: 349 average time/residue: 0.1456 time to fit residues: 81.8213 Evaluate side-chains 326 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 299 time to evaluate : 0.753 ------------------------------------------------------------------------------- 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 652 ILE 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 116 LEU 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 562 SER 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: 0.0570 chunk 66 optimal weight: 0.4980 chunk 164 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 106 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 28 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 181 GLN A 288 HIS ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 585 HIS A 683 ASN B 420 GLN B 569 GLN ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 250 GLN ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 703 HIS D 64 ASN D 163 GLN D 532 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.208074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.171290 restraints weight = 29425.371| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 2.23 r_work: 0.3913 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22552 Z= 0.107 Angle : 0.459 7.229 30537 Z= 0.241 Chirality : 0.036 0.156 3421 Planarity : 0.004 0.060 3805 Dihedral : 4.675 58.865 2936 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.37 % Allowed : 20.87 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.16), residues: 2641 helix: 1.83 (0.12), residues: 1992 sheet: None (None), residues: 0 loop : -0.81 (0.25), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 246 TYR 0.018 0.001 TYR A 408 PHE 0.017 0.001 PHE D 539 TRP 0.011 0.001 TRP D 409 HIS 0.005 0.000 HIS B 472 Details of bonding type rmsd covalent geometry : bond 0.00229 (22532) covalent geometry : angle 0.45812 (30517) SS BOND : bond 0.00188 ( 4) SS BOND : angle 0.52264 ( 8) hydrogen bonds : bond 0.03853 ( 1441) hydrogen bonds : angle 3.63137 ( 4248) metal coordination : bond 0.00296 ( 16) metal coordination : angle 1.16556 ( 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 393 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 336 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.5283 (ptp) cc_final: 0.4965 (ptp) REVERT: A 652 ILE cc_start: 0.8165 (OUTLIER) cc_final: 0.7859 (mp) REVERT: A 682 PHE cc_start: 0.7653 (m-80) cc_final: 0.7421 (m-80) REVERT: A 746 MET cc_start: 0.7188 (tmm) cc_final: 0.6736 (tpp) REVERT: B 378 PHE cc_start: 0.6244 (t80) cc_final: 0.6038 (t80) REVERT: B 421 MET cc_start: 0.6570 (tpp) cc_final: 0.6163 (mmm) REVERT: C 88 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8646 (tp) REVERT: C 509 LEU cc_start: 0.7233 (OUTLIER) cc_final: 0.6711 (mp) REVERT: D 208 LEU cc_start: 0.8786 (tp) cc_final: 0.8520 (tt) REVERT: D 563 THR cc_start: 0.8097 (t) cc_final: 0.7888 (m) REVERT: D 723 ARG cc_start: 0.7073 (ttm110) cc_final: 0.6816 (ttm110) outliers start: 57 outliers final: 32 residues processed: 370 average time/residue: 0.1440 time to fit residues: 85.5294 Evaluate side-chains 343 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 308 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 379 ILE Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 652 ILE 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 340 PHE 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 B residue 652 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 199 ILE 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 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 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 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: 3.9990 chunk 138 optimal weight: 0.0870 chunk 250 optimal weight: 3.9990 chunk 170 optimal weight: 10.0000 chunk 171 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 34 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 chunk 224 optimal weight: 0.0270 chunk 157 optimal weight: 2.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 264 GLN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 603 HIS B 735 ASN ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN C 707 GLN D 250 GLN D 442 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.197061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.158966 restraints weight = 29378.074| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.27 r_work: 0.3779 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22552 Z= 0.114 Angle : 0.464 6.817 30537 Z= 0.242 Chirality : 0.036 0.160 3421 Planarity : 0.004 0.058 3805 Dihedral : 4.544 58.287 2936 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.79 % Allowed : 21.12 % Favored : 76.09 % 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 aren not related in a simple way. whole: 2.09 (0.17), residues: 2641 helix: 2.07 (0.12), residues: 1985 sheet: None (None), residues: 0 loop : -0.77 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 246 TYR 0.018 0.001 TYR A 408 PHE 0.018 0.001 PHE D 59 TRP 0.010 0.001 TRP C 314 HIS 0.004 0.000 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00251 (22532) covalent geometry : angle 0.46356 (30517) SS BOND : bond 0.00135 ( 4) SS BOND : angle 0.37200 ( 8) hydrogen bonds : bond 0.03783 ( 1441) hydrogen bonds : angle 3.56013 ( 4248) metal coordination : bond 0.00312 ( 16) metal coordination : angle 0.87526 ( 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 391 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 324 time to evaluate : 0.876 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ASN cc_start: 0.7603 (t0) cc_final: 0.7347 (t0) REVERT: A 652 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7769 (mp) REVERT: A 682 PHE cc_start: 0.7601 (m-80) cc_final: 0.7320 (m-80) REVERT: A 746 MET cc_start: 0.7027 (tmm) cc_final: 0.6758 (tpp) REVERT: B 421 MET cc_start: 0.6460 (tpp) cc_final: 0.5977 (tpp) REVERT: B 437 MET cc_start: 0.6233 (mmt) cc_final: 0.5979 (ttt) REVERT: C 509 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6652 (mp) REVERT: C 587 LYS cc_start: 0.7252 (OUTLIER) cc_final: 0.6648 (pttm) REVERT: D 67 ASP cc_start: 0.6897 (t0) cc_final: 0.6600 (t0) REVERT: D 256 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8738 (mm) REVERT: D 582 TYR cc_start: 0.9089 (p90) cc_final: 0.8772 (p90) REVERT: D 723 ARG cc_start: 0.6940 (ttm110) cc_final: 0.6701 (ttm110) outliers start: 67 outliers final: 41 residues processed: 363 average time/residue: 0.1557 time to fit residues: 89.8479 Evaluate side-chains 347 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 302 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 170 ASN 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 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 63 ILE 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 505 LEU Chi-restraints excluded: chain B residue 709 VAL 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 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 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 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: 3.9990 chunk 109 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 172 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 205 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 109 GLN A 170 ASN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 740 HIS ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN B 735 ASN ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS C 621 ASN C 707 GLN D 163 GLN D 247 GLN D 369 HIS D 536 GLN D 590 HIS D 605 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.181989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.143124 restraints weight = 30016.335| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.58 r_work: 0.3559 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 22552 Z= 0.243 Angle : 0.609 10.294 30537 Z= 0.314 Chirality : 0.041 0.173 3421 Planarity : 0.004 0.058 3805 Dihedral : 4.740 55.777 2934 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.41 % Allowed : 21.04 % Favored : 75.55 % 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 aren not related in a simple way. whole: 1.72 (0.16), residues: 2641 helix: 1.81 (0.12), residues: 1983 sheet: None (None), residues: 0 loop : -0.92 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 169 TYR 0.025 0.002 TYR A 408 PHE 0.018 0.002 PHE D 340 TRP 0.017 0.001 TRP B 314 HIS 0.004 0.001 HIS D 704 Details of bonding type rmsd covalent geometry : bond 0.00579 (22532) covalent geometry : angle 0.60859 (30517) SS BOND : bond 0.00203 ( 4) SS BOND : angle 0.60386 ( 8) hydrogen bonds : bond 0.04791 ( 1441) hydrogen bonds : angle 3.88572 ( 4248) metal coordination : bond 0.00759 ( 16) metal coordination : angle 0.95585 ( 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 384 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 302 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ASN cc_start: 0.7718 (t0) cc_final: 0.7107 (m-40) REVERT: A 339 MET cc_start: 0.5270 (ptp) cc_final: 0.5053 (ptp) REVERT: A 652 ILE cc_start: 0.8082 (OUTLIER) cc_final: 0.7766 (mp) REVERT: A 746 MET cc_start: 0.7088 (tmm) cc_final: 0.6785 (tpp) REVERT: B 437 MET cc_start: 0.6406 (mmt) cc_final: 0.6047 (ttp) REVERT: B 739 LEU cc_start: 0.8278 (tt) cc_final: 0.8067 (tp) REVERT: C 509 LEU cc_start: 0.7521 (OUTLIER) cc_final: 0.6718 (mp) REVERT: C 587 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7048 (pttm) REVERT: C 619 MET cc_start: 0.8602 (tmm) cc_final: 0.8356 (tmm) REVERT: D 67 ASP cc_start: 0.7126 (t0) cc_final: 0.6718 (t0) REVERT: D 456 PHE cc_start: 0.8115 (t80) cc_final: 0.7879 (t80) REVERT: D 582 TYR cc_start: 0.9160 (p90) cc_final: 0.8814 (p90) outliers start: 82 outliers final: 58 residues processed: 356 average time/residue: 0.1525 time to fit residues: 86.6362 Evaluate side-chains 346 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 285 time to evaluate : 0.829 ------------------------------------------------------------------------------- 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 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 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 342 VAL 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 505 LEU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 78 ILE 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 515 ASP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 552 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 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 436 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 107 optimal weight: 0.4980 chunk 117 optimal weight: 0.8980 chunk 203 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 204 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 197 optimal weight: 0.8980 chunk 61 optimal weight: 7.9990 chunk 241 optimal weight: 7.9990 chunk 226 optimal weight: 0.9990 chunk 59 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 ASN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4222 r_free = 0.4222 target = 0.186284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.147890 restraints weight = 29800.220| |-----------------------------------------------------------------------------| r_work (start): 0.3787 rms_B_bonded: 2.66 r_work: 0.3604 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 22552 Z= 0.119 Angle : 0.489 13.111 30537 Z= 0.253 Chirality : 0.037 0.184 3421 Planarity : 0.004 0.060 3805 Dihedral : 4.531 57.172 2933 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.74 % Allowed : 22.16 % Favored : 75.09 % 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 aren not related in a simple way. whole: 2.11 (0.17), residues: 2641 helix: 2.12 (0.12), residues: 1978 sheet: None (None), residues: 0 loop : -0.86 (0.25), residues: 663 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 0.014 0.001 TRP C 314 HIS 0.004 0.000 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00261 (22532) covalent geometry : angle 0.48917 (30517) SS BOND : bond 0.00124 ( 4) SS BOND : angle 0.46324 ( 8) hydrogen bonds : bond 0.03966 ( 1441) hydrogen bonds : angle 3.62428 ( 4248) metal coordination : bond 0.00452 ( 16) metal coordination : angle 0.96998 ( 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 383 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 317 time to evaluate : 1.020 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ASN cc_start: 0.7636 (t0) cc_final: 0.7095 (m-40) REVERT: A 427 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6880 (mp) REVERT: A 514 PHE cc_start: 0.8737 (m-10) cc_final: 0.8501 (m-10) REVERT: A 652 ILE cc_start: 0.7881 (OUTLIER) cc_final: 0.7603 (mp) REVERT: A 682 PHE cc_start: 0.7746 (m-80) cc_final: 0.7522 (m-80) REVERT: A 746 MET cc_start: 0.7014 (tmm) cc_final: 0.6736 (tpp) REVERT: B 79 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6701 (mp0) REVERT: B 88 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7108 (mp) REVERT: B 421 MET cc_start: 0.6481 (tpp) cc_final: 0.5946 (tpp) REVERT: B 437 MET cc_start: 0.6304 (mmt) cc_final: 0.5920 (ttt) REVERT: B 634 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7349 (mm-30) REVERT: B 710 MET cc_start: 0.8538 (tpp) cc_final: 0.8155 (tpp) REVERT: C 509 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.6592 (mp) REVERT: C 587 LYS cc_start: 0.7384 (OUTLIER) cc_final: 0.6898 (pttm) REVERT: C 740 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7959 (mtmt) REVERT: D 67 ASP cc_start: 0.7200 (t0) cc_final: 0.6803 (t0) REVERT: D 256 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8762 (mm) REVERT: D 456 PHE cc_start: 0.8049 (t80) cc_final: 0.7826 (t80) REVERT: D 511 ARG cc_start: 0.8180 (mmm-85) cc_final: 0.7909 (mmm-85) REVERT: D 557 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.6583 (mt0) REVERT: D 582 TYR cc_start: 0.9122 (p90) cc_final: 0.8757 (p90) REVERT: D 723 ARG cc_start: 0.6931 (ttm110) cc_final: 0.6656 (ttm110) outliers start: 66 outliers final: 43 residues processed: 362 average time/residue: 0.1533 time to fit residues: 88.3478 Evaluate side-chains 353 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 300 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 170 ASN 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 B residue 63 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 88 LEU 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 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 230 LEU 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 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 174 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 442 ASN Chi-restraints excluded: chain D residue 457 VAL 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: 1.9990 chunk 122 optimal weight: 5.9990 chunk 222 optimal weight: 1.9990 chunk 264 optimal weight: 9.9990 chunk 172 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 232 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 201 optimal weight: 7.9990 chunk 243 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 ASN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 506 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 ASN ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 GLN D 442 ASN D 536 GLN D 605 ASN D 625 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.183424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.143602 restraints weight = 29812.723| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.80 r_work: 0.3560 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 22552 Z= 0.172 Angle : 0.541 12.588 30537 Z= 0.276 Chirality : 0.038 0.187 3421 Planarity : 0.004 0.061 3805 Dihedral : 4.559 55.862 2933 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.99 % Allowed : 22.25 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.02 (0.17), residues: 2641 helix: 2.05 (0.12), residues: 1981 sheet: None (None), residues: 0 loop : -0.89 (0.25), residues: 660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 105 TYR 0.020 0.002 TYR D 523 PHE 0.026 0.001 PHE B 343 TRP 0.014 0.001 TRP B 314 HIS 0.004 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00405 (22532) covalent geometry : angle 0.54074 (30517) SS BOND : bond 0.00135 ( 4) SS BOND : angle 0.49923 ( 8) hydrogen bonds : bond 0.04225 ( 1441) hydrogen bonds : angle 3.69163 ( 4248) metal coordination : bond 0.00585 ( 16) metal coordination : angle 0.91015 ( 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 372 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 300 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 427 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.6962 (mp) REVERT: A 514 PHE cc_start: 0.8768 (m-10) cc_final: 0.8508 (m-10) REVERT: A 652 ILE cc_start: 0.7970 (OUTLIER) cc_final: 0.7636 (mp) REVERT: A 746 MET cc_start: 0.7075 (tmm) cc_final: 0.6755 (tpp) REVERT: B 79 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.6394 (mp0) REVERT: B 421 MET cc_start: 0.6509 (tpp) cc_final: 0.5955 (tpp) REVERT: B 437 MET cc_start: 0.6436 (mmt) cc_final: 0.6027 (ttt) REVERT: B 634 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7424 (mm-30) REVERT: C 509 LEU cc_start: 0.7417 (OUTLIER) cc_final: 0.6705 (mp) REVERT: C 587 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.6902 (pttm) REVERT: C 723 ARG cc_start: 0.7552 (tpt170) cc_final: 0.7097 (tmt-80) REVERT: C 740 LYS cc_start: 0.8284 (OUTLIER) cc_final: 0.8021 (mtmt) REVERT: D 67 ASP cc_start: 0.7226 (t0) cc_final: 0.6811 (t0) REVERT: D 456 PHE cc_start: 0.8114 (t80) cc_final: 0.7858 (t80) REVERT: D 511 ARG cc_start: 0.8208 (mmm-85) cc_final: 0.7946 (mmm-85) REVERT: D 557 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.6663 (mt0) REVERT: D 582 TYR cc_start: 0.9144 (p90) cc_final: 0.8803 (p90) REVERT: D 723 ARG cc_start: 0.7063 (ttm110) cc_final: 0.6733 (ttm110) outliers start: 72 outliers final: 52 residues processed: 351 average time/residue: 0.1456 time to fit residues: 81.6024 Evaluate side-chains 354 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 294 time to evaluate : 0.842 ------------------------------------------------------------------------------- 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 98 ASP 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 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 499 GLU 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 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 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 395 GLN Chi-restraints excluded: chain B residue 453 ILE 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 230 LEU 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 552 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 342 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 89 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 151 optimal weight: 3.9990 chunk 130 optimal weight: 8.9990 chunk 21 optimal weight: 0.9990 chunk 118 optimal weight: 0.0870 chunk 72 optimal weight: 6.9990 chunk 170 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 ASN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4197 r_free = 0.4197 target = 0.184305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.144102 restraints weight = 29657.742| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.61 r_work: 0.3564 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2093 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= 0.149 Angle : 0.526 11.637 30537 Z= 0.270 Chirality : 0.038 0.194 3421 Planarity : 0.004 0.061 3805 Dihedral : 4.545 55.943 2933 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.24 % Allowed : 22.45 % Favored : 74.30 % 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 aren not related in a simple way. whole: 2.08 (0.17), residues: 2641 helix: 2.09 (0.12), residues: 1980 sheet: None (None), residues: 0 loop : -0.86 (0.25), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 105 TYR 0.019 0.001 TYR D 523 PHE 0.028 0.001 PHE B 343 TRP 0.013 0.001 TRP C 314 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00346 (22532) covalent geometry : angle 0.52583 (30517) SS BOND : bond 0.00126 ( 4) SS BOND : angle 0.46963 ( 8) hydrogen bonds : bond 0.04130 ( 1441) hydrogen bonds : angle 3.66872 ( 4248) metal coordination : bond 0.00511 ( 16) metal coordination : angle 0.94689 ( 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 376 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 298 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6989 (mp) REVERT: A 514 PHE cc_start: 0.8766 (m-10) cc_final: 0.8483 (m-10) REVERT: A 652 ILE cc_start: 0.7920 (OUTLIER) cc_final: 0.7607 (mp) REVERT: A 746 MET cc_start: 0.7093 (tmm) cc_final: 0.6750 (tpp) REVERT: B 79 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6383 (mp0) REVERT: B 421 MET cc_start: 0.6511 (tpp) cc_final: 0.5943 (tpp) REVERT: B 437 MET cc_start: 0.6410 (mmt) cc_final: 0.6010 (ttt) REVERT: B 634 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7423 (mm-30) REVERT: B 739 LEU cc_start: 0.8249 (tt) cc_final: 0.8041 (tp) REVERT: C 404 TRP cc_start: 0.5942 (OUTLIER) cc_final: 0.4214 (m-90) REVERT: C 509 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.6661 (mp) REVERT: C 587 LYS cc_start: 0.7418 (OUTLIER) cc_final: 0.6922 (pttm) REVERT: C 723 ARG cc_start: 0.7585 (tpt170) cc_final: 0.7123 (tmt-80) REVERT: C 740 LYS cc_start: 0.8282 (OUTLIER) cc_final: 0.8042 (mtmt) REVERT: D 67 ASP cc_start: 0.7208 (t0) cc_final: 0.6768 (t0) REVERT: D 456 PHE cc_start: 0.8122 (t80) cc_final: 0.7870 (t80) REVERT: D 511 ARG cc_start: 0.8177 (mmm-85) cc_final: 0.7924 (mmm-85) REVERT: D 557 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.6694 (mt0) REVERT: D 582 TYR cc_start: 0.9131 (p90) cc_final: 0.8771 (p90) REVERT: D 723 ARG cc_start: 0.7072 (ttm110) cc_final: 0.6751 (ttm110) REVERT: D 733 GLU cc_start: 0.7701 (mm-30) cc_final: 0.7367 (mm-30) outliers start: 78 outliers final: 56 residues processed: 353 average time/residue: 0.1560 time to fit residues: 87.3652 Evaluate side-chains 358 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 293 time to evaluate : 1.027 ------------------------------------------------------------------------------- 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 98 ASP Chi-restraints excluded: chain A residue 121 GLU 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 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 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 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 230 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 438 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 552 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 441 MET 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 148 optimal weight: 2.9990 chunk 228 optimal weight: 10.0000 chunk 181 optimal weight: 4.9990 chunk 227 optimal weight: 5.9990 chunk 174 optimal weight: 4.9990 chunk 168 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.3980 chunk 86 optimal weight: 4.9990 chunk 220 optimal weight: 0.8980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 655 HIS A 683 ASN B 385 GLN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.183529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.142700 restraints weight = 29794.520| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 2.40 r_work: 0.3585 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 22552 Z= 0.164 Angle : 0.541 11.188 30537 Z= 0.277 Chirality : 0.038 0.203 3421 Planarity : 0.004 0.061 3805 Dihedral : 4.565 56.062 2933 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.28 % Allowed : 22.08 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.03 (0.17), residues: 2641 helix: 2.06 (0.12), residues: 1979 sheet: None (None), residues: 0 loop : -0.90 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 105 TYR 0.019 0.002 TYR D 523 PHE 0.018 0.001 PHE D 59 TRP 0.017 0.001 TRP B 409 HIS 0.013 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00386 (22532) covalent geometry : angle 0.54067 (30517) SS BOND : bond 0.00130 ( 4) SS BOND : angle 0.49844 ( 8) hydrogen bonds : bond 0.04207 ( 1441) hydrogen bonds : angle 3.69522 ( 4248) metal coordination : bond 0.00564 ( 16) metal coordination : angle 0.95565 ( 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 380 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 301 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 427 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.7004 (mp) REVERT: A 652 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7594 (mp) REVERT: A 746 MET cc_start: 0.7072 (tmm) cc_final: 0.6772 (tpp) REVERT: B 79 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.6349 (mp0) REVERT: B 421 MET cc_start: 0.6549 (tpp) cc_final: 0.5970 (tpp) REVERT: B 437 MET cc_start: 0.6421 (mmt) cc_final: 0.6031 (ttt) REVERT: B 634 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: B 739 LEU cc_start: 0.8267 (tt) cc_final: 0.8054 (tp) REVERT: C 404 TRP cc_start: 0.6016 (OUTLIER) cc_final: 0.4281 (m-90) REVERT: C 509 LEU cc_start: 0.7425 (OUTLIER) cc_final: 0.6719 (mp) REVERT: C 587 LYS cc_start: 0.7410 (OUTLIER) cc_final: 0.6945 (pttm) REVERT: C 723 ARG cc_start: 0.7600 (tpt170) cc_final: 0.7137 (tmt-80) REVERT: C 740 LYS cc_start: 0.8318 (OUTLIER) cc_final: 0.8098 (mtmt) REVERT: D 67 ASP cc_start: 0.7209 (t0) cc_final: 0.6865 (t0) REVERT: D 511 ARG cc_start: 0.8184 (mmm-85) cc_final: 0.7933 (mmm-85) REVERT: D 557 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.6806 (mt0) REVERT: D 723 ARG cc_start: 0.7073 (ttm110) cc_final: 0.6746 (ttm110) REVERT: D 733 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7369 (mm-30) outliers start: 79 outliers final: 60 residues processed: 353 average time/residue: 0.1543 time to fit residues: 86.3596 Evaluate side-chains 360 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 291 time to evaluate : 0.795 ------------------------------------------------------------------------------- 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 98 ASP Chi-restraints excluded: chain A residue 121 GLU 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 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 427 LEU Chi-restraints excluded: chain A residue 499 GLU 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 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 655 HIS 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 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 505 LEU Chi-restraints excluded: chain B residue 525 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 230 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 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 552 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 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 150 optimal weight: 0.4980 chunk 167 optimal weight: 0.4980 chunk 137 optimal weight: 1.9990 chunk 245 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 197 optimal weight: 6.9990 chunk 42 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 212 optimal weight: 0.9990 chunk 195 optimal weight: 3.9990 chunk 250 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 655 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4217 r_free = 0.4217 target = 0.186187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.146306 restraints weight = 29670.183| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.62 r_work: 0.3603 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22552 Z= 0.116 Angle : 0.504 10.911 30537 Z= 0.260 Chirality : 0.037 0.206 3421 Planarity : 0.004 0.060 3805 Dihedral : 4.509 56.700 2933 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.49 % Allowed : 22.87 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.18 (0.17), residues: 2641 helix: 2.18 (0.12), residues: 1981 sheet: None (None), residues: 0 loop : -0.86 (0.25), residues: 660 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 0.020 0.001 PHE D 59 TRP 0.019 0.001 TRP B 409 HIS 0.018 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00255 (22532) covalent geometry : angle 0.50406 (30517) SS BOND : bond 0.00107 ( 4) SS BOND : angle 0.43872 ( 8) hydrogen bonds : bond 0.03889 ( 1441) hydrogen bonds : angle 3.59448 ( 4248) metal coordination : bond 0.00412 ( 16) metal coordination : angle 0.97251 ( 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 363 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 303 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: A 652 ILE cc_start: 0.7768 (OUTLIER) cc_final: 0.7467 (mp) REVERT: A 746 MET cc_start: 0.7053 (tmm) cc_final: 0.6731 (tpp) REVERT: B 79 GLU cc_start: 0.7309 (OUTLIER) cc_final: 0.6275 (mp0) REVERT: B 421 MET cc_start: 0.6513 (tpp) cc_final: 0.5945 (tpp) REVERT: B 437 MET cc_start: 0.6361 (mmt) cc_final: 0.5948 (ttt) REVERT: B 634 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7375 (mm-30) REVERT: B 710 MET cc_start: 0.8535 (tpp) cc_final: 0.8085 (tpp) REVERT: C 404 TRP cc_start: 0.6002 (OUTLIER) cc_final: 0.4474 (m-90) REVERT: C 509 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.6590 (mp) REVERT: C 541 TYR cc_start: 0.7836 (m-10) cc_final: 0.7634 (m-80) REVERT: C 587 LYS cc_start: 0.7373 (OUTLIER) cc_final: 0.6791 (pttm) REVERT: C 723 ARG cc_start: 0.7557 (tpt170) cc_final: 0.7184 (tmt-80) REVERT: C 740 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.7986 (mtmt) REVERT: D 67 ASP cc_start: 0.7238 (t0) cc_final: 0.6914 (t0) REVERT: D 511 ARG cc_start: 0.8091 (mmm-85) cc_final: 0.7857 (mmm-85) REVERT: D 557 GLN cc_start: 0.8500 (OUTLIER) cc_final: 0.6766 (mt0) REVERT: D 604 TYR cc_start: 0.8908 (t80) cc_final: 0.8495 (t80) REVERT: D 723 ARG cc_start: 0.6981 (ttm110) cc_final: 0.6705 (ttm110) REVERT: D 733 GLU cc_start: 0.7632 (mm-30) cc_final: 0.7328 (mm-30) outliers start: 60 outliers final: 50 residues processed: 346 average time/residue: 0.1509 time to fit residues: 82.7279 Evaluate side-chains 349 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 291 time to evaluate : 0.779 ------------------------------------------------------------------------------- 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 219 CYS 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 499 GLU 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 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 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 525 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 230 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 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 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 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 Chi-restraints excluded: chain D residue 750 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 104 optimal weight: 9.9990 chunk 13 optimal weight: 0.0020 chunk 191 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 258 optimal weight: 3.9990 chunk 232 optimal weight: 0.6980 chunk 181 optimal weight: 0.4980 chunk 80 optimal weight: 5.9990 chunk 133 optimal weight: 0.0980 chunk 53 optimal weight: 6.9990 overall best weight: 0.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 622 ASN ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.188193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.147935 restraints weight = 29470.236| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 2.40 r_work: 0.3652 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 22552 Z= 0.108 Angle : 0.491 10.567 30537 Z= 0.253 Chirality : 0.036 0.205 3421 Planarity : 0.004 0.060 3805 Dihedral : 4.452 57.199 2933 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.25 % Allowed : 23.08 % Favored : 74.68 % 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 aren not related in a simple way. whole: 2.33 (0.17), residues: 2641 helix: 2.30 (0.12), residues: 1976 sheet: None (None), residues: 0 loop : -0.82 (0.25), residues: 665 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 0.023 0.001 PHE D 746 TRP 0.018 0.001 TRP B 409 HIS 0.004 0.000 HIS B 472 Details of bonding type rmsd covalent geometry : bond 0.00227 (22532) covalent geometry : angle 0.49062 (30517) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.37968 ( 8) hydrogen bonds : bond 0.03681 ( 1441) hydrogen bonds : angle 3.53302 ( 4248) metal coordination : bond 0.00321 ( 16) metal coordination : angle 0.88424 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5003.57 seconds wall clock time: 86 minutes 41.83 seconds (5201.83 seconds total)