Starting phenix.real_space_refine on Wed May 21 20:44:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpm_37719/05_2025/8wpm_37719.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpm_37719/05_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_37719/05_2025/8wpm_37719.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpm_37719/05_2025/8wpm_37719.map" model { file = "/net/cci-nas-00/data/ceres_data/8wpm_37719/05_2025/8wpm_37719.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpm_37719/05_2025/8wpm_37719.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 13.57, per 1000 atoms: 0.62 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: 5.34 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 2.49 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: 6.80 Time building geometry restraints manager: 6.18 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 754 or resid 1001 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 754 or resid 1001 through 1 \ 003)) 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 754 or resid 1001 through 1 \ 003)) } 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: 3.410 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: 0.790 Check model and map are aligned: 0.160 Set scattering table: 0.190 Process input model: 53.720 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.080 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.480 ------------------------------------------------------------------------------- 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 : 5.65 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.034 0.002 TRP D 468 HIS 0.015 0.001 HIS A 493 PHE 0.046 0.002 PHE D 746 TYR 0.029 0.002 TYR A 510 ARG 0.012 0.001 ARG D 511 Details of bonding type rmsd hydrogen bonds : bond 0.13239 ( 1441) hydrogen bonds : angle 5.17368 ( 4248) metal coordination : bond 0.00618 ( 16) metal coordination : angle 0.93367 ( 12) SS BOND : bond 0.00215 ( 4) SS BOND : angle 0.58259 ( 8) covalent geometry : bond 0.00545 (22532) covalent geometry : angle 0.80079 (30517) *********************** 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 : 2.534 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: 0.3199 time to fit residues: 167.9978 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 : 2.465 ------------------------------------------------------------------------------- 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 224 optimal weight: 4.9990 chunk 201 optimal weight: 6.9990 chunk 111 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 107 optimal weight: 0.2980 chunk 208 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 126 optimal weight: 4.9990 chunk 155 optimal weight: 0.3980 chunk 241 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 585 HIS 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 420 GLN B 605 ASN B 614 ASN B 621 ASN B 622 ASN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 ASN C 250 GLN C 442 ASN C 472 HIS C 485 ASN C 559 ASN C 569 GLN C 621 ASN C 630 HIS 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.207475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.170698 restraints weight = 29359.280| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 2.22 r_work: 0.3908 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.0980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22552 Z= 0.123 Angle : 0.490 8.302 30537 Z= 0.259 Chirality : 0.037 0.201 3421 Planarity : 0.004 0.058 3805 Dihedral : 4.994 59.755 2941 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.08 % Allowed : 20.79 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.16), residues: 2641 helix: 1.39 (0.11), residues: 1991 sheet: None (None), residues: 0 loop : -0.90 (0.25), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 409 HIS 0.007 0.001 HIS A 493 PHE 0.020 0.001 PHE D 539 TYR 0.025 0.001 TYR A 510 ARG 0.003 0.000 ARG D 511 Details of bonding type rmsd hydrogen bonds : bond 0.04202 ( 1441) hydrogen bonds : angle 3.82295 ( 4248) metal coordination : bond 0.00479 ( 16) metal coordination : angle 1.43280 ( 12) SS BOND : bond 0.00127 ( 4) SS BOND : angle 0.55903 ( 8) covalent geometry : bond 0.00268 (22532) covalent geometry : angle 0.48972 (30517) *********************** 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 376 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 326 time to evaluate : 2.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.5326 (ptp) cc_final: 0.5109 (ptp) REVERT: A 652 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7976 (mp) REVERT: B 378 PHE cc_start: 0.6300 (t80) cc_final: 0.6096 (t80) REVERT: B 421 MET cc_start: 0.6557 (tpp) cc_final: 0.6167 (tpp) outliers start: 50 outliers final: 25 residues processed: 355 average time/residue: 0.3198 time to fit residues: 181.2883 Evaluate side-chains 325 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 299 time to evaluate : 2.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 89 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain 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 652 THR Chi-restraints excluded: chain C residue 88 LEU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 340 PHE Chi-restraints excluded: chain D residue 436 LEU Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 518 LYS Chi-restraints excluded: chain D residue 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 62 optimal weight: 1.9990 chunk 209 optimal weight: 7.9990 chunk 30 optimal weight: 5.9990 chunk 235 optimal weight: 0.4980 chunk 63 optimal weight: 0.9990 chunk 56 optimal weight: 0.0050 chunk 82 optimal weight: 4.9990 chunk 206 optimal weight: 0.5980 chunk 160 optimal weight: 0.7980 chunk 181 optimal weight: 0.2980 chunk 184 optimal weight: 1.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 288 HIS ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 532 ASN D 735 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.201498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.168036 restraints weight = 28911.316| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 2.07 r_work: 0.3948 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22552 Z= 0.102 Angle : 0.450 6.863 30537 Z= 0.237 Chirality : 0.035 0.159 3421 Planarity : 0.004 0.060 3805 Dihedral : 4.664 59.290 2936 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.04 % Allowed : 21.16 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.16), residues: 2641 helix: 1.87 (0.12), residues: 1988 sheet: None (None), residues: 0 loop : -0.81 (0.25), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 314 HIS 0.005 0.000 HIS A 493 PHE 0.017 0.001 PHE D 59 TYR 0.019 0.001 TYR A 408 ARG 0.004 0.000 ARG B 246 Details of bonding type rmsd hydrogen bonds : bond 0.03774 ( 1441) hydrogen bonds : angle 3.62219 ( 4248) metal coordination : bond 0.00267 ( 16) metal coordination : angle 1.14305 ( 12) SS BOND : bond 0.00271 ( 4) SS BOND : angle 0.46414 ( 8) covalent geometry : bond 0.00207 (22532) covalent geometry : angle 0.44906 (30517) *********************** 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 380 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 331 time to evaluate : 2.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.5227 (ptp) cc_final: 0.4918 (ptp) REVERT: A 652 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7833 (mp) REVERT: A 682 PHE cc_start: 0.7602 (m-80) cc_final: 0.7365 (m-80) REVERT: A 746 MET cc_start: 0.7184 (tmm) cc_final: 0.6694 (tpp) REVERT: B 421 MET cc_start: 0.6550 (tpp) cc_final: 0.6135 (tpp) REVERT: B 710 MET cc_start: 0.8374 (tpt) cc_final: 0.7767 (tpt) REVERT: B 739 LEU cc_start: 0.8279 (tt) cc_final: 0.8021 (tp) REVERT: C 88 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8626 (tp) REVERT: C 509 LEU cc_start: 0.7191 (OUTLIER) cc_final: 0.6705 (mp) REVERT: D 67 ASP cc_start: 0.7229 (t0) cc_final: 0.7018 (t0) REVERT: D 208 LEU cc_start: 0.8765 (tp) cc_final: 0.8498 (tt) REVERT: D 563 THR cc_start: 0.8056 (t) cc_final: 0.7853 (m) REVERT: D 723 ARG cc_start: 0.6991 (ttm110) cc_final: 0.6753 (ttm110) outliers start: 49 outliers final: 30 residues processed: 359 average time/residue: 0.3118 time to fit residues: 177.4203 Evaluate side-chains 341 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 308 time to evaluate : 2.267 ------------------------------------------------------------------------------- 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 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 436 LEU 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 721 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 10 optimal weight: 10.0000 chunk 223 optimal weight: 3.9990 chunk 250 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 179 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 112 optimal weight: 0.7980 chunk 56 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 207 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 GLN A 170 ASN A 181 GLN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 308 GLN B 569 GLN ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 HIS ** C 532 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN D 250 GLN D 369 HIS D 442 ASN D 590 HIS D 605 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.187979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.150852 restraints weight = 29399.905| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 2.22 r_work: 0.3721 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1622 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= 0.180 Angle : 0.531 7.929 30537 Z= 0.275 Chirality : 0.039 0.170 3421 Planarity : 0.004 0.058 3805 Dihedral : 4.652 56.621 2936 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.20 % Allowed : 20.96 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.17), residues: 2641 helix: 1.91 (0.12), residues: 1987 sheet: None (None), residues: 0 loop : -0.81 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 314 HIS 0.004 0.001 HIS A 493 PHE 0.016 0.002 PHE D 59 TYR 0.021 0.002 TYR A 408 ARG 0.004 0.000 ARG B 723 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 1441) hydrogen bonds : angle 3.71223 ( 4248) metal coordination : bond 0.00568 ( 16) metal coordination : angle 0.90490 ( 12) SS BOND : bond 0.00228 ( 4) SS BOND : angle 0.46213 ( 8) covalent geometry : bond 0.00424 (22532) covalent geometry : angle 0.53112 (30517) *********************** 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 398 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 321 time to evaluate : 2.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.5219 (ptp) cc_final: 0.4972 (ptp) REVERT: A 652 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7848 (mp) REVERT: A 682 PHE cc_start: 0.7688 (m-80) cc_final: 0.7440 (m-80) REVERT: A 746 MET cc_start: 0.7041 (tmm) cc_final: 0.6789 (tpp) REVERT: B 421 MET cc_start: 0.6542 (tpp) cc_final: 0.6051 (tpp) REVERT: B 710 MET cc_start: 0.8637 (tpt) cc_final: 0.8065 (tpp) REVERT: C 509 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6663 (mp) REVERT: C 587 LYS cc_start: 0.7457 (OUTLIER) cc_final: 0.6869 (pttm) REVERT: D 67 ASP cc_start: 0.7438 (t0) cc_final: 0.7206 (t0) REVERT: D 256 LEU cc_start: 0.9113 (OUTLIER) cc_final: 0.8813 (mm) REVERT: D 582 TYR cc_start: 0.9127 (p90) cc_final: 0.8778 (p90) REVERT: D 723 ARG cc_start: 0.7060 (ttm110) cc_final: 0.6803 (ttm110) outliers start: 77 outliers final: 47 residues processed: 369 average time/residue: 0.3200 time to fit residues: 187.7750 Evaluate side-chains 349 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 298 time to evaluate : 3.942 ------------------------------------------------------------------------------- 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 252 VAL 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 588 ILE Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain C residue 63 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 353 SER Chi-restraints excluded: chain C residue 407 LEU Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 740 LYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 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 379 LEU Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 454 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 496 PHE Chi-restraints excluded: chain D residue 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 107 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 126 optimal weight: 9.9990 chunk 169 optimal weight: 10.0000 chunk 159 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 105 optimal weight: 7.9990 chunk 186 optimal weight: 4.9990 chunk 158 optimal weight: 0.2980 chunk 217 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 735 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 532 ASN 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 = 0.4267 r_free = 0.4267 target = 0.188095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.151107 restraints weight = 29123.462| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.22 r_work: 0.3737 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22552 Z= 0.145 Angle : 0.507 12.921 30537 Z= 0.261 Chirality : 0.037 0.178 3421 Planarity : 0.004 0.060 3805 Dihedral : 4.546 57.508 2933 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.20 % Allowed : 21.08 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.17), residues: 2641 helix: 1.99 (0.12), residues: 1990 sheet: None (None), residues: 0 loop : -0.79 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 409 HIS 0.005 0.001 HIS A 655 PHE 0.019 0.001 PHE B 92 TYR 0.019 0.001 TYR D 523 ARG 0.004 0.000 ARG B 246 Details of bonding type rmsd hydrogen bonds : bond 0.04102 ( 1441) hydrogen bonds : angle 3.66076 ( 4248) metal coordination : bond 0.00468 ( 16) metal coordination : angle 0.86709 ( 12) SS BOND : bond 0.00138 ( 4) SS BOND : angle 0.45920 ( 8) covalent geometry : bond 0.00336 (22532) covalent geometry : angle 0.50640 (30517) *********************** 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 388 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 311 time to evaluate : 2.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 MET cc_start: 0.5143 (ptp) cc_final: 0.4897 (ptp) REVERT: A 545 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8362 (mm) REVERT: A 652 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7833 (mp) REVERT: A 682 PHE cc_start: 0.7769 (m-80) cc_final: 0.7509 (m-80) REVERT: A 746 MET cc_start: 0.7047 (tmm) cc_final: 0.6812 (tpp) REVERT: B 421 MET cc_start: 0.6595 (tpp) cc_final: 0.6075 (tpp) REVERT: B 437 MET cc_start: 0.6260 (mmt) cc_final: 0.5929 (ttp) REVERT: B 634 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: B 710 MET cc_start: 0.8646 (tpt) cc_final: 0.8198 (tpp) REVERT: C 509 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6721 (mp) REVERT: C 587 LYS cc_start: 0.7466 (OUTLIER) cc_final: 0.6899 (pttm) REVERT: C 594 GLU cc_start: 0.7980 (mm-30) cc_final: 0.7648 (mm-30) REVERT: D 256 LEU cc_start: 0.9128 (OUTLIER) cc_final: 0.8801 (mm) REVERT: D 563 THR cc_start: 0.8134 (t) cc_final: 0.7857 (p) REVERT: D 582 TYR cc_start: 0.9106 (p90) cc_final: 0.8773 (p90) REVERT: D 723 ARG cc_start: 0.7047 (ttm110) cc_final: 0.6737 (ttm110) outliers start: 77 outliers final: 55 residues processed: 360 average time/residue: 0.3235 time to fit residues: 184.9531 Evaluate side-chains 357 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 296 time to evaluate : 2.306 ------------------------------------------------------------------------------- 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 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 545 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 620 MET Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 109 VAL Chi-restraints excluded: chain D residue 140 THR Chi-restraints excluded: chain D residue 174 VAL 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 436 LEU Chi-restraints excluded: chain D residue 442 ASN Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 496 PHE Chi-restraints excluded: chain D residue 535 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 60 optimal weight: 3.9990 chunk 31 optimal weight: 0.0030 chunk 93 optimal weight: 7.9990 chunk 108 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 200 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 chunk 248 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 10.0000 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN ** A 324 GLN ** 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 = 0.4306 r_free = 0.4306 target = 0.194891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.155813 restraints weight = 29222.086| |-----------------------------------------------------------------------------| r_work (start): 0.3901 rms_B_bonded: 2.30 r_work: 0.3731 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7972 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22552 Z= 0.132 Angle : 0.496 11.009 30537 Z= 0.254 Chirality : 0.037 0.183 3421 Planarity : 0.004 0.058 3805 Dihedral : 4.502 57.636 2933 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.33 % Allowed : 21.58 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.10 (0.17), residues: 2641 helix: 2.10 (0.12), residues: 1983 sheet: None (None), residues: 0 loop : -0.82 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 314 HIS 0.004 0.001 HIS A 493 PHE 0.018 0.001 PHE D 59 TYR 0.018 0.001 TYR D 523 ARG 0.004 0.000 ARG A 765 Details of bonding type rmsd hydrogen bonds : bond 0.03986 ( 1441) hydrogen bonds : angle 3.60699 ( 4248) metal coordination : bond 0.00444 ( 16) metal coordination : angle 0.85160 ( 12) SS BOND : bond 0.00128 ( 4) SS BOND : angle 0.43387 ( 8) covalent geometry : bond 0.00300 (22532) covalent geometry : angle 0.49590 (30517) *********************** 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 391 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 311 time to evaluate : 2.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 171 ASN cc_start: 0.7584 (t0) cc_final: 0.7126 (m-40) REVERT: A 339 MET cc_start: 0.5127 (ptp) cc_final: 0.4887 (ptp) REVERT: A 427 LEU cc_start: 0.7214 (OUTLIER) cc_final: 0.6962 (mp) REVERT: A 545 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8369 (mm) REVERT: A 652 ILE cc_start: 0.8053 (OUTLIER) cc_final: 0.7752 (mp) REVERT: A 682 PHE cc_start: 0.7763 (m-80) cc_final: 0.7516 (m-80) REVERT: A 746 MET cc_start: 0.7047 (tmm) cc_final: 0.6771 (tpp) REVERT: B 79 GLU cc_start: 0.7233 (OUTLIER) cc_final: 0.6686 (mp0) REVERT: B 88 LEU cc_start: 0.7261 (OUTLIER) cc_final: 0.7009 (mp) REVERT: B 421 MET cc_start: 0.6516 (tpp) cc_final: 0.5996 (tpp) REVERT: B 437 MET cc_start: 0.6192 (mmt) cc_final: 0.5899 (ttt) REVERT: B 634 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7305 (mm-30) REVERT: C 88 LEU cc_start: 0.8843 (tp) cc_final: 0.8611 (tp) REVERT: C 509 LEU cc_start: 0.7315 (OUTLIER) cc_final: 0.6606 (mp) REVERT: C 587 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6941 (pttm) REVERT: C 594 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7648 (mm-30) REVERT: D 67 ASP cc_start: 0.6832 (t0) cc_final: 0.6631 (t0) REVERT: D 256 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8808 (mm) REVERT: D 557 GLN cc_start: 0.8455 (OUTLIER) cc_final: 0.6559 (mt0) REVERT: D 563 THR cc_start: 0.8131 (t) cc_final: 0.7838 (p) REVERT: D 582 TYR cc_start: 0.9108 (p90) cc_final: 0.8747 (p90) REVERT: D 723 ARG cc_start: 0.6993 (ttm110) cc_final: 0.6697 (ttm110) outliers start: 80 outliers final: 54 residues processed: 365 average time/residue: 0.3079 time to fit residues: 178.4380 Evaluate side-chains 364 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 300 time to evaluate : 2.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 219 CYS Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 553 ILE Chi-restraints excluded: chain A residue 588 ILE Chi-restraints excluded: chain A residue 611 PHE Chi-restraints excluded: chain A residue 652 ILE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain B residue 59 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 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 440 VAL Chi-restraints excluded: chain B residue 488 SER Chi-restraints excluded: chain B residue 505 LEU Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 63 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 515 ASP 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 23 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 109 VAL 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 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 633 ILE 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 39 optimal weight: 6.9990 chunk 139 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 101 optimal weight: 0.2980 chunk 29 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 740 HIS ** 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 = 0.4281 r_free = 0.4281 target = 0.189366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.152779 restraints weight = 28836.528| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.21 r_work: 0.3741 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22552 Z= 0.135 Angle : 0.497 9.703 30537 Z= 0.255 Chirality : 0.037 0.183 3421 Planarity : 0.004 0.058 3805 Dihedral : 4.483 57.123 2933 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 3.28 % Allowed : 21.66 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.17), residues: 2641 helix: 2.12 (0.12), residues: 1985 sheet: None (None), residues: 0 loop : -0.82 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 314 HIS 0.003 0.000 HIS A 493 PHE 0.019 0.001 PHE D 59 TYR 0.018 0.001 TYR C 541 ARG 0.006 0.000 ARG B 511 Details of bonding type rmsd hydrogen bonds : bond 0.03951 ( 1441) hydrogen bonds : angle 3.59258 ( 4248) metal coordination : bond 0.00444 ( 16) metal coordination : angle 0.84931 ( 12) SS BOND : bond 0.00122 ( 4) SS BOND : angle 0.43198 ( 8) covalent geometry : bond 0.00311 (22532) covalent geometry : angle 0.49691 (30517) *********************** 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 397 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 318 time to evaluate : 2.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 171 ASN cc_start: 0.7516 (t0) cc_final: 0.7034 (m-40) REVERT: A 339 MET cc_start: 0.5143 (ptp) cc_final: 0.4918 (ptp) REVERT: A 427 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6981 (mp) REVERT: A 545 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8365 (mm) REVERT: A 652 ILE cc_start: 0.8076 (OUTLIER) cc_final: 0.7767 (mp) REVERT: A 746 MET cc_start: 0.7044 (tmm) cc_final: 0.6770 (tpp) REVERT: B 79 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6679 (mp0) REVERT: B 421 MET cc_start: 0.6469 (tpp) cc_final: 0.5951 (tpp) REVERT: B 437 MET cc_start: 0.6220 (mmt) cc_final: 0.5941 (ttt) REVERT: B 634 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7334 (mm-30) REVERT: B 710 MET cc_start: 0.8545 (tpp) cc_final: 0.8171 (tpp) REVERT: C 88 LEU cc_start: 0.8831 (tp) cc_final: 0.8611 (tp) REVERT: C 509 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.6760 (mp) REVERT: C 587 LYS cc_start: 0.7588 (OUTLIER) cc_final: 0.6939 (pttm) REVERT: C 594 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7627 (mm-30) REVERT: D 67 ASP cc_start: 0.6867 (t0) cc_final: 0.6586 (t0) REVERT: D 256 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8857 (mm) REVERT: D 511 ARG cc_start: 0.8023 (mmm-85) cc_final: 0.7820 (mmm-85) REVERT: D 557 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.6601 (mt0) REVERT: D 563 THR cc_start: 0.8113 (t) cc_final: 0.7827 (p) REVERT: D 582 TYR cc_start: 0.9107 (p90) cc_final: 0.8779 (p90) REVERT: D 723 ARG cc_start: 0.7019 (ttm110) cc_final: 0.6758 (ttm110) REVERT: D 733 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7415 (mm-30) outliers start: 79 outliers final: 63 residues processed: 372 average time/residue: 0.3244 time to fit residues: 189.2448 Evaluate side-chains 379 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 307 time to evaluate : 2.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 74 ASP Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 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 252 VAL Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 427 LEU Chi-restraints excluded: chain A residue 545 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 59 PHE Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 79 GLU Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 395 GLN Chi-restraints excluded: chain B residue 440 VAL Chi-restraints excluded: chain B residue 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 655 THR Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 212 SER Chi-restraints excluded: chain C residue 305 ASN Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 740 LYS Chi-restraints excluded: chain C residue 753 LEU Chi-restraints excluded: chain D residue 23 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 109 VAL 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 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 633 ILE Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 750 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 164 optimal weight: 0.5980 chunk 167 optimal weight: 5.9990 chunk 122 optimal weight: 5.9990 chunk 172 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 105 optimal weight: 7.9990 chunk 78 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 236 optimal weight: 6.9990 chunk 97 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- 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 101 GLN A 170 ASN A 264 GLN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 683 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 605 ASN ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 621 ASN C 707 GLN D 247 GLN D 625 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.189826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.155209 restraints weight = 28892.198| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 2.33 r_work: 0.3789 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 22552 Z= 0.325 Angle : 0.715 13.843 30537 Z= 0.363 Chirality : 0.045 0.189 3421 Planarity : 0.005 0.057 3805 Dihedral : 4.881 56.271 2933 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 3.41 % Allowed : 21.79 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.16), residues: 2641 helix: 1.55 (0.11), residues: 1984 sheet: None (None), residues: 0 loop : -1.09 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 314 HIS 0.004 0.001 HIS A 603 PHE 0.028 0.002 PHE B 657 TYR 0.027 0.002 TYR D 523 ARG 0.009 0.001 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.05313 ( 1441) hydrogen bonds : angle 4.09990 ( 4248) metal coordination : bond 0.00989 ( 16) metal coordination : angle 1.13548 ( 12) SS BOND : bond 0.00235 ( 4) SS BOND : angle 0.73321 ( 8) covalent geometry : bond 0.00778 (22532) covalent geometry : angle 0.71492 (30517) *********************** 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 375 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 293 time to evaluate : 2.341 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 555 LEU cc_start: 0.8931 (mt) cc_final: 0.8725 (mt) REVERT: A 652 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.8011 (mp) REVERT: A 746 MET cc_start: 0.7201 (tmm) cc_final: 0.6900 (tpp) REVERT: B 79 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.6376 (mp0) REVERT: B 235 ASN cc_start: 0.7249 (m110) cc_final: 0.6955 (m110) REVERT: B 437 MET cc_start: 0.6597 (mmt) cc_final: 0.6244 (ttp) REVERT: B 710 MET cc_start: 0.8625 (tpp) cc_final: 0.8285 (tpp) REVERT: C 404 TRP cc_start: 0.6006 (OUTLIER) cc_final: 0.4219 (m-90) REVERT: C 587 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7221 (pttm) REVERT: C 723 ARG cc_start: 0.7713 (tpt170) cc_final: 0.7316 (tmt170) REVERT: D 45 TYR cc_start: 0.8143 (t80) cc_final: 0.7618 (t80) REVERT: D 67 ASP cc_start: 0.6977 (t0) cc_final: 0.6638 (t0) REVERT: D 557 GLN cc_start: 0.8549 (OUTLIER) cc_final: 0.6823 (mt0) REVERT: D 563 THR cc_start: 0.8073 (t) cc_final: 0.7863 (p) REVERT: D 746 PHE cc_start: 0.7829 (t80) cc_final: 0.7553 (t80) outliers start: 82 outliers final: 63 residues processed: 353 average time/residue: 0.3183 time to fit residues: 176.9011 Evaluate side-chains 342 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 274 time to evaluate : 2.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 75 LEU Chi-restraints excluded: chain A residue 98 ASP Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 252 VAL Chi-restraints excluded: chain A residue 314 ILE 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 572 VAL Chi-restraints excluded: chain A residue 588 ILE 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 525 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 267 ILE Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 404 TRP Chi-restraints excluded: chain C residue 438 ASP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 515 ASP Chi-restraints excluded: chain C residue 516 ILE Chi-restraints excluded: chain C residue 587 LYS Chi-restraints excluded: chain C residue 612 LEU Chi-restraints excluded: chain C residue 700 LEU Chi-restraints excluded: chain C residue 731 LEU Chi-restraints excluded: chain C residue 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 174 VAL 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 454 VAL Chi-restraints excluded: chain D residue 457 VAL Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain D residue 496 PHE Chi-restraints excluded: chain D residue 535 ASN Chi-restraints excluded: chain D residue 557 GLN Chi-restraints excluded: chain D residue 603 THR Chi-restraints excluded: chain D residue 633 ILE 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 27 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 233 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 263 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 262 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 257 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 A 683 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN B 605 ASN ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 GLN D 442 ASN D 605 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.192815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.154922 restraints weight = 29284.794| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 2.22 r_work: 0.3730 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 22552 Z= 0.126 Angle : 0.531 14.003 30537 Z= 0.272 Chirality : 0.038 0.193 3421 Planarity : 0.004 0.061 3805 Dihedral : 4.619 56.031 2933 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.49 % Allowed : 22.58 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.17), residues: 2641 helix: 2.02 (0.12), residues: 1974 sheet: None (None), residues: 0 loop : -1.00 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 314 HIS 0.012 0.001 HIS A 655 PHE 0.020 0.001 PHE D 59 TYR 0.018 0.001 TYR D 523 ARG 0.005 0.000 ARG B 246 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 1441) hydrogen bonds : angle 3.69097 ( 4248) metal coordination : bond 0.00525 ( 16) metal coordination : angle 1.09995 ( 12) SS BOND : bond 0.00121 ( 4) SS BOND : angle 0.52664 ( 8) covalent geometry : bond 0.00280 (22532) covalent geometry : angle 0.53061 (30517) *********************** 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 355 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 295 time to evaluate : 2.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 545 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8427 (mm) REVERT: A 652 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7645 (mp) REVERT: A 746 MET cc_start: 0.7078 (tmm) cc_final: 0.6790 (tpp) REVERT: B 79 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.6191 (mp0) REVERT: B 421 MET cc_start: 0.6495 (tpp) cc_final: 0.5927 (mmm) REVERT: B 437 MET cc_start: 0.6431 (mmt) cc_final: 0.6018 (ttt) REVERT: C 404 TRP cc_start: 0.6036 (OUTLIER) cc_final: 0.4390 (m-90) REVERT: C 509 LEU cc_start: 0.7455 (OUTLIER) cc_final: 0.6748 (mp) REVERT: C 587 LYS cc_start: 0.7609 (OUTLIER) cc_final: 0.7080 (pttm) REVERT: C 594 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7698 (mm-30) REVERT: C 723 ARG cc_start: 0.7566 (tpt170) cc_final: 0.7170 (tmt-80) REVERT: D 67 ASP cc_start: 0.7030 (t0) cc_final: 0.6727 (t0) REVERT: D 511 ARG cc_start: 0.8126 (mmm-85) cc_final: 0.7852 (mmm-85) REVERT: D 557 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.6717 (mt0) REVERT: D 563 THR cc_start: 0.8079 (t) cc_final: 0.7807 (p) REVERT: D 733 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7373 (mm-30) outliers start: 60 outliers final: 38 residues processed: 336 average time/residue: 0.3241 time to fit residues: 172.3733 Evaluate side-chains 329 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 284 time to evaluate : 2.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 196 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 545 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 572 VAL 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 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 488 SER Chi-restraints excluded: chain B residue 655 THR Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 340 PHE Chi-restraints excluded: chain C residue 404 TRP Chi-restraints excluded: chain C residue 509 LEU Chi-restraints excluded: chain C residue 515 ASP 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 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 535 ASN Chi-restraints excluded: chain D residue 557 GLN Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 750 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 225 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 149 optimal weight: 0.8980 chunk 110 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 201 optimal weight: 7.9990 chunk 34 optimal weight: 20.0000 chunk 139 optimal weight: 3.9990 chunk 186 optimal weight: 0.4980 chunk 17 optimal weight: 0.4980 chunk 70 optimal weight: 0.0980 overall best weight: 0.5982 ------------------------------------------------------------------------------- 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 171 ASN A 264 GLN ** A 324 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 655 HIS A 683 ASN A 773 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 247 GLN D 442 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.186906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.147763 restraints weight = 29722.140| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.62 r_work: 0.3614 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 22552 Z= 0.115 Angle : 0.517 14.425 30537 Z= 0.265 Chirality : 0.037 0.195 3421 Planarity : 0.004 0.060 3805 Dihedral : 4.512 56.920 2933 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 1.91 % Allowed : 23.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.17), residues: 2641 helix: 2.19 (0.12), residues: 1978 sheet: None (None), residues: 0 loop : -0.94 (0.25), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP D 409 HIS 0.003 0.000 HIS B 472 PHE 0.020 0.001 PHE D 59 TYR 0.017 0.001 TYR D 523 ARG 0.005 0.000 ARG B 246 Details of bonding type rmsd hydrogen bonds : bond 0.03839 ( 1441) hydrogen bonds : angle 3.57257 ( 4248) metal coordination : bond 0.00420 ( 16) metal coordination : angle 0.95173 ( 12) SS BOND : bond 0.00087 ( 4) SS BOND : angle 0.42172 ( 8) covalent geometry : bond 0.00250 (22532) covalent geometry : angle 0.51701 (30517) ********************** 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 361 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 315 time to evaluate : 2.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 545 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8351 (mm) REVERT: A 652 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7312 (mp) REVERT: A 746 MET cc_start: 0.7068 (tmm) cc_final: 0.6683 (tpp) REVERT: B 79 GLU cc_start: 0.7255 (OUTLIER) cc_final: 0.6617 (mp0) REVERT: B 421 MET cc_start: 0.6430 (tpp) cc_final: 0.5871 (tpp) REVERT: B 437 MET cc_start: 0.6288 (mmt) cc_final: 0.5852 (ttt) REVERT: C 88 LEU cc_start: 0.8541 (tp) cc_final: 0.8317 (tp) REVERT: C 509 LEU cc_start: 0.7230 (OUTLIER) cc_final: 0.6602 (mp) REVERT: C 587 LYS cc_start: 0.7591 (OUTLIER) cc_final: 0.6957 (pttm) REVERT: C 723 ARG cc_start: 0.7393 (tpt170) cc_final: 0.6902 (tmt-80) REVERT: D 67 ASP cc_start: 0.7213 (t0) cc_final: 0.6879 (t0) REVERT: D 511 ARG cc_start: 0.8015 (mmm-85) cc_final: 0.7801 (mmm-85) REVERT: D 557 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.6765 (mt0) REVERT: D 604 TYR cc_start: 0.8901 (t80) cc_final: 0.8338 (t80) REVERT: D 723 ARG cc_start: 0.6913 (ttm110) cc_final: 0.6606 (ttm110) REVERT: D 733 GLU cc_start: 0.7569 (mm-30) cc_final: 0.7249 (mm-30) outliers start: 46 outliers final: 32 residues processed: 349 average time/residue: 0.3165 time to fit residues: 174.5606 Evaluate side-chains 332 residues out of total 2405 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 294 time to evaluate : 2.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 156 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 314 ILE Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 545 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 652 ILE Chi-restraints excluded: chain A residue 654 ASN Chi-restraints excluded: chain A residue 658 LYS Chi-restraints excluded: chain B residue 59 PHE 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 488 SER Chi-restraints excluded: chain B residue 709 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 321 TRP Chi-restraints excluded: chain C residue 340 PHE 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 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 557 GLN Chi-restraints excluded: chain D residue 659 VAL Chi-restraints excluded: chain D residue 700 LEU Chi-restraints excluded: chain D residue 721 MET Chi-restraints excluded: chain D residue 750 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 157 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 220 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 208 optimal weight: 7.9990 chunk 183 optimal weight: 3.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 585 HIS A 683 ASN A 773 ASN ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 442 ASN ** B 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 741 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 707 GLN D 250 GLN D 605 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.182096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.141823 restraints weight = 30037.352| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 2.37 r_work: 0.3537 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 22552 Z= 0.213 Angle : 0.603 14.177 30537 Z= 0.309 Chirality : 0.041 0.200 3421 Planarity : 0.004 0.058 3805 Dihedral : 4.642 56.275 2933 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.12 % Allowed : 23.04 % Favored : 74.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.17), residues: 2641 helix: 1.98 (0.12), residues: 1974 sheet: None (None), residues: 0 loop : -0.99 (0.24), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP D 409 HIS 0.004 0.001 HIS A 646 PHE 0.021 0.002 PHE D 539 TYR 0.022 0.002 TYR D 523 ARG 0.006 0.000 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.04472 ( 1441) hydrogen bonds : angle 3.79123 ( 4248) metal coordination : bond 0.00706 ( 16) metal coordination : angle 1.04689 ( 12) SS BOND : bond 0.00148 ( 4) SS BOND : angle 0.56343 ( 8) covalent geometry : bond 0.00509 (22532) covalent geometry : angle 0.60268 (30517) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10184.71 seconds wall clock time: 177 minutes 30.84 seconds (10650.84 seconds total)