Starting phenix.real_space_refine on Mon May 4 15:46:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpn_37720/05_2026/8wpn_37720_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpn_37720/05_2026/8wpn_37720.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wpn_37720/05_2026/8wpn_37720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpn_37720/05_2026/8wpn_37720.map" model { file = "/net/cci-nas-00/data/ceres_data/8wpn_37720/05_2026/8wpn_37720_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpn_37720/05_2026/8wpn_37720_neut.cif" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.075 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: 7 Type Number sf(0) Gaussians Ca 4 9.91 5 Zn 4 6.06 5 P 4 5.49 5 S 104 5.16 5 C 14704 2.51 5 N 3712 2.21 5 O 3992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 91 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22524 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5550 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 655} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 5550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5550 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 655} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 5550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5550 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 655} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 5550 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5550 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 24, 'TRANS': 655} Chain breaks: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {' CA': 1, ' ZN': 1, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {' CA': 1, ' ZN': 1, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {' CA': 1, ' ZN': 1, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 81 Unusual residues: {' CA': 1, ' ZN': 1, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1159 SG CYS A 176 76.984 105.503 62.223 1.00112.69 S ATOM 1173 SG CYS A 178 77.294 108.810 60.346 1.00126.23 S ATOM 1195 SG CYS A 181 74.160 106.576 59.846 1.00113.75 S ATOM 6709 SG CYS B 176 22.944 76.984 62.205 1.00112.69 S ATOM 6723 SG CYS B 178 19.640 77.297 60.323 1.00126.23 S ATOM 6745 SG CYS B 181 21.876 74.165 59.819 1.00113.75 S ATOM 12259 SG CYS C 176 51.544 22.922 62.279 1.00112.69 S ATOM 12273 SG CYS C 178 51.230 19.616 60.401 1.00126.23 S ATOM 12295 SG CYS C 181 54.364 21.848 59.898 1.00113.75 S ATOM 17809 SG CYS D 176 105.520 51.626 62.300 1.00112.69 S ATOM 17823 SG CYS D 178 108.829 51.323 60.425 1.00126.23 S ATOM 17845 SG CYS D 181 106.586 54.450 59.920 1.00113.75 S Time building chain proxies: 6.13, per 1000 atoms: 0.27 Number of scatterers: 22524 At special positions: 0 Unit cell: (129.591, 129.591, 137.088, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 Ca 4 19.99 S 104 16.00 P 4 15.00 O 3992 8.00 N 3712 7.00 C 14704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 549 " - pdb=" SG CYS A 554 " distance=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 554 " distance=2.03 Simple disulfide: pdb=" SG CYS C 549 " - pdb=" SG CYS C 554 " distance=2.03 Simple disulfide: pdb=" SG CYS D 549 " - pdb=" SG CYS D 554 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1002 " pdb="ZN ZN A1002 " - pdb=" ND1 HIS A 172 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 176 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 178 " pdb="ZN ZN A1002 " - pdb=" SG CYS A 181 " pdb=" ZN B1002 " pdb="ZN ZN B1002 " - pdb=" ND1 HIS B 172 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 176 " pdb="ZN ZN B1002 " - pdb=" SG CYS B 178 " 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 176 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 178 " pdb="ZN ZN C1002 " - pdb=" SG CYS C 181 " pdb=" ZN D1003 " pdb="ZN ZN D1003 " - pdb=" ND1 HIS D 172 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 176 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 178 " pdb="ZN ZN D1003 " - pdb=" SG CYS D 181 " Number of angles added : 12 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5240 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 4 sheets defined 77.2% alpha, 0.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 30 through 43 Processing helix chain 'A' and resid 44 through 59 Processing helix chain 'A' and resid 72 through 80 Processing helix chain 'A' and resid 82 through 92 removed outlier: 3.731A pdb=" N PHE A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 106 Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 144 through 153 Processing helix chain 'A' and resid 154 through 164 removed outlier: 3.568A pdb=" N LYS A 164 " --> pdb=" O LEU A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 188 Processing helix chain 'A' and resid 188 through 204 Processing helix chain 'A' and resid 205 through 213 Processing helix chain 'A' and resid 215 through 234 Processing helix chain 'A' and resid 237 through 257 Processing helix chain 'A' and resid 261 through 270 Processing helix chain 'A' and resid 286 through 295 Processing helix chain 'A' and resid 297 through 302 Processing helix chain 'A' and resid 303 through 315 Processing helix chain 'A' and resid 320 through 324 Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 339 through 350 Processing helix chain 'A' and resid 361 through 386 Processing helix chain 'A' and resid 400 through 424 Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 425 through 432 removed outlier: 4.104A pdb=" N ASP A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 459 removed outlier: 3.671A pdb=" N LEU A 436 " --> pdb=" O ASP A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 464 through 468 Processing helix chain 'A' and resid 472 through 491 Processing helix chain 'A' and resid 492 through 498 removed outlier: 3.718A pdb=" N THR A 497 " --> pdb=" O SER A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 539 removed outlier: 4.056A pdb=" N LEU A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU A 514 " --> pdb=" O GLY A 510 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASP A 515 " --> pdb=" O ARG A 511 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 574 Processing helix chain 'A' and resid 580 through 585 removed outlier: 3.790A pdb=" N VAL A 583 " --> pdb=" O ASN A 580 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A 584 " --> pdb=" O LEU A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 Processing helix chain 'A' and resid 611 through 629 removed outlier: 4.107A pdb=" N ASP A 629 " --> pdb=" O GLN A 625 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 645 Processing helix chain 'A' and resid 696 through 721 Processing helix chain 'A' and resid 721 through 728 removed outlier: 3.750A pdb=" N LYS A 726 " --> pdb=" O ILE A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 732 through 755 removed outlier: 3.545A pdb=" N PHE A 736 " --> pdb=" O THR A 732 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU A 749 " --> pdb=" O SER A 745 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL A 750 " --> pdb=" O PHE A 746 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU A 751 " --> pdb=" O ARG A 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 43 Processing helix chain 'B' and resid 44 through 59 Processing helix chain 'B' and resid 72 through 80 Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.731A pdb=" N PHE B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 98 through 106 Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 144 through 153 Processing helix chain 'B' and resid 154 through 164 removed outlier: 3.568A pdb=" N LYS B 164 " --> pdb=" O LEU B 160 " (cutoff:3.500A) 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 257 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 320 through 324 Processing helix chain 'B' and resid 325 through 339 Processing helix chain 'B' and resid 339 through 350 Processing helix chain 'B' and resid 361 through 386 Processing helix chain 'B' and resid 400 through 424 Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 425 through 432 removed outlier: 4.103A pdb=" N ASP B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 459 removed outlier: 3.671A pdb=" N LEU B 436 " --> pdb=" O ASP B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 468 Processing helix chain 'B' and resid 472 through 491 Processing helix chain 'B' and resid 492 through 498 removed outlier: 3.718A pdb=" N THR B 497 " --> pdb=" O SER B 494 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 539 removed outlier: 4.055A pdb=" N LEU B 505 " --> pdb=" O HIS B 501 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B 514 " --> pdb=" O GLY B 510 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASP B 515 " --> pdb=" O ARG B 511 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) removed outlier: 3.604A 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: 3.791A pdb=" N VAL B 583 " --> pdb=" O ASN B 580 " (cutoff:3.500A) removed outlier: 3.619A 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 629 removed outlier: 4.107A pdb=" N ASP B 629 " --> pdb=" O GLN B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 630 through 645 Processing helix chain 'B' and resid 696 through 721 Processing helix chain 'B' and resid 721 through 728 removed outlier: 3.750A pdb=" N LYS B 726 " --> pdb=" O ILE B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 732 through 755 removed outlier: 3.545A pdb=" N PHE B 736 " --> pdb=" O THR B 732 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU B 749 " --> pdb=" O SER B 745 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL B 750 " --> pdb=" O PHE B 746 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU B 751 " --> pdb=" O ARG B 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 43 Processing helix chain 'C' and resid 44 through 59 Processing helix chain 'C' and resid 72 through 80 Processing helix chain 'C' and resid 82 through 92 removed outlier: 3.731A 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 111 through 116 Processing helix chain 'C' and resid 144 through 153 Processing helix chain 'C' and resid 154 through 164 removed outlier: 3.568A pdb=" N LYS C 164 " --> pdb=" O LEU C 160 " (cutoff:3.500A) 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 257 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 320 through 324 Processing helix chain 'C' and resid 325 through 339 Processing helix chain 'C' and resid 339 through 350 Processing helix chain 'C' and resid 361 through 386 Processing helix chain 'C' and resid 400 through 424 Proline residue: C 408 - end of helix Processing helix chain 'C' and resid 425 through 432 removed outlier: 4.103A pdb=" N ASP C 432 " --> pdb=" O ASP C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 432 through 459 removed outlier: 3.670A pdb=" N LEU C 436 " --> pdb=" O ASP C 432 " (cutoff:3.500A) 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 498 removed outlier: 3.717A pdb=" N THR C 497 " --> pdb=" O SER C 494 " (cutoff:3.500A) Processing helix chain 'C' and resid 501 through 539 removed outlier: 4.055A pdb=" N LEU C 505 " --> pdb=" O HIS C 501 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU C 514 " --> pdb=" O GLY C 510 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASP C 515 " --> pdb=" O ARG C 511 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE C 516 " --> pdb=" O MET C 512 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE C 521 " --> pdb=" O LEU C 517 " (cutoff:3.500A) removed outlier: 3.604A 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: 3.790A pdb=" N VAL C 583 " --> pdb=" O ASN C 580 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR C 584 " --> pdb=" O LEU C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 610 Processing helix chain 'C' and resid 611 through 629 removed outlier: 4.107A pdb=" N ASP C 629 " --> pdb=" O GLN C 625 " (cutoff:3.500A) Processing helix chain 'C' and resid 630 through 645 Processing helix chain 'C' and resid 696 through 721 Processing helix chain 'C' and resid 721 through 728 removed outlier: 3.750A pdb=" N LYS C 726 " --> pdb=" O ILE C 722 " (cutoff:3.500A) Processing helix chain 'C' and resid 732 through 755 removed outlier: 3.545A pdb=" N PHE C 736 " --> pdb=" O THR C 732 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU C 749 " --> pdb=" O SER C 745 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL C 750 " --> pdb=" O PHE C 746 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU C 751 " --> pdb=" O ARG C 747 " (cutoff:3.500A) Processing helix chain 'D' and resid 30 through 43 Processing helix chain 'D' and resid 44 through 59 Processing helix chain 'D' and resid 72 through 80 Processing helix chain 'D' and resid 82 through 92 removed outlier: 3.732A pdb=" N PHE D 92 " --> pdb=" O LEU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 111 through 116 Processing helix chain 'D' and resid 144 through 153 Processing helix chain 'D' and resid 154 through 164 removed outlier: 3.568A pdb=" N LYS D 164 " --> pdb=" O LEU D 160 " (cutoff:3.500A) 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 257 Processing helix chain 'D' and resid 261 through 270 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 320 through 324 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 Processing helix chain 'D' and resid 400 through 424 Proline residue: D 408 - end of helix Processing helix chain 'D' and resid 425 through 432 removed outlier: 4.103A pdb=" N ASP D 432 " --> pdb=" O ASP D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 459 removed outlier: 3.671A 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 491 Processing helix chain 'D' and resid 492 through 498 removed outlier: 3.717A pdb=" N THR D 497 " --> pdb=" O SER D 494 " (cutoff:3.500A) Processing helix chain 'D' and resid 501 through 539 removed outlier: 4.056A pdb=" N LEU D 505 " --> pdb=" O HIS D 501 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU D 514 " --> pdb=" O GLY D 510 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N ASP D 515 " --> pdb=" O ARG D 511 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE D 516 " --> pdb=" O MET D 512 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N PHE D 521 " --> pdb=" O LEU D 517 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE D 522 " --> pdb=" O LYS D 518 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 574 Processing helix chain 'D' and resid 580 through 585 removed outlier: 3.790A pdb=" N VAL D 583 " --> pdb=" O ASN D 580 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR D 584 " --> pdb=" O LEU D 581 " (cutoff:3.500A) Processing helix chain 'D' and resid 590 through 610 Processing helix chain 'D' and resid 611 through 629 removed outlier: 4.106A pdb=" N ASP D 629 " --> pdb=" O GLN D 625 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 645 Processing helix chain 'D' and resid 696 through 721 Processing helix chain 'D' and resid 721 through 728 removed outlier: 3.750A pdb=" N LYS D 726 " --> pdb=" O ILE D 722 " (cutoff:3.500A) Processing helix chain 'D' and resid 732 through 755 removed outlier: 3.546A pdb=" N PHE D 736 " --> pdb=" O THR D 732 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU D 749 " --> pdb=" O SER D 745 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL D 750 " --> pdb=" O PHE D 746 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU D 751 " --> pdb=" O ARG D 747 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 Processing sheet with id=AA2, first strand: chain 'A' and resid 168 through 169 Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 18 Processing sheet with id=AA4, first strand: chain 'C' and resid 17 through 18 1460 hydrogen bonds defined for protein. 4272 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.93 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3572 1.32 - 1.44: 6277 1.44 - 1.56: 13035 1.56 - 1.69: 4 1.69 - 1.81: 160 Bond restraints: 23048 Sorted by residual: bond pdb=" O5 LPP C1004 " pdb=" P1 LPP C1004 " ideal model delta sigma weight residual 2.278 1.605 0.673 2.00e-02 2.50e+03 1.13e+03 bond pdb=" O5 LPP D1001 " pdb=" P1 LPP D1001 " ideal model delta sigma weight residual 2.278 1.605 0.673 2.00e-02 2.50e+03 1.13e+03 bond pdb=" O5 LPP A1004 " pdb=" P1 LPP A1004 " ideal model delta sigma weight residual 2.278 1.605 0.673 2.00e-02 2.50e+03 1.13e+03 bond pdb=" O5 LPP B1004 " pdb=" P1 LPP B1004 " ideal model delta sigma weight residual 2.278 1.605 0.673 2.00e-02 2.50e+03 1.13e+03 bond pdb=" O4 LPP B1004 " pdb=" P1 LPP B1004 " ideal model delta sigma weight residual 1.764 1.506 0.258 2.00e-02 2.50e+03 1.66e+02 ... (remaining 23043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.14: 31180 8.14 - 16.29: 16 16.29 - 24.43: 4 24.43 - 32.58: 4 32.58 - 40.72: 8 Bond angle restraints: 31212 Sorted by residual: angle pdb=" O4 LPP B1004 " pdb=" P1 LPP B1004 " pdb=" O5 LPP B1004 " ideal model delta sigma weight residual 62.99 103.71 -40.72 3.00e+00 1.11e-01 1.84e+02 angle pdb=" O4 LPP D1001 " pdb=" P1 LPP D1001 " pdb=" O5 LPP D1001 " ideal model delta sigma weight residual 62.99 103.70 -40.71 3.00e+00 1.11e-01 1.84e+02 angle pdb=" O4 LPP A1004 " pdb=" P1 LPP A1004 " pdb=" O5 LPP A1004 " ideal model delta sigma weight residual 62.99 103.68 -40.69 3.00e+00 1.11e-01 1.84e+02 angle pdb=" O4 LPP C1004 " pdb=" P1 LPP C1004 " pdb=" O5 LPP C1004 " ideal model delta sigma weight residual 62.99 103.68 -40.69 3.00e+00 1.11e-01 1.84e+02 angle pdb=" C6 LPP C1004 " pdb=" O5 LPP C1004 " pdb=" P1 LPP C1004 " ideal model delta sigma weight residual 82.33 118.96 -36.63 3.00e+00 1.11e-01 1.49e+02 ... (remaining 31207 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.79: 12624 23.79 - 47.58: 1172 47.58 - 71.38: 212 71.38 - 95.17: 20 95.17 - 118.96: 12 Dihedral angle restraints: 14040 sinusoidal: 5996 harmonic: 8044 Sorted by residual: 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 93.00 156.61 -63.61 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS A 549 " pdb=" SG CYS A 549 " pdb=" SG CYS A 554 " pdb=" CB CYS A 554 " ideal model delta sinusoidal sigma weight residual 93.00 156.58 -63.58 1 1.00e+01 1.00e-02 5.33e+01 dihedral pdb=" CB CYS D 549 " pdb=" SG CYS D 549 " pdb=" SG CYS D 554 " pdb=" CB CYS D 554 " ideal model delta sinusoidal sigma weight residual 93.00 156.58 -63.58 1 1.00e+01 1.00e-02 5.33e+01 ... (remaining 14037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2717 0.039 - 0.078: 646 0.078 - 0.117: 100 0.117 - 0.156: 26 0.156 - 0.195: 7 Chirality restraints: 3496 Sorted by residual: chirality pdb=" CA GLU D 708 " pdb=" N GLU D 708 " pdb=" C GLU D 708 " pdb=" CB GLU D 708 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.53e-01 chirality pdb=" CA GLU B 708 " pdb=" N GLU B 708 " pdb=" C GLU B 708 " pdb=" CB GLU B 708 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" CA GLU A 708 " pdb=" N GLU A 708 " pdb=" C GLU A 708 " pdb=" CB GLU A 708 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.22e-01 ... (remaining 3493 not shown) Planarity restraints: 3880 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 624 " -0.009 2.00e-02 2.50e+03 1.36e-02 3.67e+00 pdb=" CG TYR B 624 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR B 624 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 624 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR B 624 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 624 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 624 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 624 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 624 " -0.008 2.00e-02 2.50e+03 1.34e-02 3.57e+00 pdb=" CG TYR A 624 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR A 624 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 624 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 624 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 624 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 624 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 624 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 624 " -0.008 2.00e-02 2.50e+03 1.32e-02 3.50e+00 pdb=" CG TYR D 624 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR D 624 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR D 624 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR D 624 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 624 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 624 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 624 " 0.001 2.00e-02 2.50e+03 ... (remaining 3877 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 936 2.73 - 3.27: 23269 3.27 - 3.81: 38595 3.81 - 4.36: 47284 4.36 - 4.90: 80508 Nonbonded interactions: 190592 Sorted by model distance: nonbonded pdb=" NH1 ARG A 747 " pdb=" OE2 GLU B 749 " model vdw 2.185 3.120 nonbonded pdb=" NH1 ARG B 747 " pdb=" OE2 GLU C 749 " model vdw 2.201 3.120 nonbonded pdb=" OE2 GLU A 749 " pdb=" NH1 ARG D 747 " model vdw 2.267 3.120 nonbonded pdb=" OH TYR A 315 " pdb=" OAF Y01 A1001 " model vdw 2.274 3.040 nonbonded pdb=" OH TYR C 315 " pdb=" OAF Y01 C1001 " model vdw 2.275 3.040 ... (remaining 190587 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: 0.08 Found NCS groups: ncs_group { reference = (chain 'A' and resid 15 through 755) selection = (chain 'B' and resid 15 through 755) selection = (chain 'C' and resid 15 through 755) selection = (chain 'D' and resid 15 through 755) } 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: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 24.820 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 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:6.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 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 : 0.010 0.673 23068 Z= 0.517 Angle : 0.942 40.722 31232 Z= 0.380 Chirality : 0.037 0.195 3496 Planarity : 0.003 0.034 3880 Dihedral : 18.141 118.961 8788 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.33 % Allowed : 26.19 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.16), residues: 2688 helix: 1.71 (0.11), residues: 1932 sheet: None (None), residues: 0 loop : -0.81 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 747 TYR 0.033 0.001 TYR B 624 PHE 0.014 0.001 PHE B 340 TRP 0.020 0.001 TRP D 415 HIS 0.004 0.001 HIS D 630 Details of bonding type rmsd covalent geometry : bond 0.01040 (23048) covalent geometry : angle 0.94195 (31212) SS BOND : bond 0.00320 ( 4) SS BOND : angle 2.06683 ( 8) hydrogen bonds : bond 0.20427 ( 1460) hydrogen bonds : angle 6.10168 ( 4272) metal coordination : bond 0.00177 ( 16) metal coordination : angle 1.12062 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 291 time to evaluate : 0.899 Fit side-chains REVERT: A 272 ARG cc_start: 0.7355 (ptp90) cc_final: 0.6845 (ttp80) REVERT: A 469 ASP cc_start: 0.6728 (t0) cc_final: 0.6478 (m-30) REVERT: A 632 ASP cc_start: 0.8348 (OUTLIER) cc_final: 0.7891 (t70) REVERT: A 700 LEU cc_start: 0.7154 (tp) cc_final: 0.6745 (mm) REVERT: B 106 LYS cc_start: 0.8276 (mmmt) cc_final: 0.7812 (tptm) REVERT: C 106 LYS cc_start: 0.8401 (mmmt) cc_final: 0.8022 (tptp) REVERT: C 239 SER cc_start: 0.8493 (p) cc_final: 0.8288 (m) REVERT: C 632 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7845 (t70) REVERT: D 632 ASP cc_start: 0.8288 (OUTLIER) cc_final: 0.7888 (t70) outliers start: 8 outliers final: 4 residues processed: 295 average time/residue: 0.5901 time to fit residues: 201.0619 Evaluate side-chains 267 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 260 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 632 ASP Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 632 ASP Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 632 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 0.0570 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 62 ASN A 64 ASN A 163 GLN A 305 ASN A 393 ASN A 499 ASN A 532 ASN A 558 ASN A 590 HIS ** A 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 ASN B 38 ASN B 62 ASN B 64 ASN B 163 GLN B 305 ASN B 393 ASN B 499 ASN B 532 ASN B 558 ASN B 589 GLN B 590 HIS B 735 ASN C 38 ASN C 62 ASN C 64 ASN C 163 GLN C 305 ASN C 393 ASN C 499 ASN C 558 ASN C 590 HIS ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 735 ASN D 38 ASN D 62 ASN D 64 ASN D 163 GLN D 305 ASN D 393 ASN D 499 ASN D 532 ASN D 558 ASN D 590 HIS D 735 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.160040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.121415 restraints weight = 22550.280| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.83 r_work: 0.3175 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23068 Z= 0.145 Angle : 0.523 9.001 31232 Z= 0.270 Chirality : 0.037 0.148 3496 Planarity : 0.004 0.030 3880 Dihedral : 7.691 58.000 3426 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.29 % Allowed : 23.15 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.16), residues: 2688 helix: 2.19 (0.11), residues: 1956 sheet: None (None), residues: 0 loop : -0.93 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 747 TYR 0.014 0.001 TYR B 523 PHE 0.014 0.001 PHE A 340 TRP 0.017 0.001 TRP A 415 HIS 0.004 0.001 HIS D 118 Details of bonding type rmsd covalent geometry : bond 0.00334 (23048) covalent geometry : angle 0.52132 (31212) SS BOND : bond 0.00360 ( 4) SS BOND : angle 2.39096 ( 8) hydrogen bonds : bond 0.04421 ( 1460) hydrogen bonds : angle 4.20346 ( 4272) metal coordination : bond 0.00263 ( 16) metal coordination : angle 1.30649 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 295 time to evaluate : 0.791 Fit side-chains REVERT: A 112 VAL cc_start: 0.7187 (OUTLIER) cc_final: 0.6888 (m) REVERT: A 272 ARG cc_start: 0.7690 (ptp90) cc_final: 0.7160 (ttp80) REVERT: A 469 ASP cc_start: 0.7153 (t0) cc_final: 0.6663 (m-30) REVERT: A 470 MET cc_start: 0.8817 (OUTLIER) cc_final: 0.8460 (tmm) REVERT: A 700 LEU cc_start: 0.6898 (tp) cc_final: 0.6573 (mm) REVERT: A 728 GLU cc_start: 0.6682 (OUTLIER) cc_final: 0.6132 (mp0) REVERT: B 106 LYS cc_start: 0.8264 (mmmt) cc_final: 0.7856 (tptp) REVERT: B 112 VAL cc_start: 0.7193 (OUTLIER) cc_final: 0.6773 (m) REVERT: B 469 ASP cc_start: 0.6950 (t0) cc_final: 0.6520 (m-30) REVERT: B 520 LEU cc_start: 0.7212 (OUTLIER) cc_final: 0.6225 (mp) REVERT: B 700 LEU cc_start: 0.6966 (tp) cc_final: 0.6496 (mm) REVERT: B 728 GLU cc_start: 0.6620 (OUTLIER) cc_final: 0.6173 (mp0) REVERT: C 106 LYS cc_start: 0.8377 (mmmt) cc_final: 0.7983 (tptp) REVERT: C 112 VAL cc_start: 0.7136 (OUTLIER) cc_final: 0.6754 (m) REVERT: C 469 ASP cc_start: 0.6943 (t0) cc_final: 0.6499 (m-30) REVERT: C 520 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6301 (mp) REVERT: C 700 LEU cc_start: 0.6893 (tp) cc_final: 0.6425 (mm) REVERT: C 728 GLU cc_start: 0.6849 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: D 239 SER cc_start: 0.8664 (p) cc_final: 0.8455 (m) REVERT: D 469 ASP cc_start: 0.6929 (t0) cc_final: 0.6427 (m-30) REVERT: D 520 LEU cc_start: 0.7571 (OUTLIER) cc_final: 0.6598 (mp) REVERT: D 700 LEU cc_start: 0.6818 (tp) cc_final: 0.6387 (mm) REVERT: D 728 GLU cc_start: 0.6706 (OUTLIER) cc_final: 0.6180 (mp0) outliers start: 80 outliers final: 37 residues processed: 350 average time/residue: 0.5586 time to fit residues: 227.4333 Evaluate side-chains 314 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 266 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 520 LEU Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain C residue 728 GLU Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 520 LEU Chi-restraints excluded: chain D residue 708 GLU Chi-restraints excluded: chain D residue 728 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 61 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 179 optimal weight: 0.8980 chunk 80 optimal weight: 0.6980 chunk 81 optimal weight: 3.9990 chunk 217 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 111 optimal weight: 0.6980 chunk 169 optimal weight: 0.8980 chunk 231 optimal weight: 7.9990 chunk 37 optimal weight: 3.9990 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 38 ASN A 163 GLN A 297 GLN A 532 ASN A 589 GLN B 163 GLN B 532 ASN B 589 GLN C 38 ASN C 163 GLN C 305 ASN C 589 GLN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.159013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.120546 restraints weight = 22824.190| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 1.84 r_work: 0.3160 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23068 Z= 0.120 Angle : 0.457 5.962 31232 Z= 0.241 Chirality : 0.036 0.148 3496 Planarity : 0.003 0.034 3880 Dihedral : 6.508 55.967 3420 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.50 % Allowed : 23.85 % Favored : 72.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.16), residues: 2688 helix: 2.34 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.96 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 196 TYR 0.015 0.001 TYR A 523 PHE 0.015 0.001 PHE A 340 TRP 0.011 0.001 TRP D 415 HIS 0.004 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00269 (23048) covalent geometry : angle 0.45518 (31212) SS BOND : bond 0.00318 ( 4) SS BOND : angle 2.12539 ( 8) hydrogen bonds : bond 0.03929 ( 1460) hydrogen bonds : angle 3.96896 ( 4272) metal coordination : bond 0.00119 ( 16) metal coordination : angle 0.94167 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 284 time to evaluate : 0.893 Fit side-chains REVERT: A 272 ARG cc_start: 0.7811 (ptp90) cc_final: 0.7241 (ttp80) REVERT: A 441 MET cc_start: 0.7884 (OUTLIER) cc_final: 0.7562 (ttm) REVERT: A 469 ASP cc_start: 0.7121 (t0) cc_final: 0.6452 (m-30) REVERT: A 470 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8462 (tmm) REVERT: A 519 PHE cc_start: 0.8027 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: A 700 LEU cc_start: 0.6937 (tp) cc_final: 0.6532 (mm) REVERT: A 728 GLU cc_start: 0.6687 (OUTLIER) cc_final: 0.6288 (mp0) REVERT: B 106 LYS cc_start: 0.8356 (mmmt) cc_final: 0.7933 (tptp) REVERT: B 116 LEU cc_start: 0.8020 (pp) cc_final: 0.7702 (mm) REVERT: B 440 VAL cc_start: 0.8247 (t) cc_final: 0.8015 (t) REVERT: B 441 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7454 (ttm) REVERT: B 469 ASP cc_start: 0.7075 (t0) cc_final: 0.6568 (m-30) REVERT: B 519 PHE cc_start: 0.7905 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: B 700 LEU cc_start: 0.6960 (tp) cc_final: 0.6488 (mm) REVERT: B 721 MET cc_start: 0.8155 (mmm) cc_final: 0.7897 (mmt) REVERT: C 106 LYS cc_start: 0.8372 (mmmt) cc_final: 0.7981 (tptp) REVERT: C 116 LEU cc_start: 0.8079 (pp) cc_final: 0.7637 (mm) REVERT: C 469 ASP cc_start: 0.7113 (t0) cc_final: 0.6592 (m-30) REVERT: C 700 LEU cc_start: 0.6874 (tp) cc_final: 0.6410 (mm) REVERT: C 728 GLU cc_start: 0.6740 (OUTLIER) cc_final: 0.6419 (mp0) REVERT: D 106 LYS cc_start: 0.8423 (mmmt) cc_final: 0.8010 (tptp) REVERT: D 116 LEU cc_start: 0.8148 (pp) cc_final: 0.7713 (mm) REVERT: D 441 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7222 (ttm) REVERT: D 456 PHE cc_start: 0.8070 (t80) cc_final: 0.7830 (t80) REVERT: D 469 ASP cc_start: 0.7078 (t0) cc_final: 0.6522 (m-30) REVERT: D 519 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: D 700 LEU cc_start: 0.6929 (tp) cc_final: 0.6414 (mm) outliers start: 85 outliers final: 45 residues processed: 338 average time/residue: 0.5678 time to fit residues: 222.6436 Evaluate side-chains 312 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 258 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 519 PHE Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 433 TRP Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain C residue 728 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 519 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 71 optimal weight: 5.9990 chunk 149 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 179 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 231 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 265 optimal weight: 0.1980 chunk 100 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 240 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 163 GLN B 163 GLN B 589 GLN C 82 ASN C 163 GLN C 305 ASN C 589 GLN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN D 297 GLN D 589 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.157628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.119365 restraints weight = 22854.754| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.81 r_work: 0.3162 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23068 Z= 0.117 Angle : 0.451 5.963 31232 Z= 0.238 Chirality : 0.036 0.147 3496 Planarity : 0.003 0.032 3880 Dihedral : 6.543 59.617 3420 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.79 % Allowed : 24.55 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.16), residues: 2688 helix: 2.38 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : -0.96 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 196 TYR 0.016 0.001 TYR D 523 PHE 0.019 0.001 PHE A 519 TRP 0.014 0.001 TRP A 415 HIS 0.003 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00267 (23048) covalent geometry : angle 0.44981 (31212) SS BOND : bond 0.00280 ( 4) SS BOND : angle 2.12558 ( 8) hydrogen bonds : bond 0.03695 ( 1460) hydrogen bonds : angle 3.86907 ( 4272) metal coordination : bond 0.00108 ( 16) metal coordination : angle 0.80211 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 274 time to evaluate : 0.782 Fit side-chains REVERT: A 106 LYS cc_start: 0.8143 (mmmt) cc_final: 0.7703 (tptp) REVERT: A 116 LEU cc_start: 0.7926 (pp) cc_final: 0.7667 (mm) REVERT: A 163 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8318 (mt0) REVERT: A 272 ARG cc_start: 0.7623 (ptp90) cc_final: 0.6993 (ttp80) REVERT: A 441 MET cc_start: 0.7513 (OUTLIER) cc_final: 0.7186 (ttm) REVERT: A 469 ASP cc_start: 0.7138 (t0) cc_final: 0.6481 (m-30) REVERT: A 470 MET cc_start: 0.8645 (OUTLIER) cc_final: 0.8317 (tmm) REVERT: A 700 LEU cc_start: 0.6595 (tp) cc_final: 0.6247 (mm) REVERT: A 728 GLU cc_start: 0.6417 (OUTLIER) cc_final: 0.5978 (mp0) REVERT: B 106 LYS cc_start: 0.8127 (mmmt) cc_final: 0.7698 (tptp) REVERT: B 116 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7551 (mm) REVERT: B 440 VAL cc_start: 0.7873 (t) cc_final: 0.7628 (t) REVERT: B 469 ASP cc_start: 0.7095 (t0) cc_final: 0.6544 (m-30) REVERT: B 519 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.7313 (m-80) REVERT: B 700 LEU cc_start: 0.6609 (tp) cc_final: 0.6193 (mm) REVERT: B 721 MET cc_start: 0.8002 (mmm) cc_final: 0.7697 (mmt) REVERT: B 728 GLU cc_start: 0.6437 (OUTLIER) cc_final: 0.6108 (mp0) REVERT: C 106 LYS cc_start: 0.8091 (mmmt) cc_final: 0.7679 (tptp) REVERT: C 440 VAL cc_start: 0.8076 (t) cc_final: 0.7834 (t) REVERT: C 456 PHE cc_start: 0.7849 (t80) cc_final: 0.7574 (t80) REVERT: C 469 ASP cc_start: 0.7168 (t0) cc_final: 0.6621 (m-30) REVERT: C 512 MET cc_start: 0.7926 (ttp) cc_final: 0.7714 (ttp) REVERT: C 519 PHE cc_start: 0.7417 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: C 700 LEU cc_start: 0.6586 (tp) cc_final: 0.6155 (mm) REVERT: C 721 MET cc_start: 0.8026 (mmm) cc_final: 0.7746 (mmt) REVERT: C 728 GLU cc_start: 0.6405 (OUTLIER) cc_final: 0.6111 (mp0) REVERT: D 106 LYS cc_start: 0.8115 (mmmt) cc_final: 0.7688 (tptp) REVERT: D 441 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.6836 (ttm) REVERT: D 456 PHE cc_start: 0.7849 (t80) cc_final: 0.7616 (t80) REVERT: D 469 ASP cc_start: 0.7145 (t0) cc_final: 0.6525 (m-30) REVERT: D 512 MET cc_start: 0.8033 (ttp) cc_final: 0.7815 (ttp) REVERT: D 519 PHE cc_start: 0.7924 (OUTLIER) cc_final: 0.7355 (m-80) REVERT: D 700 LEU cc_start: 0.6558 (tp) cc_final: 0.6098 (mm) REVERT: D 728 GLU cc_start: 0.6427 (OUTLIER) cc_final: 0.6096 (mp0) outliers start: 92 outliers final: 50 residues processed: 335 average time/residue: 0.5319 time to fit residues: 207.2948 Evaluate side-chains 321 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 259 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 519 PHE Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain C residue 728 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 519 PHE Chi-restraints excluded: chain D residue 708 GLU Chi-restraints excluded: chain D residue 728 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 24 optimal weight: 4.9990 chunk 67 optimal weight: 3.9990 chunk 219 optimal weight: 5.9990 chunk 50 optimal weight: 0.0170 chunk 121 optimal weight: 0.7980 chunk 167 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 160 optimal weight: 4.9990 chunk 253 optimal weight: 3.9990 chunk 5 optimal weight: 5.9990 overall best weight: 1.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 ASN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 HIS A 589 GLN A 621 ASN B 82 ASN B 163 GLN B 297 GLN B 305 ASN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 435 ASN B 589 GLN C 38 ASN C 163 GLN C 297 GLN C 305 ASN C 435 ASN C 589 GLN C 621 ASN D 82 ASN D 163 GLN D 305 ASN D 308 GLN ** D 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 435 ASN D 472 HIS D 589 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.153495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.114774 restraints weight = 22687.847| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 1.82 r_work: 0.3070 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 23068 Z= 0.213 Angle : 0.547 9.730 31232 Z= 0.283 Chirality : 0.040 0.154 3496 Planarity : 0.004 0.033 3880 Dihedral : 7.030 59.066 3420 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 5.56 % Allowed : 22.65 % Favored : 71.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.16), residues: 2688 helix: 1.97 (0.11), residues: 2000 sheet: None (None), residues: 0 loop : -1.07 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 747 TYR 0.020 0.002 TYR D 523 PHE 0.016 0.002 PHE A 340 TRP 0.019 0.002 TRP A 415 HIS 0.004 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00520 (23048) covalent geometry : angle 0.53492 (31212) SS BOND : bond 0.00389 ( 4) SS BOND : angle 3.33044 ( 8) hydrogen bonds : bond 0.04237 ( 1460) hydrogen bonds : angle 4.04821 ( 4272) metal coordination : bond 0.02405 ( 16) metal coordination : angle 5.25125 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 285 time to evaluate : 0.832 Fit side-chains REVERT: A 163 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8035 (mt0) REVERT: A 245 SER cc_start: 0.9218 (OUTLIER) cc_final: 0.8794 (t) REVERT: A 469 ASP cc_start: 0.7229 (t0) cc_final: 0.6587 (m-30) REVERT: A 700 LEU cc_start: 0.6823 (tp) cc_final: 0.6472 (mm) REVERT: A 713 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8728 (mp) REVERT: A 728 GLU cc_start: 0.6792 (OUTLIER) cc_final: 0.6366 (mp0) REVERT: B 245 SER cc_start: 0.9222 (OUTLIER) cc_final: 0.8797 (t) REVERT: B 330 MET cc_start: 0.6356 (OUTLIER) cc_final: 0.5936 (ttt) REVERT: B 456 PHE cc_start: 0.8018 (t80) cc_final: 0.7762 (t80) REVERT: B 469 ASP cc_start: 0.7227 (t0) cc_final: 0.6701 (m-30) REVERT: B 700 LEU cc_start: 0.6895 (tp) cc_final: 0.6453 (mm) REVERT: B 713 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8737 (mp) REVERT: B 721 MET cc_start: 0.8053 (mmm) cc_final: 0.7785 (mmt) REVERT: B 728 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6330 (mp0) REVERT: C 106 LYS cc_start: 0.8441 (mmmt) cc_final: 0.8023 (tptp) REVERT: C 245 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.8824 (t) REVERT: C 456 PHE cc_start: 0.7947 (t80) cc_final: 0.7691 (t80) REVERT: C 469 ASP cc_start: 0.7246 (t0) cc_final: 0.6781 (m-30) REVERT: C 700 LEU cc_start: 0.6889 (tp) cc_final: 0.6460 (mm) REVERT: C 713 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8743 (mp) REVERT: C 728 GLU cc_start: 0.6822 (OUTLIER) cc_final: 0.6472 (mp0) REVERT: C 741 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7004 (tp40) REVERT: D 106 LYS cc_start: 0.8375 (mmmt) cc_final: 0.7936 (tptp) REVERT: D 245 SER cc_start: 0.9201 (OUTLIER) cc_final: 0.8794 (t) REVERT: D 330 MET cc_start: 0.6333 (OUTLIER) cc_final: 0.5974 (ttt) REVERT: D 469 ASP cc_start: 0.7261 (t0) cc_final: 0.6720 (m-30) REVERT: D 519 PHE cc_start: 0.8084 (t80) cc_final: 0.7747 (m-80) REVERT: D 700 LEU cc_start: 0.6831 (tp) cc_final: 0.6363 (mm) REVERT: D 713 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8746 (mp) REVERT: D 728 GLU cc_start: 0.6688 (OUTLIER) cc_final: 0.6278 (mp0) outliers start: 135 outliers final: 66 residues processed: 377 average time/residue: 0.5299 time to fit residues: 233.0751 Evaluate side-chains 349 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 267 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 433 TRP Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 160 LEU Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 433 TRP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 433 TRP Chi-restraints excluded: chain C residue 435 ASN Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 728 GLU Chi-restraints excluded: chain C residue 741 GLN Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 160 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 223 LEU Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 330 MET Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 433 TRP Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 708 GLU Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 728 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 244 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 202 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 166 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 43 optimal weight: 0.9980 chunk 237 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 58 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 163 GLN A 305 ASN A 435 ASN A 589 GLN B 82 ASN B 163 GLN B 305 ASN B 589 GLN C 38 ASN C 163 GLN C 305 ASN C 589 GLN D 163 GLN D 305 ASN D 589 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.155977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.117351 restraints weight = 22961.087| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.84 r_work: 0.3117 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23068 Z= 0.127 Angle : 0.492 11.662 31232 Z= 0.252 Chirality : 0.037 0.152 3496 Planarity : 0.004 0.034 3880 Dihedral : 6.903 59.831 3420 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.32 % Allowed : 24.14 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.16), residues: 2688 helix: 2.23 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : -1.06 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 196 TYR 0.017 0.001 TYR D 523 PHE 0.018 0.001 PHE A 340 TRP 0.014 0.001 TRP B 415 HIS 0.006 0.001 HIS B 172 Details of bonding type rmsd covalent geometry : bond 0.00292 (23048) covalent geometry : angle 0.46515 (31212) SS BOND : bond 0.00271 ( 4) SS BOND : angle 2.36642 ( 8) hydrogen bonds : bond 0.03730 ( 1460) hydrogen bonds : angle 3.92087 ( 4272) metal coordination : bond 0.02199 ( 16) metal coordination : angle 8.02917 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 288 time to evaluate : 0.872 Fit side-chains REVERT: A 84 GLU cc_start: 0.7783 (mp0) cc_final: 0.7355 (mp0) REVERT: A 106 LYS cc_start: 0.8397 (mmmt) cc_final: 0.7963 (tptp) REVERT: A 163 GLN cc_start: 0.8798 (OUTLIER) cc_final: 0.8405 (mt0) REVERT: A 245 SER cc_start: 0.9190 (OUTLIER) cc_final: 0.8805 (t) REVERT: A 469 ASP cc_start: 0.7370 (t0) cc_final: 0.6791 (m-30) REVERT: A 470 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8481 (tmm) REVERT: A 700 LEU cc_start: 0.6827 (tp) cc_final: 0.6493 (mm) REVERT: A 713 LEU cc_start: 0.9032 (OUTLIER) cc_final: 0.8733 (mp) REVERT: B 106 LYS cc_start: 0.8401 (mmmt) cc_final: 0.7960 (tptp) REVERT: B 245 SER cc_start: 0.9212 (OUTLIER) cc_final: 0.8821 (t) REVERT: B 330 MET cc_start: 0.6347 (OUTLIER) cc_final: 0.5913 (ttt) REVERT: B 440 VAL cc_start: 0.8257 (t) cc_final: 0.8017 (t) REVERT: B 456 PHE cc_start: 0.8068 (t80) cc_final: 0.7791 (t80) REVERT: B 469 ASP cc_start: 0.7266 (t0) cc_final: 0.6761 (m-30) REVERT: B 519 PHE cc_start: 0.8047 (OUTLIER) cc_final: 0.7810 (m-80) REVERT: B 700 LEU cc_start: 0.6901 (tp) cc_final: 0.6540 (mm) REVERT: B 713 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8758 (mp) REVERT: B 721 MET cc_start: 0.8021 (mmm) cc_final: 0.7799 (mmt) REVERT: B 728 GLU cc_start: 0.6684 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: C 84 GLU cc_start: 0.7794 (mp0) cc_final: 0.7390 (mp0) REVERT: C 106 LYS cc_start: 0.8424 (mmmt) cc_final: 0.8016 (tptp) REVERT: C 440 VAL cc_start: 0.8380 (t) cc_final: 0.8136 (t) REVERT: C 441 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7640 (ttm) REVERT: C 469 ASP cc_start: 0.7230 (t0) cc_final: 0.6775 (m-30) REVERT: C 700 LEU cc_start: 0.6904 (tp) cc_final: 0.6514 (mm) REVERT: C 713 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8748 (mp) REVERT: C 728 GLU cc_start: 0.6737 (OUTLIER) cc_final: 0.6456 (mp0) REVERT: D 106 LYS cc_start: 0.8415 (mmmt) cc_final: 0.7982 (tptp) REVERT: D 440 VAL cc_start: 0.8408 (t) cc_final: 0.8188 (t) REVERT: D 469 ASP cc_start: 0.7334 (t0) cc_final: 0.6841 (m-30) REVERT: D 512 MET cc_start: 0.8280 (ttp) cc_final: 0.8079 (ttp) REVERT: D 519 PHE cc_start: 0.7934 (t80) cc_final: 0.7644 (m-80) REVERT: D 700 LEU cc_start: 0.6836 (tp) cc_final: 0.6380 (mm) REVERT: D 713 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8747 (mp) REVERT: D 728 GLU cc_start: 0.6700 (OUTLIER) cc_final: 0.6391 (mp0) outliers start: 105 outliers final: 69 residues processed: 358 average time/residue: 0.5677 time to fit residues: 235.3763 Evaluate side-chains 360 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 277 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 441 MET Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 619 MET Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 728 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 294 LYS Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 441 MET Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 708 GLU Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 728 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 5 optimal weight: 4.9990 chunk 241 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 227 optimal weight: 1.9990 chunk 181 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 240 optimal weight: 1.9990 chunk 217 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 179 optimal weight: 0.5980 chunk 222 optimal weight: 0.7980 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 163 GLN A 435 ASN A 589 GLN B 82 ASN B 163 GLN B 589 GLN C 163 GLN C 589 GLN D 163 GLN D 589 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.156778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.118018 restraints weight = 22974.778| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.86 r_work: 0.3118 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23068 Z= 0.121 Angle : 0.481 9.775 31232 Z= 0.247 Chirality : 0.036 0.151 3496 Planarity : 0.004 0.035 3880 Dihedral : 6.842 58.891 3420 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 4.41 % Allowed : 24.38 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.17 (0.16), residues: 2688 helix: 2.28 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : -1.04 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 196 TYR 0.016 0.001 TYR D 523 PHE 0.017 0.001 PHE A 340 TRP 0.015 0.001 TRP A 415 HIS 0.004 0.001 HIS B 172 Details of bonding type rmsd covalent geometry : bond 0.00276 (23048) covalent geometry : angle 0.46136 (31212) SS BOND : bond 0.00261 ( 4) SS BOND : angle 2.25216 ( 8) hydrogen bonds : bond 0.03633 ( 1460) hydrogen bonds : angle 3.86852 ( 4272) metal coordination : bond 0.01661 ( 16) metal coordination : angle 6.63912 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 291 time to evaluate : 0.856 Fit side-chains REVERT: A 84 GLU cc_start: 0.7780 (mp0) cc_final: 0.7344 (mp0) REVERT: A 106 LYS cc_start: 0.8390 (mmmt) cc_final: 0.7971 (tptp) REVERT: A 163 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8096 (mt0) REVERT: A 440 VAL cc_start: 0.8344 (t) cc_final: 0.7986 (t) REVERT: A 469 ASP cc_start: 0.7418 (t0) cc_final: 0.6818 (m-30) REVERT: A 470 MET cc_start: 0.8761 (OUTLIER) cc_final: 0.8438 (tmm) REVERT: A 700 LEU cc_start: 0.6767 (tp) cc_final: 0.6418 (mm) REVERT: A 713 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8674 (mp) REVERT: B 98 ASP cc_start: 0.8239 (p0) cc_final: 0.8037 (p0) REVERT: B 106 LYS cc_start: 0.8345 (mmmt) cc_final: 0.7908 (tptp) REVERT: B 330 MET cc_start: 0.6202 (OUTLIER) cc_final: 0.5793 (ttt) REVERT: B 440 VAL cc_start: 0.8224 (t) cc_final: 0.7982 (t) REVERT: B 456 PHE cc_start: 0.8010 (t80) cc_final: 0.7716 (t80) REVERT: B 469 ASP cc_start: 0.7310 (t0) cc_final: 0.6790 (m-30) REVERT: B 519 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.7609 (m-80) REVERT: B 700 LEU cc_start: 0.6845 (tp) cc_final: 0.6480 (mm) REVERT: B 713 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8715 (mp) REVERT: B 721 MET cc_start: 0.8000 (mmm) cc_final: 0.7769 (mmt) REVERT: B 728 GLU cc_start: 0.6553 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: C 84 GLU cc_start: 0.7854 (mp0) cc_final: 0.7443 (mp0) REVERT: C 106 LYS cc_start: 0.8375 (mmmt) cc_final: 0.7963 (tptp) REVERT: C 245 SER cc_start: 0.9160 (OUTLIER) cc_final: 0.8806 (t) REVERT: C 440 VAL cc_start: 0.8343 (t) cc_final: 0.7974 (t) REVERT: C 469 ASP cc_start: 0.7392 (t0) cc_final: 0.6942 (m-30) REVERT: C 700 LEU cc_start: 0.6846 (tp) cc_final: 0.6463 (mm) REVERT: C 713 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8674 (mp) REVERT: C 728 GLU cc_start: 0.6457 (OUTLIER) cc_final: 0.6135 (mp0) REVERT: D 98 ASP cc_start: 0.8200 (p0) cc_final: 0.7944 (p0) REVERT: D 106 LYS cc_start: 0.8407 (mmmt) cc_final: 0.7985 (tptp) REVERT: D 245 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8785 (t) REVERT: D 469 ASP cc_start: 0.7410 (t0) cc_final: 0.6853 (m-30) REVERT: D 519 PHE cc_start: 0.7949 (t80) cc_final: 0.7523 (m-80) REVERT: D 700 LEU cc_start: 0.6771 (tp) cc_final: 0.6316 (mm) REVERT: D 713 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8660 (mp) REVERT: D 728 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.6070 (mp0) outliers start: 107 outliers final: 75 residues processed: 359 average time/residue: 0.5513 time to fit residues: 230.0027 Evaluate side-chains 372 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 284 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 728 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 294 LYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 708 GLU Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 728 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 180 optimal weight: 0.9990 chunk 267 optimal weight: 0.8980 chunk 235 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 215 optimal weight: 0.4980 chunk 204 optimal weight: 4.9990 chunk 248 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 435 ASN A 589 GLN B 82 ASN B 163 GLN B 472 HIS B 589 GLN C 163 GLN C 472 HIS C 589 GLN D 163 GLN D 589 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.156581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.117893 restraints weight = 22842.568| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.85 r_work: 0.3130 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23068 Z= 0.128 Angle : 0.482 8.619 31232 Z= 0.249 Chirality : 0.037 0.150 3496 Planarity : 0.004 0.034 3880 Dihedral : 6.878 58.806 3420 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.53 % Allowed : 24.05 % Favored : 71.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.16), residues: 2688 helix: 2.25 (0.11), residues: 1976 sheet: None (None), residues: 0 loop : -1.00 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 196 TYR 0.017 0.001 TYR D 523 PHE 0.017 0.001 PHE A 340 TRP 0.017 0.001 TRP A 415 HIS 0.004 0.001 HIS B 172 Details of bonding type rmsd covalent geometry : bond 0.00298 (23048) covalent geometry : angle 0.46663 (31212) SS BOND : bond 0.00270 ( 4) SS BOND : angle 2.33572 ( 8) hydrogen bonds : bond 0.03654 ( 1460) hydrogen bonds : angle 3.84186 ( 4272) metal coordination : bond 0.01432 ( 16) metal coordination : angle 5.92069 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 287 time to evaluate : 0.829 Fit side-chains REVERT: A 84 GLU cc_start: 0.7831 (mp0) cc_final: 0.7399 (mp0) REVERT: A 106 LYS cc_start: 0.8381 (mmmt) cc_final: 0.7965 (tptp) REVERT: A 163 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.7996 (mt0) REVERT: A 173 GLU cc_start: 0.7707 (mt-10) cc_final: 0.7307 (pm20) REVERT: A 245 SER cc_start: 0.9157 (OUTLIER) cc_final: 0.8814 (t) REVERT: A 439 PHE cc_start: 0.8324 (t80) cc_final: 0.8046 (t80) REVERT: A 469 ASP cc_start: 0.7407 (t0) cc_final: 0.6780 (m-30) REVERT: A 470 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8435 (tmm) REVERT: A 700 LEU cc_start: 0.6811 (tp) cc_final: 0.6492 (mm) REVERT: A 713 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8717 (mp) REVERT: A 721 MET cc_start: 0.8061 (mmm) cc_final: 0.7857 (mmt) REVERT: B 106 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7952 (tptp) REVERT: B 245 SER cc_start: 0.9184 (OUTLIER) cc_final: 0.8832 (t) REVERT: B 330 MET cc_start: 0.6265 (OUTLIER) cc_final: 0.5837 (ttt) REVERT: B 440 VAL cc_start: 0.8273 (t) cc_final: 0.8035 (t) REVERT: B 456 PHE cc_start: 0.8117 (t80) cc_final: 0.7853 (t80) REVERT: B 469 ASP cc_start: 0.7335 (t0) cc_final: 0.6916 (m-30) REVERT: B 519 PHE cc_start: 0.7869 (OUTLIER) cc_final: 0.7667 (m-80) REVERT: B 700 LEU cc_start: 0.6897 (tp) cc_final: 0.6549 (mm) REVERT: B 713 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8757 (mp) REVERT: B 721 MET cc_start: 0.8025 (mmm) cc_final: 0.7803 (mmt) REVERT: B 728 GLU cc_start: 0.6642 (OUTLIER) cc_final: 0.6249 (mp0) REVERT: C 84 GLU cc_start: 0.7924 (mp0) cc_final: 0.7494 (mp0) REVERT: C 106 LYS cc_start: 0.8416 (mmmt) cc_final: 0.8012 (tptp) REVERT: C 245 SER cc_start: 0.9176 (OUTLIER) cc_final: 0.8823 (t) REVERT: C 469 ASP cc_start: 0.7407 (t0) cc_final: 0.7021 (m-30) REVERT: C 700 LEU cc_start: 0.6887 (tp) cc_final: 0.6530 (mm) REVERT: C 713 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8718 (mp) REVERT: C 728 GLU cc_start: 0.6514 (OUTLIER) cc_final: 0.6189 (mp0) REVERT: D 98 ASP cc_start: 0.8212 (p0) cc_final: 0.7992 (p0) REVERT: D 106 LYS cc_start: 0.8391 (mmmt) cc_final: 0.7964 (tptp) REVERT: D 245 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8818 (t) REVERT: D 469 ASP cc_start: 0.7438 (t0) cc_final: 0.6971 (m-30) REVERT: D 519 PHE cc_start: 0.8005 (t80) cc_final: 0.7622 (m-80) REVERT: D 700 LEU cc_start: 0.6815 (tp) cc_final: 0.6357 (mm) REVERT: D 713 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8725 (mp) REVERT: D 728 GLU cc_start: 0.6486 (OUTLIER) cc_final: 0.6121 (mp0) outliers start: 110 outliers final: 76 residues processed: 356 average time/residue: 0.5538 time to fit residues: 229.0354 Evaluate side-chains 371 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 280 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 409 TRP Chi-restraints excluded: chain A residue 441 MET Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 61 ILE Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 519 PHE Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 406 ILE Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 728 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 294 LYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 708 GLU Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 728 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 98 optimal weight: 5.9990 chunk 28 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 182 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 248 optimal weight: 0.7980 chunk 226 optimal weight: 0.5980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 589 GLN B 82 ASN B 163 GLN B 589 GLN C 163 GLN C 589 GLN D 163 GLN D 589 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.155489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.116870 restraints weight = 22913.617| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.84 r_work: 0.3100 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2956 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 23068 Z= 0.157 Angle : 0.509 7.764 31232 Z= 0.262 Chirality : 0.038 0.152 3496 Planarity : 0.004 0.031 3880 Dihedral : 7.052 59.334 3420 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 4.57 % Allowed : 24.26 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.16), residues: 2688 helix: 2.16 (0.11), residues: 1976 sheet: None (None), residues: 0 loop : -1.02 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 196 TYR 0.018 0.001 TYR D 523 PHE 0.017 0.001 PHE D 340 TRP 0.021 0.001 TRP B 415 HIS 0.004 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00376 (23048) covalent geometry : angle 0.49486 (31212) SS BOND : bond 0.00322 ( 4) SS BOND : angle 2.70292 ( 8) hydrogen bonds : bond 0.03823 ( 1460) hydrogen bonds : angle 3.88934 ( 4272) metal coordination : bond 0.01351 ( 16) metal coordination : angle 5.58315 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 391 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 280 time to evaluate : 0.719 Fit side-chains REVERT: A 84 GLU cc_start: 0.7809 (mp0) cc_final: 0.7359 (mp0) REVERT: A 163 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7993 (mt0) REVERT: A 173 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7283 (pm20) REVERT: A 245 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8791 (t) REVERT: A 469 ASP cc_start: 0.7428 (t0) cc_final: 0.6833 (m-30) REVERT: A 470 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.8394 (tmm) REVERT: A 700 LEU cc_start: 0.6791 (tp) cc_final: 0.6472 (mm) REVERT: A 713 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8731 (mp) REVERT: A 721 MET cc_start: 0.8080 (mmm) cc_final: 0.7867 (mmt) REVERT: A 728 GLU cc_start: 0.6634 (OUTLIER) cc_final: 0.6187 (mp0) REVERT: B 106 LYS cc_start: 0.8359 (mmmt) cc_final: 0.7931 (tptp) REVERT: B 245 SER cc_start: 0.9172 (OUTLIER) cc_final: 0.8804 (t) REVERT: B 330 MET cc_start: 0.6245 (OUTLIER) cc_final: 0.5823 (ttt) REVERT: B 440 VAL cc_start: 0.8277 (t) cc_final: 0.8042 (t) REVERT: B 469 ASP cc_start: 0.7418 (t0) cc_final: 0.6977 (m-30) REVERT: B 700 LEU cc_start: 0.6881 (tp) cc_final: 0.6539 (mm) REVERT: B 713 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8723 (mp) REVERT: B 721 MET cc_start: 0.8051 (mmm) cc_final: 0.7818 (mmt) REVERT: B 728 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6142 (mp0) REVERT: C 84 GLU cc_start: 0.7897 (mp0) cc_final: 0.7459 (mp0) REVERT: C 106 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8034 (tptp) REVERT: C 163 GLN cc_start: 0.8789 (OUTLIER) cc_final: 0.8402 (mt0) REVERT: C 245 SER cc_start: 0.9165 (OUTLIER) cc_final: 0.8803 (t) REVERT: C 469 ASP cc_start: 0.7410 (t0) cc_final: 0.7030 (m-30) REVERT: C 700 LEU cc_start: 0.6847 (tp) cc_final: 0.6521 (mm) REVERT: C 713 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8713 (mp) REVERT: C 728 GLU cc_start: 0.6549 (OUTLIER) cc_final: 0.6195 (mp0) REVERT: D 98 ASP cc_start: 0.8189 (p0) cc_final: 0.7974 (p0) REVERT: D 106 LYS cc_start: 0.8427 (mmmt) cc_final: 0.8008 (tptp) REVERT: D 245 SER cc_start: 0.9158 (OUTLIER) cc_final: 0.8790 (t) REVERT: D 469 ASP cc_start: 0.7448 (t0) cc_final: 0.6991 (m-30) REVERT: D 700 LEU cc_start: 0.6808 (tp) cc_final: 0.6360 (mm) REVERT: D 713 LEU cc_start: 0.9034 (OUTLIER) cc_final: 0.8714 (mp) REVERT: D 728 GLU cc_start: 0.6603 (OUTLIER) cc_final: 0.6149 (mp0) outliers start: 111 outliers final: 75 residues processed: 353 average time/residue: 0.5711 time to fit residues: 233.3696 Evaluate side-chains 367 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 276 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 330 MET Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 223 LEU Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 728 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 235 ASN Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 294 LYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 708 GLU Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 728 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 99 optimal weight: 0.0570 chunk 246 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 251 optimal weight: 0.9990 chunk 196 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 238 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 119 optimal weight: 0.7980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 589 GLN B 82 ASN B 163 GLN B 589 GLN C 163 GLN C 589 GLN D 163 GLN D 589 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.156269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.118243 restraints weight = 23013.051| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 1.81 r_work: 0.3146 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23068 Z= 0.116 Angle : 0.487 13.122 31232 Z= 0.251 Chirality : 0.037 0.148 3496 Planarity : 0.003 0.031 3880 Dihedral : 6.950 58.687 3420 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.95 % Allowed : 24.79 % Favored : 71.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.16), residues: 2688 helix: 2.27 (0.11), residues: 1976 sheet: None (None), residues: 0 loop : -0.97 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 196 TYR 0.016 0.001 TYR D 523 PHE 0.017 0.001 PHE A 340 TRP 0.019 0.001 TRP A 409 HIS 0.004 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00261 (23048) covalent geometry : angle 0.47479 (31212) SS BOND : bond 0.00243 ( 4) SS BOND : angle 2.16426 ( 8) hydrogen bonds : bond 0.03589 ( 1460) hydrogen bonds : angle 3.83459 ( 4272) metal coordination : bond 0.01309 ( 16) metal coordination : angle 5.35755 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5376 Ramachandran restraints generated. 2688 Oldfield, 0 Emsley, 2688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 283 time to evaluate : 0.892 Fit side-chains REVERT: A 84 GLU cc_start: 0.7819 (mp0) cc_final: 0.7388 (mp0) REVERT: A 106 LYS cc_start: 0.8321 (mmmt) cc_final: 0.7902 (tptp) REVERT: A 173 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7300 (pm20) REVERT: A 245 SER cc_start: 0.9146 (OUTLIER) cc_final: 0.8806 (t) REVERT: A 469 ASP cc_start: 0.7395 (t0) cc_final: 0.6851 (m-30) REVERT: A 470 MET cc_start: 0.8713 (OUTLIER) cc_final: 0.8398 (tmm) REVERT: A 512 MET cc_start: 0.8279 (ttm) cc_final: 0.8049 (ttp) REVERT: A 700 LEU cc_start: 0.6798 (tp) cc_final: 0.6484 (mm) REVERT: A 713 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8717 (mp) REVERT: B 106 LYS cc_start: 0.8420 (mmmt) cc_final: 0.8014 (tptp) REVERT: B 163 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.8421 (mt0) REVERT: B 245 SER cc_start: 0.9167 (OUTLIER) cc_final: 0.8822 (t) REVERT: B 440 VAL cc_start: 0.8283 (t) cc_final: 0.8060 (t) REVERT: B 469 ASP cc_start: 0.7396 (t0) cc_final: 0.6995 (m-30) REVERT: B 619 MET cc_start: 0.7152 (ttp) cc_final: 0.6339 (tpp) REVERT: B 700 LEU cc_start: 0.6886 (tp) cc_final: 0.6542 (mm) REVERT: B 713 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8738 (mp) REVERT: B 721 MET cc_start: 0.8000 (mmm) cc_final: 0.7785 (mmt) REVERT: B 728 GLU cc_start: 0.6547 (OUTLIER) cc_final: 0.6167 (mp0) REVERT: C 84 GLU cc_start: 0.7811 (mp0) cc_final: 0.7385 (mp0) REVERT: C 98 ASP cc_start: 0.8200 (p0) cc_final: 0.7968 (p0) REVERT: C 106 LYS cc_start: 0.8397 (mmmt) cc_final: 0.7991 (tptp) REVERT: C 163 GLN cc_start: 0.8613 (OUTLIER) cc_final: 0.8173 (mt0) REVERT: C 245 SER cc_start: 0.9151 (OUTLIER) cc_final: 0.8803 (t) REVERT: C 440 VAL cc_start: 0.8350 (t) cc_final: 0.7978 (t) REVERT: C 469 ASP cc_start: 0.7365 (t0) cc_final: 0.6996 (m-30) REVERT: C 512 MET cc_start: 0.8211 (ttp) cc_final: 0.8010 (ttp) REVERT: C 700 LEU cc_start: 0.6852 (tp) cc_final: 0.6530 (mm) REVERT: C 713 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8714 (mp) REVERT: C 728 GLU cc_start: 0.6632 (OUTLIER) cc_final: 0.6328 (mp0) REVERT: D 84 GLU cc_start: 0.7762 (mp0) cc_final: 0.7333 (mp0) REVERT: D 98 ASP cc_start: 0.8225 (p0) cc_final: 0.8015 (p0) REVERT: D 106 LYS cc_start: 0.8326 (mmmt) cc_final: 0.7906 (tptp) REVERT: D 245 SER cc_start: 0.9157 (OUTLIER) cc_final: 0.8812 (t) REVERT: D 440 VAL cc_start: 0.8403 (t) cc_final: 0.8062 (t) REVERT: D 469 ASP cc_start: 0.7447 (t0) cc_final: 0.7022 (m-30) REVERT: D 519 PHE cc_start: 0.7948 (t80) cc_final: 0.7664 (m-80) REVERT: D 700 LEU cc_start: 0.6790 (tp) cc_final: 0.6363 (mm) REVERT: D 713 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8683 (mp) REVERT: D 728 GLU cc_start: 0.6551 (OUTLIER) cc_final: 0.6181 (mp0) outliers start: 96 outliers final: 69 residues processed: 347 average time/residue: 0.5525 time to fit residues: 222.6438 Evaluate side-chains 360 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 277 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 189 SER Chi-restraints excluded: chain A residue 235 ASN Chi-restraints excluded: chain A residue 239 SER Chi-restraints excluded: chain A residue 245 SER Chi-restraints excluded: chain A residue 294 LYS Chi-restraints excluded: chain A residue 318 PHE Chi-restraints excluded: chain A residue 342 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 372 SER Chi-restraints excluded: chain A residue 405 MET Chi-restraints excluded: chain A residue 406 ILE Chi-restraints excluded: chain A residue 470 MET Chi-restraints excluded: chain A residue 500 SER Chi-restraints excluded: chain A residue 562 SER Chi-restraints excluded: chain A residue 708 GLU Chi-restraints excluded: chain A residue 713 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 144 THR Chi-restraints excluded: chain B residue 163 GLN Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 235 ASN Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain B residue 245 SER Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 318 PHE Chi-restraints excluded: chain B residue 342 VAL Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 405 MET Chi-restraints excluded: chain B residue 406 ILE Chi-restraints excluded: chain B residue 441 MET Chi-restraints excluded: chain B residue 500 SER Chi-restraints excluded: chain B residue 562 SER Chi-restraints excluded: chain B residue 708 GLU Chi-restraints excluded: chain B residue 713 LEU Chi-restraints excluded: chain B residue 728 GLU Chi-restraints excluded: chain C residue 61 ILE Chi-restraints excluded: chain C residue 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 235 ASN Chi-restraints excluded: chain C residue 239 SER Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 294 LYS Chi-restraints excluded: chain C residue 318 PHE Chi-restraints excluded: chain C residue 342 VAL Chi-restraints excluded: chain C residue 345 VAL Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 405 MET Chi-restraints excluded: chain C residue 500 SER Chi-restraints excluded: chain C residue 562 SER Chi-restraints excluded: chain C residue 708 GLU Chi-restraints excluded: chain C residue 713 LEU Chi-restraints excluded: chain C residue 728 GLU Chi-restraints excluded: chain D residue 61 ILE Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 116 LEU Chi-restraints excluded: chain D residue 144 THR Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain D residue 239 SER Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 294 LYS Chi-restraints excluded: chain D residue 318 PHE Chi-restraints excluded: chain D residue 342 VAL Chi-restraints excluded: chain D residue 345 VAL Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 562 SER Chi-restraints excluded: chain D residue 708 GLU Chi-restraints excluded: chain D residue 713 LEU Chi-restraints excluded: chain D residue 728 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 250 optimal weight: 1.9990 chunk 50 optimal weight: 0.0970 chunk 58 optimal weight: 4.9990 chunk 163 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 170 optimal weight: 4.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 589 GLN B 82 ASN B 163 GLN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 GLN C 163 GLN C 589 GLN D 163 GLN D 589 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.153091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.114729 restraints weight = 22925.518| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 1.80 r_work: 0.3080 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2936 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23068 Z= 0.203 Angle : 0.560 16.680 31232 Z= 0.286 Chirality : 0.040 0.162 3496 Planarity : 0.004 0.032 3880 Dihedral : 7.315 59.832 3420 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 4.12 % Allowed : 24.55 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.16), residues: 2688 helix: 1.94 (0.11), residues: 2004 sheet: None (None), residues: 0 loop : -1.03 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 196 TYR 0.020 0.002 TYR A 523 PHE 0.017 0.002 PHE A 340 TRP 0.027 0.002 TRP A 409 HIS 0.004 0.001 HIS B 118 Details of bonding type rmsd covalent geometry : bond 0.00495 (23048) covalent geometry : angle 0.54791 (31212) SS BOND : bond 0.00378 ( 4) SS BOND : angle 3.17842 ( 8) hydrogen bonds : bond 0.04057 ( 1460) hydrogen bonds : angle 3.98196 ( 4272) metal coordination : bond 0.01355 ( 16) metal coordination : angle 5.44868 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7448.42 seconds wall clock time: 127 minutes 37.14 seconds (7657.14 seconds total)