Starting phenix.real_space_refine on Sat Jul 4 17:41:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wpn_37720/07_2026/8wpn_37720_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wpn_37720/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/8wpn_37720/07_2026/8wpn_37720_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wpn_37720/07_2026/8wpn_37720_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8wpn_37720/07_2026/8wpn_37720.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wpn_37720/07_2026/8wpn_37720.map" } 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-dev-6108/lib/python3.11/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, 80 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 Chain: "B" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 Chain: "C" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 1} Chain breaks: 1 Chain: "D" Number of atoms: 81 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' ZN': 1, 'LPP': 1, 'Y01': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain breaks: 1 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: 5.38, per 1000 atoms: 0.24 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: 2.03 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: 0.83 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: 4.03 Time building geometry restraints manager: 2.71 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: 0.07 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: 2.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 24.540 Find NCS groups from input model: 0.700 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:8.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 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/Z covalent geometry : bond 0.01040 / 0.52 (23048) covalent geometry : angle 0.94195 / 0.38 (31212) SS BOND : bond 0.00320 / 0.16 ( 4) SS BOND : angle 2.06683 / 1.26 ( 8) hydrogen bonds : bond 0.20427 / 13.81 ( 1460) hydrogen bonds : angle 6.10168 / 4.33 ( 4272) metal coordination : bond 0.00177 / 0.10 ( 16) metal coordination : angle 1.12062 / 0.76 ( 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 : 0.819 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: 0.5740 time to fit residues: 196.8265 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 : 0.878 ------------------------------------------------------------------------------- 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... A 38 ASN A 62 ASN A 64 ASN A 163 GLN A 305 ASN A 393 ASN A 472 HIS A 499 ASN A 532 ASN A 558 ASN A 590 HIS 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: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.160084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.121449 restraints weight = 22520.856| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.82 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: 0.8200 moved from start: 0.1123 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= 0.149 Angle : 0.518 8.983 31232 Z= 0.269 Chirality : 0.037 0.149 3496 Planarity : 0.004 0.029 3880 Dihedral : 8.097 65.257 3426 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 3.29 % Allowed : 23.27 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.16 (0.16), residues: 2688 helix: 2.23 (0.11), residues: 1948 sheet: None (None), residues: 0 loop : -0.79 (0.22), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 747 TYR 0.013 0.001 TYR B 523 PHE 0.015 0.001 PHE D 340 TRP 0.015 0.001 TRP A 415 HIS 0.004 0.001 HIS D 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.15 (23048) covalent geometry : angle 0.51592 / 0.27 (31212) SS BOND : bond 0.00359 / 0.18 ( 4) SS BOND : angle 2.33231 / 1.48 ( 8) hydrogen bonds : bond 0.04821 / 3.27 ( 1460) hydrogen bonds : angle 4.25395 / 3.04 ( 4272) metal coordination : bond 0.00189 / 0.13 ( 16) metal coordination : angle 1.23303 / 0.80 ( 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 367 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 287 time to evaluate : 0.858 Fit side-chains REVERT: A 112 VAL cc_start: 0.7187 (OUTLIER) cc_final: 0.6776 (m) REVERT: A 272 ARG cc_start: 0.7690 (ptp90) cc_final: 0.7155 (ttp80) REVERT: A 469 ASP cc_start: 0.6978 (t0) cc_final: 0.6545 (m-30) REVERT: A 470 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8433 (tmm) REVERT: A 520 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6366 (mp) REVERT: A 700 LEU cc_start: 0.6890 (tp) cc_final: 0.6511 (mm) REVERT: A 728 GLU cc_start: 0.6672 (OUTLIER) cc_final: 0.6116 (mp0) REVERT: B 106 LYS cc_start: 0.8261 (mmmt) cc_final: 0.7856 (tptp) REVERT: B 112 VAL cc_start: 0.7201 (OUTLIER) cc_final: 0.6793 (m) REVERT: B 469 ASP cc_start: 0.6937 (t0) cc_final: 0.6531 (m-30) REVERT: B 520 LEU cc_start: 0.7221 (OUTLIER) cc_final: 0.6267 (mp) REVERT: B 700 LEU cc_start: 0.6938 (tp) cc_final: 0.6511 (mm) REVERT: B 728 GLU cc_start: 0.6630 (OUTLIER) cc_final: 0.6169 (mp0) REVERT: C 106 LYS cc_start: 0.8378 (mmmt) cc_final: 0.7992 (tptp) REVERT: C 112 VAL cc_start: 0.7136 (OUTLIER) cc_final: 0.6772 (m) REVERT: C 469 ASP cc_start: 0.6922 (t0) cc_final: 0.6498 (m-30) REVERT: C 700 LEU cc_start: 0.6857 (tp) cc_final: 0.6408 (mm) REVERT: C 728 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: D 112 VAL cc_start: 0.7260 (OUTLIER) cc_final: 0.6846 (m) REVERT: D 239 SER cc_start: 0.8659 (p) cc_final: 0.8443 (m) REVERT: D 469 ASP cc_start: 0.6914 (t0) cc_final: 0.6425 (m-30) outliers start: 80 outliers final: 36 residues processed: 342 average time/residue: 0.5388 time to fit residues: 215.1626 Evaluate side-chains 308 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 262 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 520 LEU 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 619 MET 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 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 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 708 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 61 optimal weight: 0.9990 chunk 180 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 217 optimal weight: 1.9990 chunk 85 optimal weight: 0.5980 chunk 111 optimal weight: 0.7980 chunk 169 optimal weight: 0.9990 chunk 231 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN A 163 GLN A 532 ASN A 589 GLN B 163 GLN B 589 GLN C 38 ASN C 163 GLN C 589 GLN ** C 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.159586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.121214 restraints weight = 22768.134| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.84 r_work: 0.3169 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1502 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 : 0.455 5.974 31232 Z= 0.239 Chirality : 0.036 0.147 3496 Planarity : 0.003 0.031 3880 Dihedral : 6.507 54.354 3420 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.46 % Allowed : 23.64 % Favored : 72.90 % 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: 2.24 (0.16), residues: 2688 helix: 2.33 (0.11), residues: 1968 sheet: None (None), residues: 0 loop : -0.97 (0.22), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 196 TYR 0.014 0.001 TYR B 523 PHE 0.016 0.001 PHE A 340 TRP 0.012 0.001 TRP C 415 HIS 0.003 0.001 HIS C 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (23048) covalent geometry : angle 0.45342 / 0.24 (31212) SS BOND : bond 0.00310 / 0.16 ( 4) SS BOND : angle 2.06628 / 1.31 ( 8) hydrogen bonds : bond 0.03937 / 2.67 ( 1460) hydrogen bonds : angle 3.99236 / 2.86 ( 4272) metal coordination : bond 0.00140 / 0.09 ( 16) metal coordination : angle 0.99286 / 0.66 ( 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 376 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 292 time to evaluate : 0.711 Fit side-chains REVERT: A 68 PRO cc_start: 0.8253 (Cg_exo) cc_final: 0.8026 (Cg_endo) REVERT: A 116 LEU cc_start: 0.8109 (pp) cc_final: 0.7709 (mm) REVERT: A 272 ARG cc_start: 0.7732 (ptp90) cc_final: 0.7185 (ttp80) REVERT: A 441 MET cc_start: 0.7872 (OUTLIER) cc_final: 0.7561 (ttm) REVERT: A 469 ASP cc_start: 0.7117 (t0) cc_final: 0.6535 (m-30) REVERT: A 470 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.8472 (tmm) REVERT: A 519 PHE cc_start: 0.7893 (OUTLIER) cc_final: 0.7579 (m-80) REVERT: A 700 LEU cc_start: 0.6928 (tp) cc_final: 0.6519 (mm) REVERT: A 728 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: B 106 LYS cc_start: 0.8340 (mmmt) cc_final: 0.7916 (tptp) REVERT: B 116 LEU cc_start: 0.8032 (pp) cc_final: 0.7677 (mm) REVERT: B 469 ASP cc_start: 0.7124 (t0) cc_final: 0.6644 (m-30) REVERT: B 700 LEU cc_start: 0.6961 (tp) cc_final: 0.6490 (mm) REVERT: B 721 MET cc_start: 0.8151 (mmm) cc_final: 0.7888 (mmt) REVERT: B 747 ARG cc_start: 0.7982 (tpt-90) cc_final: 0.7772 (tpt-90) REVERT: C 106 LYS cc_start: 0.8355 (mmmt) cc_final: 0.7955 (tptp) REVERT: C 469 ASP cc_start: 0.7098 (t0) cc_final: 0.6570 (m-30) REVERT: C 700 LEU cc_start: 0.6881 (tp) cc_final: 0.6422 (mm) REVERT: C 728 GLU cc_start: 0.6779 (OUTLIER) cc_final: 0.6441 (mp0) REVERT: D 106 LYS cc_start: 0.8415 (mmmt) cc_final: 0.8006 (tptp) REVERT: D 441 MET cc_start: 0.7817 (OUTLIER) cc_final: 0.7220 (ttm) REVERT: D 456 PHE cc_start: 0.8064 (t80) cc_final: 0.7842 (t80) REVERT: D 469 ASP cc_start: 0.7091 (t0) cc_final: 0.6519 (m-30) REVERT: D 519 PHE cc_start: 0.8031 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: D 520 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.6509 (mp) REVERT: D 700 LEU cc_start: 0.6914 (tp) cc_final: 0.6405 (mm) REVERT: D 728 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6336 (mp0) outliers start: 84 outliers final: 44 residues processed: 345 average time/residue: 0.4862 time to fit residues: 196.2016 Evaluate side-chains 316 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 263 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 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 500 SER 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 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 500 SER 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 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 520 LEU Chi-restraints excluded: chain D residue 728 GLU 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: 3.9990 chunk 80 optimal weight: 0.6980 chunk 179 optimal weight: 4.9990 chunk 261 optimal weight: 0.8980 chunk 231 optimal weight: 7.9990 chunk 52 optimal weight: 0.8980 chunk 265 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 174 optimal weight: 7.9990 chunk 240 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 297 GLN A 621 ASN B 163 GLN B 589 GLN C 163 GLN C 621 ASN D 82 ASN D 163 GLN D 297 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.157950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.119389 restraints weight = 22853.747| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 1.84 r_work: 0.3146 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1730 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= 0.126 Angle : 0.458 5.993 31232 Z= 0.242 Chirality : 0.037 0.147 3496 Planarity : 0.003 0.030 3880 Dihedral : 6.557 58.903 3420 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.62 % Allowed : 24.51 % Favored : 71.87 % 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: 2.25 (0.16), residues: 2688 helix: 2.33 (0.11), residues: 1972 sheet: None (None), residues: 0 loop : -0.97 (0.22), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 196 TYR 0.017 0.001 TYR C 624 PHE 0.017 0.001 PHE A 519 TRP 0.014 0.001 TRP A 415 HIS 0.003 0.001 HIS D 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (23048) covalent geometry : angle 0.45634 / 0.24 (31212) SS BOND : bond 0.00301 / 0.15 ( 4) SS BOND : angle 2.26130 / 1.43 ( 8) hydrogen bonds : bond 0.03761 / 2.55 ( 1460) hydrogen bonds : angle 3.89371 / 2.79 ( 4272) metal coordination : bond 0.00127 / 0.09 ( 16) metal coordination : angle 0.87633 / 0.56 ( 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 378 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 290 time to evaluate : 0.911 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.8381 (mmmt) cc_final: 0.7952 (tptp) REVERT: A 116 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7723 (mm) REVERT: A 163 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8493 (mt0) REVERT: A 441 MET cc_start: 0.7865 (OUTLIER) cc_final: 0.7533 (ttm) REVERT: A 469 ASP cc_start: 0.7226 (t0) cc_final: 0.6666 (m-30) REVERT: A 470 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8514 (tmm) REVERT: A 700 LEU cc_start: 0.6955 (tp) cc_final: 0.6545 (mm) REVERT: A 728 GLU cc_start: 0.6749 (OUTLIER) cc_final: 0.6293 (mp0) REVERT: B 106 LYS cc_start: 0.8459 (mmmt) cc_final: 0.8045 (tptp) REVERT: B 116 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7707 (mm) REVERT: B 440 VAL cc_start: 0.8231 (t) cc_final: 0.7995 (t) REVERT: B 469 ASP cc_start: 0.7163 (t0) cc_final: 0.6709 (m-30) REVERT: B 519 PHE cc_start: 0.7932 (OUTLIER) cc_final: 0.7725 (m-80) REVERT: B 520 LEU cc_start: 0.7404 (OUTLIER) cc_final: 0.6455 (mp) REVERT: B 700 LEU cc_start: 0.7036 (tp) cc_final: 0.6528 (mm) REVERT: B 721 MET cc_start: 0.8163 (mmm) cc_final: 0.7902 (mmt) REVERT: B 728 GLU cc_start: 0.6735 (OUTLIER) cc_final: 0.6399 (mp0) REVERT: B 747 ARG cc_start: 0.8110 (tpt-90) cc_final: 0.7807 (tpt-90) REVERT: C 106 LYS cc_start: 0.8391 (mmmt) cc_final: 0.7999 (tptp) REVERT: C 440 VAL cc_start: 0.8424 (t) cc_final: 0.8189 (t) REVERT: C 469 ASP cc_start: 0.7242 (t0) cc_final: 0.6787 (m-30) REVERT: C 519 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7674 (m-80) REVERT: C 700 LEU cc_start: 0.6983 (tp) cc_final: 0.6501 (mm) REVERT: C 728 GLU cc_start: 0.6726 (OUTLIER) cc_final: 0.6416 (mp0) REVERT: D 106 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8028 (tptp) REVERT: D 441 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7242 (ttm) REVERT: D 456 PHE cc_start: 0.8132 (t80) cc_final: 0.7892 (t80) REVERT: D 469 ASP cc_start: 0.7228 (t0) cc_final: 0.6699 (m-30) REVERT: D 519 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7680 (m-80) REVERT: D 520 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6546 (mp) REVERT: D 700 LEU cc_start: 0.6959 (tp) cc_final: 0.6430 (mm) REVERT: D 728 GLU cc_start: 0.6713 (OUTLIER) cc_final: 0.6323 (mp0) outliers start: 88 outliers final: 53 residues processed: 345 average time/residue: 0.5334 time to fit residues: 214.7247 Evaluate side-chains 333 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 265 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 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 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 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 520 LEU 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 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 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 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 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 520 LEU 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: 4.9990 chunk 219 optimal weight: 9.9990 chunk 50 optimal weight: 0.0170 chunk 121 optimal weight: 0.2980 chunk 167 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 253 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.8622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN B 163 GLN B 297 GLN B 305 ASN ** B 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 589 GLN C 38 ASN C 82 ASN C 163 GLN C 297 GLN C 305 ASN C 589 GLN D 82 ASN D 163 GLN D 305 ASN ** D 386 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 589 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.152919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.114519 restraints weight = 22834.164| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.80 r_work: 0.3091 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 23068 Z= 0.203 Angle : 0.531 6.663 31232 Z= 0.278 Chirality : 0.040 0.154 3496 Planarity : 0.004 0.036 3880 Dihedral : 6.955 58.974 3420 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 5.40 % Allowed : 22.69 % Favored : 71.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.85 (0.16), residues: 2688 helix: 1.98 (0.11), residues: 2000 sheet: None (None), residues: 0 loop : -1.08 (0.22), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 747 TYR 0.020 0.002 TYR D 523 PHE 0.017 0.002 PHE D 519 TRP 0.021 0.002 TRP A 415 HIS 0.004 0.001 HIS B 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.20 (23048) covalent geometry : angle 0.52847 / 0.28 (31212) SS BOND : bond 0.00368 / 0.18 ( 4) SS BOND : angle 3.20778 / 2.04 ( 8) hydrogen bonds : bond 0.04178 / 2.83 ( 1460) hydrogen bonds : angle 4.03740 / 2.89 ( 4272) metal coordination : bond 0.00266 / 0.20 ( 16) metal coordination : angle 1.09287 / 0.66 ( 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: 131 poor density : 289 time to evaluate : 0.704 Fit side-chains REVERT: A 163 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8010 (mt0) REVERT: A 245 SER cc_start: 0.9167 (OUTLIER) cc_final: 0.8784 (t) REVERT: A 469 ASP cc_start: 0.7225 (t0) cc_final: 0.6607 (m-30) REVERT: A 700 LEU cc_start: 0.6840 (tp) cc_final: 0.6474 (mm) REVERT: A 728 GLU cc_start: 0.6843 (OUTLIER) cc_final: 0.6410 (mp0) REVERT: B 245 SER cc_start: 0.9245 (OUTLIER) cc_final: 0.8825 (t) REVERT: B 330 MET cc_start: 0.6408 (OUTLIER) cc_final: 0.5982 (ttt) REVERT: B 469 ASP cc_start: 0.7208 (t0) cc_final: 0.6710 (m-30) REVERT: B 700 LEU cc_start: 0.6941 (tp) cc_final: 0.6499 (mm) REVERT: B 713 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8763 (mp) REVERT: B 721 MET cc_start: 0.8054 (mmm) cc_final: 0.7798 (mmt) REVERT: B 728 GLU cc_start: 0.6731 (OUTLIER) cc_final: 0.6361 (mp0) REVERT: B 747 ARG cc_start: 0.8222 (tpt-90) cc_final: 0.7670 (tpt-90) REVERT: C 106 LYS cc_start: 0.8463 (mmmt) cc_final: 0.8045 (tptp) REVERT: C 245 SER cc_start: 0.9238 (OUTLIER) cc_final: 0.8846 (t) REVERT: C 456 PHE cc_start: 0.8038 (t80) cc_final: 0.7830 (t80) REVERT: C 469 ASP cc_start: 0.7284 (t0) cc_final: 0.6836 (m-30) REVERT: C 700 LEU cc_start: 0.6943 (tp) cc_final: 0.6505 (mm) REVERT: C 713 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8768 (mp) REVERT: C 728 GLU cc_start: 0.6844 (OUTLIER) cc_final: 0.6494 (mp0) REVERT: D 106 LYS cc_start: 0.8423 (mmmt) cc_final: 0.7985 (tptp) REVERT: D 245 SER cc_start: 0.9220 (OUTLIER) cc_final: 0.8824 (t) REVERT: D 330 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.6032 (ttt) REVERT: D 469 ASP cc_start: 0.7275 (t0) cc_final: 0.6756 (m-30) REVERT: D 519 PHE cc_start: 0.8088 (t80) cc_final: 0.7781 (m-80) REVERT: D 700 LEU cc_start: 0.6873 (tp) cc_final: 0.6410 (mm) REVERT: D 713 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8761 (mp) REVERT: D 728 GLU cc_start: 0.6767 (OUTLIER) cc_final: 0.6397 (mp0) outliers start: 131 outliers final: 64 residues processed: 383 average time/residue: 0.4807 time to fit residues: 216.4153 Evaluate side-chains 349 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 271 time to evaluate : 0.696 ------------------------------------------------------------------------------- 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 160 LEU 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 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 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 112 VAL Chi-restraints excluded: chain C residue 116 LEU Chi-restraints excluded: chain C residue 144 THR Chi-restraints excluded: chain C residue 160 LEU 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 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 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 406 ILE Chi-restraints excluded: chain D residue 433 TRP 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: 0.7980 chunk 37 optimal weight: 0.7980 chunk 202 optimal weight: 1.9990 chunk 156 optimal weight: 0.9980 chunk 166 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 chunk 237 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 82 ASN A 163 GLN A 435 ASN A 589 GLN B 82 ASN B 163 GLN B 305 ASN B 435 ASN B 589 GLN C 38 ASN C 82 ASN C 163 GLN C 305 ASN C 435 ASN C 589 GLN D 82 ASN D 163 GLN D 305 ASN D 435 ASN D 472 HIS D 589 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.156086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.117571 restraints weight = 23013.339| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.85 r_work: 0.3120 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23068 Z= 0.128 Angle : 0.493 10.715 31232 Z= 0.252 Chirality : 0.037 0.153 3496 Planarity : 0.004 0.031 3880 Dihedral : 6.849 59.411 3420 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 4.45 % Allowed : 23.76 % 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: 2.11 (0.16), residues: 2688 helix: 2.23 (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 0.003 0.000 ARG C 196 TYR 0.017 0.001 TYR D 523 PHE 0.018 0.001 PHE A 340 TRP 0.016 0.001 TRP A 415 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (23048) covalent geometry : angle 0.46571 / 0.25 (31212) SS BOND : bond 0.00273 / 0.14 ( 4) SS BOND : angle 2.33454 / 1.49 ( 8) hydrogen bonds : bond 0.03693 / 2.51 ( 1460) hydrogen bonds : angle 3.91315 / 2.80 ( 4272) metal coordination : bond 0.03116 / 2.08 ( 16) metal coordination : angle 8.03240 / 5.25 ( 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 398 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 290 time to evaluate : 0.890 Fit side-chains REVERT: A 84 GLU cc_start: 0.7790 (mp0) cc_final: 0.7363 (mp0) REVERT: A 106 LYS cc_start: 0.8386 (mmmt) cc_final: 0.7955 (tptp) REVERT: A 163 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8426 (mt0) REVERT: A 245 SER cc_start: 0.9185 (OUTLIER) cc_final: 0.8832 (t) REVERT: A 469 ASP cc_start: 0.7263 (t0) cc_final: 0.6700 (m-30) REVERT: A 470 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8469 (tmm) REVERT: A 512 MET cc_start: 0.8309 (ttp) cc_final: 0.8104 (ttp) REVERT: A 700 LEU cc_start: 0.6819 (tp) cc_final: 0.6473 (mm) REVERT: B 98 ASP cc_start: 0.8225 (p0) cc_final: 0.8018 (p0) REVERT: B 106 LYS cc_start: 0.8408 (mmmt) cc_final: 0.7962 (tptp) REVERT: B 245 SER cc_start: 0.9212 (OUTLIER) cc_final: 0.8836 (t) REVERT: B 330 MET cc_start: 0.6354 (OUTLIER) cc_final: 0.5913 (ttt) REVERT: B 440 VAL cc_start: 0.8287 (t) cc_final: 0.8058 (t) REVERT: B 469 ASP cc_start: 0.7237 (t0) cc_final: 0.6733 (m-30) REVERT: B 512 MET cc_start: 0.8285 (ttp) cc_final: 0.8052 (ttp) REVERT: B 700 LEU cc_start: 0.6913 (tp) cc_final: 0.6550 (mm) REVERT: B 713 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8752 (mp) REVERT: B 721 MET cc_start: 0.8030 (mmm) cc_final: 0.7809 (mmt) REVERT: B 728 GLU cc_start: 0.6487 (OUTLIER) cc_final: 0.6129 (mp0) REVERT: B 747 ARG cc_start: 0.8158 (tpt-90) cc_final: 0.7593 (ttt180) REVERT: C 84 GLU cc_start: 0.7756 (mp0) cc_final: 0.7388 (mp0) REVERT: C 106 LYS cc_start: 0.8433 (mmmt) cc_final: 0.8020 (tptp) REVERT: C 440 VAL cc_start: 0.8449 (t) cc_final: 0.8215 (t) REVERT: C 469 ASP cc_start: 0.7232 (t0) cc_final: 0.6777 (m-30) REVERT: C 700 LEU cc_start: 0.6916 (tp) cc_final: 0.6523 (mm) REVERT: C 713 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8728 (mp) REVERT: C 728 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6483 (mp0) REVERT: C 747 ARG cc_start: 0.7981 (tpt-90) cc_final: 0.7713 (tpt-90) REVERT: D 98 ASP cc_start: 0.8211 (p0) cc_final: 0.7994 (p0) REVERT: D 106 LYS cc_start: 0.8462 (mmmt) cc_final: 0.8042 (tptp) REVERT: D 469 ASP cc_start: 0.7342 (t0) cc_final: 0.6848 (m-30) REVERT: D 700 LEU cc_start: 0.6848 (tp) cc_final: 0.6375 (mm) REVERT: D 713 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8738 (mp) REVERT: D 728 GLU cc_start: 0.6667 (OUTLIER) cc_final: 0.6327 (mp0) outliers start: 108 outliers final: 70 residues processed: 364 average time/residue: 0.5504 time to fit residues: 232.5507 Evaluate side-chains 358 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 277 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 619 MET Chi-restraints excluded: chain A residue 708 GLU 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 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 435 ASN 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 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 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 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 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 318 PHE 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 435 ASN Chi-restraints excluded: chain D residue 500 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: 0.8980 chunk 241 optimal weight: 0.7980 chunk 38 optimal weight: 9.9990 chunk 227 optimal weight: 1.9990 chunk 181 optimal weight: 0.9990 chunk 31 optimal weight: 0.1980 chunk 240 optimal weight: 0.7980 chunk 217 optimal weight: 0.2980 chunk 18 optimal weight: 0.5980 chunk 179 optimal weight: 0.7980 chunk 222 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 435 ASN A 589 GLN B 82 ASN B 163 GLN B 435 ASN B 589 GLN C 82 ASN C 163 GLN C 435 ASN C 589 GLN D 82 ASN D 163 GLN D 435 ASN D 589 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.157439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.119017 restraints weight = 22956.258| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.84 r_work: 0.3143 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2132 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= 0.112 Angle : 0.481 9.786 31232 Z= 0.246 Chirality : 0.036 0.149 3496 Planarity : 0.003 0.031 3880 Dihedral : 6.748 58.564 3420 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.61 % Allowed : 23.97 % 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: 2.21 (0.16), residues: 2688 helix: 2.30 (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 0.003 0.000 ARG C 196 TYR 0.015 0.001 TYR D 523 PHE 0.020 0.001 PHE D 519 TRP 0.015 0.001 TRP A 409 HIS 0.005 0.001 HIS B 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (23048) covalent geometry : angle 0.45931 / 0.24 (31212) SS BOND : bond 0.00220 / 0.11 ( 4) SS BOND : angle 2.03194 / 1.29 ( 8) hydrogen bonds : bond 0.03573 / 2.42 ( 1460) hydrogen bonds : angle 3.85586 / 2.77 ( 4272) metal coordination : bond 0.01913 / 1.21 ( 16) metal coordination : angle 7.15067 / 4.62 ( 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: 112 poor density : 286 time to evaluate : 0.906 Fit side-chains REVERT: A 84 GLU cc_start: 0.7830 (mp0) cc_final: 0.7402 (mp0) REVERT: A 106 LYS cc_start: 0.8423 (mmmt) cc_final: 0.8011 (tptp) REVERT: A 163 GLN cc_start: 0.8678 (OUTLIER) cc_final: 0.8220 (mt0) REVERT: A 440 VAL cc_start: 0.8366 (t) cc_final: 0.8015 (t) REVERT: A 441 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7544 (ttm) REVERT: A 469 ASP cc_start: 0.7385 (t0) cc_final: 0.6792 (m-30) REVERT: A 470 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8455 (tmm) REVERT: A 700 LEU cc_start: 0.6793 (tp) cc_final: 0.6464 (mm) REVERT: B 67 ASP cc_start: 0.7023 (t0) cc_final: 0.6777 (t0) REVERT: B 106 LYS cc_start: 0.8384 (mmmt) cc_final: 0.7950 (tptp) REVERT: B 163 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8413 (mt0) REVERT: B 330 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5813 (ttt) REVERT: B 440 VAL cc_start: 0.8270 (t) cc_final: 0.8031 (t) REVERT: B 441 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7637 (ttm) REVERT: B 469 ASP cc_start: 0.7201 (t0) cc_final: 0.6698 (m-30) REVERT: B 700 LEU cc_start: 0.6883 (tp) cc_final: 0.6512 (mm) REVERT: B 713 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8734 (mp) REVERT: B 721 MET cc_start: 0.8092 (mmm) cc_final: 0.7871 (mmt) REVERT: B 728 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.6249 (mp0) REVERT: B 747 ARG cc_start: 0.8100 (tpt-90) cc_final: 0.7299 (tpt-90) REVERT: C 84 GLU cc_start: 0.7761 (mp0) cc_final: 0.7398 (mp0) REVERT: C 106 LYS cc_start: 0.8340 (mmmt) cc_final: 0.7916 (tptp) REVERT: C 245 SER cc_start: 0.9172 (OUTLIER) cc_final: 0.8827 (t) REVERT: C 440 VAL cc_start: 0.8358 (t) cc_final: 0.7965 (t) REVERT: C 469 ASP cc_start: 0.7431 (t0) cc_final: 0.7002 (m-30) REVERT: C 615 MET cc_start: 0.9015 (mtt) cc_final: 0.8747 (mmm) REVERT: C 700 LEU cc_start: 0.6873 (tp) cc_final: 0.6530 (mm) REVERT: C 713 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8696 (mp) REVERT: C 728 GLU cc_start: 0.6522 (OUTLIER) cc_final: 0.6242 (mp0) REVERT: C 747 ARG cc_start: 0.7973 (tpt-90) cc_final: 0.7698 (tpt-90) REVERT: D 98 ASP cc_start: 0.8261 (p0) cc_final: 0.8055 (p0) REVERT: D 106 LYS cc_start: 0.8440 (mmmt) cc_final: 0.8026 (tptp) REVERT: D 245 SER cc_start: 0.9168 (OUTLIER) cc_final: 0.8825 (t) REVERT: D 440 VAL cc_start: 0.8393 (t) cc_final: 0.8029 (t) REVERT: D 469 ASP cc_start: 0.7416 (t0) cc_final: 0.6912 (m-30) REVERT: D 519 PHE cc_start: 0.7952 (OUTLIER) cc_final: 0.7479 (m-80) REVERT: D 700 LEU cc_start: 0.6814 (tp) cc_final: 0.6339 (mm) REVERT: D 713 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8711 (mp) REVERT: D 728 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.6128 (mp0) outliers start: 112 outliers final: 72 residues processed: 358 average time/residue: 0.5551 time to fit residues: 231.7026 Evaluate side-chains 373 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 286 time to evaluate : 0.681 ------------------------------------------------------------------------------- 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 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 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 163 GLN 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 239 SER Chi-restraints excluded: chain D residue 245 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 357 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 519 PHE 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: 0.7980 chunk 267 optimal weight: 0.9980 chunk 235 optimal weight: 0.7980 chunk 154 optimal weight: 1.9990 chunk 215 optimal weight: 0.5980 chunk 204 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 163 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 145 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 589 GLN B 82 ASN B 163 GLN B 472 HIS B 589 GLN C 82 ASN C 163 GLN C 589 GLN D 82 ASN D 163 GLN D 435 ASN D 589 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.157282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.118863 restraints weight = 22806.808| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.83 r_work: 0.3143 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23068 Z= 0.121 Angle : 0.481 8.696 31232 Z= 0.247 Chirality : 0.037 0.149 3496 Planarity : 0.003 0.031 3880 Dihedral : 6.761 58.366 3420 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 4.49 % Allowed : 24.01 % Favored : 71.50 % 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: 2.21 (0.16), residues: 2688 helix: 2.30 (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 0.003 0.000 ARG C 491 TYR 0.016 0.001 TYR D 523 PHE 0.020 0.001 PHE D 519 TRP 0.016 0.001 TRP D 415 HIS 0.005 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (23048) covalent geometry : angle 0.46423 / 0.24 (31212) SS BOND : bond 0.00237 / 0.12 ( 4) SS BOND : angle 2.15207 / 1.37 ( 8) hydrogen bonds : bond 0.03595 / 2.44 ( 1460) hydrogen bonds : angle 3.83445 / 2.76 ( 4272) metal coordination : bond 0.01583 / 0.99 ( 16) metal coordination : angle 6.29736 / 4.04 ( 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 395 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 286 time to evaluate : 0.857 Fit side-chains REVERT: A 84 GLU cc_start: 0.7879 (mp0) cc_final: 0.7459 (mp0) REVERT: A 106 LYS cc_start: 0.8328 (mmmt) cc_final: 0.7910 (tptp) REVERT: A 163 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.8052 (mt0) REVERT: A 245 SER cc_start: 0.9151 (OUTLIER) cc_final: 0.8811 (t) REVERT: A 439 PHE cc_start: 0.8278 (t80) cc_final: 0.8055 (t80) REVERT: A 469 ASP cc_start: 0.7385 (t0) cc_final: 0.6775 (m-30) REVERT: A 470 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8423 (tmm) REVERT: A 700 LEU cc_start: 0.6787 (tp) cc_final: 0.6453 (mm) REVERT: B 106 LYS cc_start: 0.8434 (mmmt) cc_final: 0.8018 (tptp) REVERT: B 163 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: B 245 SER cc_start: 0.9174 (OUTLIER) cc_final: 0.8833 (t) REVERT: B 330 MET cc_start: 0.6267 (OUTLIER) cc_final: 0.5828 (ttt) REVERT: B 440 VAL cc_start: 0.8304 (t) cc_final: 0.8067 (t) REVERT: B 469 ASP cc_start: 0.7412 (t0) cc_final: 0.6975 (m-30) REVERT: B 700 LEU cc_start: 0.6887 (tp) cc_final: 0.6546 (mm) REVERT: B 713 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8716 (mp) REVERT: B 721 MET cc_start: 0.8094 (mmm) cc_final: 0.7873 (mmt) REVERT: B 728 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6214 (mp0) REVERT: B 747 ARG cc_start: 0.8118 (tpt-90) cc_final: 0.7696 (ttt-90) REVERT: C 84 GLU cc_start: 0.7820 (mp0) cc_final: 0.7456 (mp0) REVERT: C 106 LYS cc_start: 0.8353 (mmmt) cc_final: 0.7934 (tptp) REVERT: C 163 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8418 (mt0) REVERT: C 245 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8819 (t) REVERT: C 439 PHE cc_start: 0.8192 (t80) cc_final: 0.7906 (t80) REVERT: C 469 ASP cc_start: 0.7450 (t0) cc_final: 0.7032 (m-30) REVERT: C 615 MET cc_start: 0.8993 (mtt) cc_final: 0.8775 (mmm) REVERT: C 700 LEU cc_start: 0.6869 (tp) cc_final: 0.6522 (mm) REVERT: C 713 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8707 (mp) REVERT: C 728 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6251 (mp0) REVERT: C 747 ARG cc_start: 0.8152 (tpt-90) cc_final: 0.7871 (tpt-90) REVERT: D 106 LYS cc_start: 0.8345 (mmmt) cc_final: 0.7926 (tptp) REVERT: D 245 SER cc_start: 0.9163 (OUTLIER) cc_final: 0.8830 (t) REVERT: D 439 PHE cc_start: 0.8253 (t80) cc_final: 0.7961 (t80) REVERT: D 469 ASP cc_start: 0.7412 (t0) cc_final: 0.6957 (m-30) REVERT: D 519 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7567 (m-80) REVERT: D 700 LEU cc_start: 0.6839 (tp) cc_final: 0.6387 (mm) REVERT: D 713 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8715 (mp) REVERT: D 728 GLU cc_start: 0.6473 (OUTLIER) cc_final: 0.6134 (mp0) outliers start: 109 outliers final: 74 residues processed: 356 average time/residue: 0.5515 time to fit residues: 228.5773 Evaluate side-chains 373 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 283 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 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 745 SER 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 163 GLN 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 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 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 239 SER Chi-restraints excluded: chain D residue 245 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 357 LEU Chi-restraints excluded: chain D residue 405 MET Chi-restraints excluded: chain D residue 406 ILE Chi-restraints excluded: chain D residue 435 ASN Chi-restraints excluded: chain D residue 500 SER Chi-restraints excluded: chain D residue 519 PHE 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 Chi-restraints excluded: chain D residue 745 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 9.9990 chunk 170 optimal weight: 1.9990 chunk 192 optimal weight: 0.9980 chunk 99 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 226 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 589 GLN B 82 ASN B 163 GLN B 589 GLN C 82 ASN C 163 GLN C 589 GLN D 82 ASN D 163 GLN D 435 ASN D 589 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.156506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.117982 restraints weight = 22913.381| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.84 r_work: 0.3130 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23068 Z= 0.139 Angle : 0.495 8.031 31232 Z= 0.255 Chirality : 0.037 0.150 3496 Planarity : 0.004 0.034 3880 Dihedral : 6.870 58.794 3420 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.57 % Allowed : 24.09 % 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: 2.14 (0.16), residues: 2688 helix: 2.24 (0.11), residues: 1976 sheet: None (None), residues: 0 loop : -0.99 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 747 TYR 0.017 0.001 TYR A 523 PHE 0.021 0.001 PHE D 519 TRP 0.019 0.001 TRP A 415 HIS 0.004 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (23048) covalent geometry : angle 0.48077 / 0.25 (31212) SS BOND : bond 0.00290 / 0.15 ( 4) SS BOND : angle 2.43955 / 1.57 ( 8) hydrogen bonds : bond 0.03686 / 2.50 ( 1460) hydrogen bonds : angle 3.86862 / 2.78 ( 4272) metal coordination : bond 0.01441 / 0.89 ( 16) metal coordination : angle 5.81643 / 3.76 ( 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 396 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 285 time to evaluate : 0.915 Fit side-chains REVERT: A 84 GLU cc_start: 0.7869 (mp0) cc_final: 0.7447 (mp0) REVERT: A 106 LYS cc_start: 0.8369 (mmmt) cc_final: 0.7955 (tptp) REVERT: A 163 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.8033 (mt0) REVERT: A 245 SER cc_start: 0.9147 (OUTLIER) cc_final: 0.8813 (t) REVERT: A 469 ASP cc_start: 0.7419 (t0) cc_final: 0.6844 (m-30) REVERT: A 470 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8335 (tmm) REVERT: A 700 LEU cc_start: 0.6782 (tp) cc_final: 0.6480 (mm) REVERT: A 728 GLU cc_start: 0.6686 (OUTLIER) cc_final: 0.6251 (mp0) REVERT: B 106 LYS cc_start: 0.8435 (mmmt) cc_final: 0.8021 (tptp) REVERT: B 163 GLN cc_start: 0.8617 (OUTLIER) cc_final: 0.8109 (mt0) REVERT: B 245 SER cc_start: 0.9177 (OUTLIER) cc_final: 0.8830 (t) REVERT: B 330 MET cc_start: 0.6246 (OUTLIER) cc_final: 0.5812 (ttt) REVERT: B 440 VAL cc_start: 0.8299 (t) cc_final: 0.8070 (t) REVERT: B 469 ASP cc_start: 0.7416 (t0) cc_final: 0.6985 (m-30) REVERT: B 619 MET cc_start: 0.8525 (ttm) cc_final: 0.8309 (ptm) REVERT: B 700 LEU cc_start: 0.6872 (tp) cc_final: 0.6523 (mm) REVERT: B 713 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8745 (mp) REVERT: B 721 MET cc_start: 0.8026 (mmm) cc_final: 0.7792 (mmt) REVERT: B 728 GLU cc_start: 0.6590 (OUTLIER) cc_final: 0.6185 (mp0) REVERT: B 747 ARG cc_start: 0.8112 (tpt-90) cc_final: 0.7523 (tpt-90) REVERT: C 106 LYS cc_start: 0.8402 (mmmt) cc_final: 0.8009 (tptp) REVERT: C 163 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8330 (mt0) REVERT: C 245 SER cc_start: 0.9169 (OUTLIER) cc_final: 0.8819 (t) REVERT: C 469 ASP cc_start: 0.7416 (t0) cc_final: 0.7041 (m-30) REVERT: C 615 MET cc_start: 0.8988 (mtt) cc_final: 0.8753 (mmm) REVERT: C 700 LEU cc_start: 0.6860 (tp) cc_final: 0.6528 (mm) REVERT: C 713 LEU cc_start: 0.9024 (OUTLIER) cc_final: 0.8711 (mp) REVERT: C 728 GLU cc_start: 0.6526 (OUTLIER) cc_final: 0.6190 (mp0) REVERT: C 747 ARG cc_start: 0.8044 (tpt-90) cc_final: 0.7776 (tpt-90) REVERT: D 106 LYS cc_start: 0.8347 (mmmt) cc_final: 0.7927 (tptp) REVERT: D 245 SER cc_start: 0.9168 (OUTLIER) cc_final: 0.8825 (t) REVERT: D 469 ASP cc_start: 0.7447 (t0) cc_final: 0.7005 (m-30) REVERT: D 519 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7735 (m-80) REVERT: D 700 LEU cc_start: 0.6813 (tp) cc_final: 0.6367 (mm) REVERT: D 713 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8712 (mp) REVERT: D 728 GLU cc_start: 0.6835 (OUTLIER) cc_final: 0.6481 (mp0) outliers start: 111 outliers final: 79 residues processed: 358 average time/residue: 0.5512 time to fit residues: 230.1294 Evaluate side-chains 377 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 281 time to evaluate : 0.876 ------------------------------------------------------------------------------- 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 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 708 GLU Chi-restraints excluded: chain A residue 728 GLU Chi-restraints excluded: chain A residue 745 SER 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 163 GLN 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 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 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 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 519 PHE 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 Chi-restraints excluded: chain D residue 745 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 99 optimal weight: 0.9990 chunk 246 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 251 optimal weight: 0.1980 chunk 196 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 238 optimal weight: 0.3980 chunk 108 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 43 optimal weight: 0.6980 chunk 119 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 589 GLN B 82 ASN B 163 GLN B 589 GLN C 82 ASN C 163 GLN C 472 HIS C 589 GLN D 82 ASN 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 = 0.3744 r_free = 0.3744 target = 0.156948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.118402 restraints weight = 22960.828| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 1.85 r_work: 0.3120 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2214 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= 0.129 Angle : 0.491 7.754 31232 Z= 0.254 Chirality : 0.037 0.154 3496 Planarity : 0.004 0.033 3880 Dihedral : 6.897 58.900 3420 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.32 % Allowed : 24.34 % 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: 2.18 (0.16), residues: 2688 helix: 2.26 (0.11), residues: 1976 sheet: None (None), residues: 0 loop : -0.97 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 196 TYR 0.016 0.001 TYR A 523 PHE 0.021 0.001 PHE D 519 TRP 0.019 0.001 TRP A 415 HIS 0.004 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (23048) covalent geometry : angle 0.47746 / 0.25 (31212) SS BOND : bond 0.00271 / 0.14 ( 4) SS BOND : angle 2.31930 / 1.49 ( 8) hydrogen bonds : bond 0.03627 / 2.46 ( 1460) hydrogen bonds : angle 3.84293 / 2.76 ( 4272) metal coordination : bond 0.01401 / 0.87 ( 16) metal coordination : angle 5.58492 / 3.58 ( 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 391 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 286 time to evaluate : 0.896 Fit side-chains REVERT: A 84 GLU cc_start: 0.7856 (mp0) cc_final: 0.7435 (mp0) REVERT: A 106 LYS cc_start: 0.8304 (mmmt) cc_final: 0.7882 (tptp) REVERT: A 163 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7978 (mt0) REVERT: A 245 SER cc_start: 0.9131 (OUTLIER) cc_final: 0.8798 (t) REVERT: A 469 ASP cc_start: 0.7393 (t0) cc_final: 0.6820 (m-30) REVERT: A 470 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.8385 (tmm) REVERT: A 700 LEU cc_start: 0.6744 (tp) cc_final: 0.6436 (mm) REVERT: A 728 GLU cc_start: 0.6633 (OUTLIER) cc_final: 0.6254 (mp0) REVERT: B 98 ASP cc_start: 0.8204 (p0) cc_final: 0.7974 (p0) REVERT: B 106 LYS cc_start: 0.8410 (mmmt) cc_final: 0.7993 (tptp) REVERT: B 163 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7995 (mt0) REVERT: B 245 SER cc_start: 0.9158 (OUTLIER) cc_final: 0.8815 (t) REVERT: B 330 MET cc_start: 0.6172 (OUTLIER) cc_final: 0.5723 (ttt) REVERT: B 440 VAL cc_start: 0.8257 (t) cc_final: 0.8029 (t) REVERT: B 469 ASP cc_start: 0.7427 (t0) cc_final: 0.6999 (m-30) REVERT: B 619 MET cc_start: 0.8510 (ttm) cc_final: 0.8268 (ptm) REVERT: B 700 LEU cc_start: 0.6829 (tp) cc_final: 0.6492 (mm) REVERT: B 713 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8730 (mp) REVERT: B 721 MET cc_start: 0.8093 (mmm) cc_final: 0.7865 (mmt) REVERT: B 728 GLU cc_start: 0.6546 (OUTLIER) cc_final: 0.6162 (mp0) REVERT: B 747 ARG cc_start: 0.8100 (tpt-90) cc_final: 0.7501 (tpt-90) REVERT: C 84 GLU cc_start: 0.7805 (mp0) cc_final: 0.7437 (mp0) REVERT: C 106 LYS cc_start: 0.8385 (mmmt) cc_final: 0.7967 (tptp) REVERT: C 163 GLN cc_start: 0.8602 (OUTLIER) cc_final: 0.8164 (mt0) REVERT: C 245 SER cc_start: 0.9150 (OUTLIER) cc_final: 0.8804 (t) REVERT: C 469 ASP cc_start: 0.7420 (t0) cc_final: 0.7044 (m-30) REVERT: C 615 MET cc_start: 0.8936 (mtt) cc_final: 0.8718 (mmm) REVERT: C 700 LEU cc_start: 0.6803 (tp) cc_final: 0.6479 (mm) REVERT: C 713 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8680 (mp) REVERT: C 728 GLU cc_start: 0.6496 (OUTLIER) cc_final: 0.6166 (mp0) REVERT: C 747 ARG cc_start: 0.8038 (tpt-90) cc_final: 0.7729 (tpt-90) REVERT: D 106 LYS cc_start: 0.8310 (mmmt) cc_final: 0.7887 (tptp) REVERT: D 245 SER cc_start: 0.9151 (OUTLIER) cc_final: 0.8812 (t) REVERT: D 469 ASP cc_start: 0.7432 (t0) cc_final: 0.6994 (m-30) REVERT: D 700 LEU cc_start: 0.6758 (tp) cc_final: 0.6325 (mm) REVERT: D 713 LEU cc_start: 0.9005 (OUTLIER) cc_final: 0.8692 (mp) REVERT: D 728 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6191 (mp0) outliers start: 105 outliers final: 78 residues processed: 355 average time/residue: 0.5533 time to fit residues: 228.8676 Evaluate side-chains 375 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 281 time to evaluate : 0.880 ------------------------------------------------------------------------------- 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 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 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 728 GLU Chi-restraints excluded: chain A residue 745 SER 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 163 GLN 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 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 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 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 Chi-restraints excluded: chain D residue 745 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 88 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 61 optimal weight: 0.0370 chunk 250 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 58 optimal weight: 0.6980 chunk 163 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 163 GLN A 589 GLN B 82 ASN B 163 GLN B 589 GLN C 82 ASN C 163 GLN C 589 GLN D 82 ASN D 163 GLN D 589 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.157878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.119514 restraints weight = 22830.775| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.84 r_work: 0.3151 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3007 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 23068 Z= 0.117 Angle : 0.484 7.566 31232 Z= 0.251 Chirality : 0.037 0.152 3496 Planarity : 0.003 0.034 3880 Dihedral : 6.877 59.139 3420 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 4.12 % Allowed : 24.96 % Favored : 70.92 % 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: 2.23 (0.16), residues: 2688 helix: 2.30 (0.11), residues: 1976 sheet: None (None), residues: 0 loop : -0.95 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 196 TYR 0.015 0.001 TYR A 523 PHE 0.017 0.001 PHE A 340 TRP 0.019 0.001 TRP B 409 HIS 0.004 0.001 HIS A 172 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (23048) covalent geometry : angle 0.47124 / 0.25 (31212) SS BOND : bond 0.00241 / 0.12 ( 4) SS BOND : angle 2.12066 / 1.36 ( 8) hydrogen bonds : bond 0.03554 / 2.41 ( 1460) hydrogen bonds : angle 3.82780 / 2.75 ( 4272) metal coordination : bond 0.01384 / 0.86 ( 16) metal coordination : angle 5.39953 / 3.44 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7100.32 seconds wall clock time: 121 minutes 59.73 seconds (7319.73 seconds total)