Starting phenix.real_space_refine on Wed Mar 4 11:43:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zel_14690/03_2026/7zel_14690.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zel_14690/03_2026/7zel_14690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zel_14690/03_2026/7zel_14690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zel_14690/03_2026/7zel_14690.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zel_14690/03_2026/7zel_14690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zel_14690/03_2026/7zel_14690.map" } resolution = 2.8 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= -0.001 sd= 0.150 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 Mg 2 5.21 5 S 86 5.16 5 C 8508 2.51 5 N 2320 2.21 5 O 2416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13334 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "B" Number of atoms: 6665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 827, 6665 Classifications: {'peptide': 827} Link IDs: {'PCIS': 3, 'PTRANS': 39, 'TRANS': 784} Chain breaks: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2033 SG CYS A 287 76.086 60.217 52.259 1.00 53.15 S ATOM 2310 SG CYS A 321 76.041 59.012 48.562 1.00 35.67 S ATOM 8698 SG CYS B 287 24.109 68.729 51.783 1.00 56.90 S ATOM 8975 SG CYS B 321 24.132 69.825 48.117 1.00 37.22 S ATOM 8981 SG CYS B 322 26.772 67.408 49.424 1.00 39.30 S Time building chain proxies: 2.56, per 1000 atoms: 0.19 Number of scatterers: 13334 At special positions: 0 Unit cell: (101.462, 130.75, 126.566, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 86 16.00 Mg 2 11.99 O 2416 8.00 N 2320 7.00 C 8508 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.78 Conformation dependent library (CDL) restraints added in 490.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 321 " pdb="ZN ZN A1001 " - pdb=" ND1 HIS A 285 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 287 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" ND1 HIS B 285 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 322 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 321 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 287 " Number of angles added : 3 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3124 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 17 sheets defined 45.0% alpha, 17.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 27 through 33 Processing helix chain 'A' and resid 35 through 56 Processing helix chain 'A' and resid 74 through 86 Processing helix chain 'A' and resid 89 through 92 Processing helix chain 'A' and resid 144 through 157 removed outlier: 3.600A pdb=" N LYS A 157 " --> pdb=" O LYS A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 189 through 195 removed outlier: 3.962A pdb=" N ILE A 193 " --> pdb=" O PRO A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 241 Proline residue: A 232 - end of helix Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 266 through 281 removed outlier: 3.664A pdb=" N LEU A 281 " --> pdb=" O ALA A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 353 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.557A pdb=" N LEU A 387 " --> pdb=" O SER A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 398 Processing helix chain 'A' and resid 409 through 420 Processing helix chain 'A' and resid 422 through 431 Processing helix chain 'A' and resid 444 through 449 Processing helix chain 'A' and resid 482 through 501 removed outlier: 3.566A pdb=" N VAL A 499 " --> pdb=" O LYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 540 Processing helix chain 'A' and resid 543 through 560 removed outlier: 3.512A pdb=" N ILE A 556 " --> pdb=" O GLN A 552 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLY A 560 " --> pdb=" O ILE A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 586 Processing helix chain 'A' and resid 587 through 589 No H-bonds generated for 'chain 'A' and resid 587 through 589' Processing helix chain 'A' and resid 604 through 621 Processing helix chain 'A' and resid 623 through 625 No H-bonds generated for 'chain 'A' and resid 623 through 625' Processing helix chain 'A' and resid 633 through 642 Processing helix chain 'A' and resid 651 through 657 Processing helix chain 'A' and resid 669 through 673 Processing helix chain 'A' and resid 679 through 690 Processing helix chain 'A' and resid 703 through 707 removed outlier: 3.917A pdb=" N THR A 707 " --> pdb=" O TYR A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 721 Processing helix chain 'A' and resid 734 through 751 Processing helix chain 'A' and resid 759 through 763 removed outlier: 3.705A pdb=" N GLU A 762 " --> pdb=" O GLY A 759 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL A 763 " --> pdb=" O CYS A 760 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 759 through 763' Processing helix chain 'A' and resid 784 through 803 Processing helix chain 'A' and resid 805 through 807 No H-bonds generated for 'chain 'A' and resid 805 through 807' Processing helix chain 'A' and resid 815 through 817 No H-bonds generated for 'chain 'A' and resid 815 through 817' Processing helix chain 'A' and resid 818 through 831 removed outlier: 3.563A pdb=" N TYR A 824 " --> pdb=" O GLU A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 834 No H-bonds generated for 'chain 'A' and resid 832 through 834' Processing helix chain 'A' and resid 855 through 858 Processing helix chain 'A' and resid 877 through 887 removed outlier: 3.676A pdb=" N LEU A 882 " --> pdb=" O LEU A 878 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ILE A 883 " --> pdb=" O PRO A 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 33 removed outlier: 3.627A pdb=" N LYS B 33 " --> pdb=" O GLU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 56 Processing helix chain 'B' and resid 74 through 86 Processing helix chain 'B' and resid 89 through 92 Processing helix chain 'B' and resid 144 through 157 removed outlier: 3.548A pdb=" N LYS B 157 " --> pdb=" O LYS B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 189 through 196 removed outlier: 4.226A pdb=" N ILE B 193 " --> pdb=" O PRO B 189 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 241 Proline residue: B 232 - end of helix Proline residue: B 236 - end of helix Processing helix chain 'B' and resid 266 through 281 removed outlier: 3.590A pdb=" N LEU B 281 " --> pdb=" O ALA B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 353 Processing helix chain 'B' and resid 383 through 389 Processing helix chain 'B' and resid 389 through 398 Processing helix chain 'B' and resid 409 through 420 Processing helix chain 'B' and resid 422 through 431 Processing helix chain 'B' and resid 444 through 449 Processing helix chain 'B' and resid 482 through 501 Processing helix chain 'B' and resid 536 through 540 Processing helix chain 'B' and resid 543 through 560 removed outlier: 3.514A pdb=" N GLY B 560 " --> pdb=" O ILE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 586 removed outlier: 3.646A pdb=" N ILE B 584 " --> pdb=" O GLN B 580 " (cutoff:3.500A) Processing helix chain 'B' and resid 587 through 589 No H-bonds generated for 'chain 'B' and resid 587 through 589' Processing helix chain 'B' and resid 604 through 621 removed outlier: 3.537A pdb=" N ARG B 617 " --> pdb=" O MET B 613 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 625 No H-bonds generated for 'chain 'B' and resid 623 through 625' Processing helix chain 'B' and resid 633 through 642 Processing helix chain 'B' and resid 651 through 657 Processing helix chain 'B' and resid 669 through 673 Processing helix chain 'B' and resid 679 through 690 removed outlier: 3.561A pdb=" N LYS B 683 " --> pdb=" O ASP B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 703 through 707 removed outlier: 3.806A pdb=" N THR B 707 " --> pdb=" O TYR B 704 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 721 removed outlier: 3.500A pdb=" N GLN B 721 " --> pdb=" O LEU B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 751 removed outlier: 3.511A pdb=" N VAL B 747 " --> pdb=" O LYS B 743 " (cutoff:3.500A) Processing helix chain 'B' and resid 759 through 763 removed outlier: 3.632A pdb=" N VAL B 763 " --> pdb=" O CYS B 760 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 803 Processing helix chain 'B' and resid 805 through 807 No H-bonds generated for 'chain 'B' and resid 805 through 807' Processing helix chain 'B' and resid 817 through 831 removed outlier: 4.495A pdb=" N HIS B 821 " --> pdb=" O LYS B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 834 No H-bonds generated for 'chain 'B' and resid 832 through 834' Processing helix chain 'B' and resid 877 through 887 removed outlier: 3.626A pdb=" N VAL B 881 " --> pdb=" O ILE B 877 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N LEU B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 11 removed outlier: 4.522A pdb=" N VAL A 18 " --> pdb=" O GLU A 11 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ILE A 19 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 8.236A pdb=" N ALA A 64 " --> pdb=" O ILE A 19 " (cutoff:3.500A) removed outlier: 8.318A pdb=" N VAL A 21 " --> pdb=" O ALA A 64 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 136 Processing sheet with id=AA3, first strand: chain 'A' and resid 198 through 200 removed outlier: 6.587A pdb=" N LEU A 199 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR A 296 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE A 315 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS A 298 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS A 313 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 300 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR A 311 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 302 " --> pdb=" O TYR A 309 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLU A 214 " --> pdb=" O PHE A 247 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 198 through 200 removed outlier: 6.587A pdb=" N LEU A 199 " --> pdb=" O LEU A 303 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N THR A 296 " --> pdb=" O ILE A 315 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ILE A 315 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N LYS A 298 " --> pdb=" O CYS A 313 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N CYS A 313 " --> pdb=" O LYS A 298 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 300 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N TYR A 311 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL A 302 " --> pdb=" O TYR A 309 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 311 " --> pdb=" O CYS A 260 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 283 through 284 removed outlier: 3.572A pdb=" N ALA A 323 " --> pdb=" O VAL A 284 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 332 through 335 Processing sheet with id=AA7, first strand: chain 'A' and resid 405 through 408 removed outlier: 6.426A pdb=" N ARG A 406 " --> pdb=" O LEU A 439 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N PHE A 441 " --> pdb=" O ARG A 406 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N THR A 408 " --> pdb=" O PHE A 441 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N CYS A 459 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 647 through 650 removed outlier: 6.264A pdb=" N LEU A 628 " --> pdb=" O VAL A 666 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE A 665 " --> pdb=" O TRP A 699 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N PHE A 701 " --> pdb=" O ILE A 665 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N ILE A 667 " --> pdb=" O PHE A 701 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY A 599 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 776 through 779 removed outlier: 7.223A pdb=" N SER A 863 " --> pdb=" O LYS A 890 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ALA A 810 " --> pdb=" O PHE A 866 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N ILE A 868 " --> pdb=" O ALA A 810 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU A 812 " --> pdb=" O ILE A 868 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 18 through 23 removed outlier: 6.213A pdb=" N ILE B 19 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ALA B 64 " --> pdb=" O ILE B 19 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N VAL B 21 " --> pdb=" O ALA B 64 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 133 through 136 Processing sheet with id=AB3, first strand: chain 'B' and resid 198 through 200 removed outlier: 6.580A pdb=" N THR B 296 " --> pdb=" O ILE B 315 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE B 315 " --> pdb=" O THR B 296 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N LYS B 298 " --> pdb=" O CYS B 313 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N CYS B 313 " --> pdb=" O LYS B 298 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL B 300 " --> pdb=" O TYR B 311 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N TYR B 311 " --> pdb=" O VAL B 300 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 302 " --> pdb=" O TYR B 309 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N GLU B 214 " --> pdb=" O PHE B 247 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 283 through 284 removed outlier: 3.614A pdb=" N ALA B 323 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 332 through 335 Processing sheet with id=AB6, first strand: chain 'B' and resid 405 through 408 removed outlier: 6.407A pdb=" N ARG B 406 " --> pdb=" O LEU B 439 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE B 441 " --> pdb=" O ARG B 406 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B 408 " --> pdb=" O PHE B 441 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N CYS B 459 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 647 through 650 removed outlier: 6.259A pdb=" N LEU B 628 " --> pdb=" O VAL B 666 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ILE B 665 " --> pdb=" O TRP B 699 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE B 701 " --> pdb=" O ILE B 665 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ILE B 667 " --> pdb=" O PHE B 701 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 776 through 779 removed outlier: 7.074A pdb=" N SER B 863 " --> pdb=" O LYS B 890 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N SER B 839 " --> pdb=" O LEU B 851 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N SER B 853 " --> pdb=" O SER B 839 " (cutoff:3.500A) 600 hydrogen bonds defined for protein. 1689 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: 2.56 Time building geometry restraints manager: 1.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3402 1.33 - 1.45: 2449 1.45 - 1.57: 7645 1.57 - 1.69: 0 1.69 - 1.81: 122 Bond restraints: 13618 Sorted by residual: bond pdb=" N VAL B 836 " pdb=" CA VAL B 836 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.88e+00 bond pdb=" N LEU B 838 " pdb=" CA LEU B 838 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.23e-02 6.61e+03 7.60e+00 bond pdb=" N GLN A 706 " pdb=" CA GLN A 706 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.16e-02 7.43e+03 7.28e+00 bond pdb=" N SER B 13 " pdb=" CA SER B 13 " ideal model delta sigma weight residual 1.456 1.485 -0.029 1.18e-02 7.18e+03 6.09e+00 bond pdb=" N ASN B 264 " pdb=" CA ASN B 264 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.28e-02 6.10e+03 5.95e+00 ... (remaining 13613 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 17386 1.12 - 2.24: 819 2.24 - 3.36: 145 3.36 - 4.49: 20 4.49 - 5.61: 14 Bond angle restraints: 18384 Sorted by residual: angle pdb=" N SER B 13 " pdb=" CA SER B 13 " pdb=" C SER B 13 " ideal model delta sigma weight residual 112.72 108.26 4.46 1.14e+00 7.69e-01 1.53e+01 angle pdb=" N VAL A 21 " pdb=" CA VAL A 21 " pdb=" C VAL A 21 " ideal model delta sigma weight residual 112.83 109.36 3.47 9.90e-01 1.02e+00 1.23e+01 angle pdb=" CA ASP B 847 " pdb=" C ASP B 847 " pdb=" O ASP B 847 " ideal model delta sigma weight residual 122.63 118.32 4.31 1.29e+00 6.01e-01 1.12e+01 angle pdb=" N VAL B 21 " pdb=" CA VAL B 21 " pdb=" C VAL B 21 " ideal model delta sigma weight residual 112.83 109.53 3.30 9.90e-01 1.02e+00 1.11e+01 angle pdb=" N ARG A 590 " pdb=" CA ARG A 590 " pdb=" C ARG A 590 " ideal model delta sigma weight residual 112.89 108.86 4.03 1.24e+00 6.50e-01 1.05e+01 ... (remaining 18379 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 7715 17.77 - 35.54: 472 35.54 - 53.31: 101 53.31 - 71.08: 23 71.08 - 88.85: 11 Dihedral angle restraints: 8322 sinusoidal: 3490 harmonic: 4832 Sorted by residual: dihedral pdb=" CA ARG A 477 " pdb=" C ARG A 477 " pdb=" N GLU A 478 " pdb=" CA GLU A 478 " ideal model delta harmonic sigma weight residual 180.00 160.41 19.59 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA LEU A 125 " pdb=" C LEU A 125 " pdb=" N CYS A 126 " pdb=" CA CYS A 126 " ideal model delta harmonic sigma weight residual 180.00 161.64 18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" C ARG A 590 " pdb=" N ARG A 590 " pdb=" CA ARG A 590 " pdb=" CB ARG A 590 " ideal model delta harmonic sigma weight residual -122.60 -113.60 -9.00 0 2.50e+00 1.60e-01 1.30e+01 ... (remaining 8319 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1665 0.053 - 0.105: 293 0.105 - 0.158: 58 0.158 - 0.210: 1 0.210 - 0.263: 1 Chirality restraints: 2018 Sorted by residual: chirality pdb=" CA ARG A 590 " pdb=" N ARG A 590 " pdb=" C ARG A 590 " pdb=" CB ARG A 590 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA VAL B 836 " pdb=" N VAL B 836 " pdb=" C VAL B 836 " pdb=" CB VAL B 836 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.25e-01 chirality pdb=" CA ILE B 756 " pdb=" N ILE B 756 " pdb=" C ILE B 756 " pdb=" CB ILE B 756 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 ... (remaining 2015 not shown) Planarity restraints: 2362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 266 " 0.043 5.00e-02 4.00e+02 6.55e-02 6.86e+00 pdb=" N PRO A 267 " -0.113 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 11 " -0.012 2.00e-02 2.50e+03 2.44e-02 5.93e+00 pdb=" C GLU B 11 " 0.042 2.00e-02 2.50e+03 pdb=" O GLU B 11 " -0.016 2.00e-02 2.50e+03 pdb=" N PRO B 12 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 531 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO B 532 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 532 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 532 " 0.019 5.00e-02 4.00e+02 ... (remaining 2359 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 184 2.68 - 3.24: 12299 3.24 - 3.79: 20110 3.79 - 4.35: 29580 4.35 - 4.90: 48257 Nonbonded interactions: 110430 Sorted by model distance: nonbonded pdb=" OE2 GLU B 214 " pdb="MG MG B1002 " model vdw 2.126 2.170 nonbonded pdb=" OD2 ASP B 567 " pdb=" OH TYR B 804 " model vdw 2.225 3.040 nonbonded pdb=" OE1 GLU A 95 " pdb=" OG SER A 538 " model vdw 2.233 3.040 nonbonded pdb=" NH2 ARG B 732 " pdb=" OE2 GLU B 861 " model vdw 2.255 3.120 nonbonded pdb=" O LEU B 718 " pdb=" NH2 ARG B 724 " model vdw 2.258 3.120 ... (remaining 110425 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.710 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 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:7.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 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 : 0.003 0.039 13625 Z= 0.168 Angle : 0.569 5.607 18387 Z= 0.333 Chirality : 0.042 0.263 2018 Planarity : 0.004 0.065 2362 Dihedral : 12.711 88.853 5198 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.20), residues: 1638 helix: 0.09 (0.19), residues: 648 sheet: 1.03 (0.31), residues: 268 loop : 0.11 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 134 TYR 0.010 0.001 TYR A 234 PHE 0.023 0.001 PHE B 218 TRP 0.007 0.001 TRP A 898 HIS 0.004 0.001 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.00348 (13618) covalent geometry : angle 0.56889 (18384) hydrogen bonds : bond 0.24332 ( 597) hydrogen bonds : angle 7.10496 ( 1689) metal coordination : bond 0.01017 ( 7) metal coordination : angle 1.80519 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.8534 (ttp) cc_final: 0.8271 (ttp) REVERT: A 256 GLU cc_start: 0.7022 (mt-10) cc_final: 0.6782 (pt0) REVERT: A 720 ASP cc_start: 0.8087 (m-30) cc_final: 0.7844 (t0) REVERT: A 858 SER cc_start: 0.8497 (m) cc_final: 0.8152 (m) REVERT: B 229 ARG cc_start: 0.6787 (ptt90) cc_final: 0.6572 (ttp-110) REVERT: B 703 ASP cc_start: 0.8416 (t0) cc_final: 0.8158 (t70) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 0.7891 time to fit residues: 175.1638 Evaluate side-chains 156 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.7980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.0670 overall best weight: 1.1724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 HIS A 395 GLN ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS A 706 GLN B 69 HIS B 222 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.161328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.122137 restraints weight = 13751.424| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.31 r_work: 0.3060 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2920 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13625 Z= 0.180 Angle : 0.571 6.111 18387 Z= 0.299 Chirality : 0.044 0.152 2018 Planarity : 0.005 0.043 2362 Dihedral : 4.348 18.809 1824 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.42 % Allowed : 7.31 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.20), residues: 1638 helix: 0.96 (0.19), residues: 670 sheet: 0.80 (0.31), residues: 268 loop : 0.03 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 119 TYR 0.013 0.001 TYR B 309 PHE 0.019 0.002 PHE A 218 TRP 0.008 0.001 TRP A 413 HIS 0.005 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00433 (13618) covalent geometry : angle 0.56997 (18384) hydrogen bonds : bond 0.05590 ( 597) hydrogen bonds : angle 4.79440 ( 1689) metal coordination : bond 0.00937 ( 7) metal coordination : angle 2.74052 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 172 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7813 (mt-10) REVERT: A 38 GLN cc_start: 0.7941 (OUTLIER) cc_final: 0.7649 (tt0) REVERT: A 337 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8202 (tptt) REVERT: A 617 ARG cc_start: 0.7048 (ttt-90) cc_final: 0.6786 (ttp-110) REVERT: A 649 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7318 (mp0) REVERT: A 720 ASP cc_start: 0.8462 (m-30) cc_final: 0.7881 (t0) REVERT: A 830 MET cc_start: 0.7363 (tpp) cc_final: 0.7060 (tpt) REVERT: A 858 SER cc_start: 0.8361 (m) cc_final: 0.8020 (m) REVERT: B 229 ARG cc_start: 0.6844 (ptt90) cc_final: 0.6473 (ttp-110) REVERT: B 686 SER cc_start: 0.8231 (t) cc_final: 0.7958 (p) REVERT: B 807 LYS cc_start: 0.8174 (pttt) cc_final: 0.7812 (ptpt) REVERT: B 840 ASP cc_start: 0.7793 (p0) cc_final: 0.7561 (p0) outliers start: 21 outliers final: 9 residues processed: 186 average time/residue: 0.7203 time to fit residues: 143.5636 Evaluate side-chains 168 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 155 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 337 LYS Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 861 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 34 optimal weight: 0.6980 chunk 100 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 156 optimal weight: 0.0970 chunk 98 optimal weight: 10.0000 chunk 131 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 150 optimal weight: 3.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS A 663 GLN A 706 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.161516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.123597 restraints weight = 13898.844| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 2.21 r_work: 0.3043 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13625 Z= 0.119 Angle : 0.490 5.080 18387 Z= 0.256 Chirality : 0.042 0.154 2018 Planarity : 0.004 0.033 2362 Dihedral : 4.091 17.739 1824 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.10 % Allowed : 9.54 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.06 (0.20), residues: 1638 helix: 1.43 (0.20), residues: 674 sheet: 0.64 (0.31), residues: 270 loop : 0.13 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 119 TYR 0.013 0.001 TYR A 704 PHE 0.014 0.001 PHE B 218 TRP 0.007 0.001 TRP A 413 HIS 0.003 0.001 HIS A 420 Details of bonding type rmsd covalent geometry : bond 0.00274 (13618) covalent geometry : angle 0.48956 (18384) hydrogen bonds : bond 0.04321 ( 597) hydrogen bonds : angle 4.43493 ( 1689) metal coordination : bond 0.00959 ( 7) metal coordination : angle 2.40231 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7730 (mt-10) REVERT: A 38 GLN cc_start: 0.7948 (OUTLIER) cc_final: 0.7680 (tt0) REVERT: A 617 ARG cc_start: 0.7125 (ttt-90) cc_final: 0.6818 (ttp-110) REVERT: A 649 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: A 720 ASP cc_start: 0.8383 (m-30) cc_final: 0.7909 (t0) REVERT: A 858 SER cc_start: 0.8385 (m) cc_final: 0.7990 (m) REVERT: B 75 LEU cc_start: 0.8576 (mt) cc_final: 0.8370 (mp) REVERT: B 229 ARG cc_start: 0.7016 (ptt90) cc_final: 0.6552 (ttp-110) REVERT: B 273 LYS cc_start: 0.6966 (tppp) cc_final: 0.6626 (tppp) REVERT: B 345 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7605 (pm20) REVERT: B 807 LYS cc_start: 0.8074 (pttt) cc_final: 0.7647 (ptpt) REVERT: B 808 ASP cc_start: 0.8756 (m-30) cc_final: 0.8402 (m-30) REVERT: B 840 ASP cc_start: 0.7886 (p0) cc_final: 0.7681 (p0) outliers start: 31 outliers final: 5 residues processed: 200 average time/residue: 0.6704 time to fit residues: 144.6718 Evaluate side-chains 176 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 861 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 120 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 159 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 661 HIS A 706 GLN B 580 GLN B 663 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.155827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.115064 restraints weight = 13981.736| |-----------------------------------------------------------------------------| r_work (start): 0.3227 rms_B_bonded: 2.19 r_work: 0.2982 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.121 13625 Z= 0.457 Angle : 0.793 10.033 18387 Z= 0.409 Chirality : 0.057 0.197 2018 Planarity : 0.006 0.075 2362 Dihedral : 5.009 24.520 1824 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.65 % Allowed : 10.22 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.20), residues: 1638 helix: 0.79 (0.19), residues: 654 sheet: 0.30 (0.31), residues: 272 loop : -0.28 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 135 TYR 0.022 0.003 TYR B 234 PHE 0.021 0.003 PHE A 705 TRP 0.014 0.003 TRP B 332 HIS 0.007 0.002 HIS B 420 Details of bonding type rmsd covalent geometry : bond 0.01143 (13618) covalent geometry : angle 0.79193 (18384) hydrogen bonds : bond 0.06817 ( 597) hydrogen bonds : angle 4.86570 ( 1689) metal coordination : bond 0.00712 ( 7) metal coordination : angle 2.69935 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 166 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: A 617 ARG cc_start: 0.7346 (ttt-90) cc_final: 0.6967 (ttp-110) REVERT: A 643 ARG cc_start: 0.7818 (mmm-85) cc_final: 0.7614 (mmm-85) REVERT: A 649 GLU cc_start: 0.8176 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: A 690 ARG cc_start: 0.7523 (mpt180) cc_final: 0.7313 (mmt180) REVERT: A 720 ASP cc_start: 0.8572 (m-30) cc_final: 0.8028 (t0) REVERT: A 778 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7601 (mtt-85) REVERT: A 885 LEU cc_start: 0.8545 (OUTLIER) cc_final: 0.8250 (tp) REVERT: B 11 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.8368 (pt0) REVERT: B 229 ARG cc_start: 0.7051 (ptt90) cc_final: 0.6685 (ttp-110) REVERT: B 482 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7114 (tm-30) REVERT: B 562 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.7739 (mmm160) REVERT: B 642 ASP cc_start: 0.7173 (m-30) cc_final: 0.6922 (m-30) REVERT: B 807 LYS cc_start: 0.8595 (pttt) cc_final: 0.8187 (ptpt) REVERT: B 882 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8565 (mp) outliers start: 54 outliers final: 19 residues processed: 204 average time/residue: 0.6879 time to fit residues: 151.0364 Evaluate side-chains 188 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 778 ARG Chi-restraints excluded: chain A residue 877 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 562 ARG Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 858 SER Chi-restraints excluded: chain B residue 881 VAL Chi-restraints excluded: chain B residue 882 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 104 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 121 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 452 GLN ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS A 706 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.160710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.120906 restraints weight = 13846.555| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.34 r_work: 0.3077 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13625 Z= 0.132 Angle : 0.514 5.342 18387 Z= 0.269 Chirality : 0.042 0.155 2018 Planarity : 0.004 0.038 2362 Dihedral : 4.344 18.947 1824 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.23 % Allowed : 12.45 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.20), residues: 1638 helix: 1.27 (0.20), residues: 674 sheet: 0.26 (0.31), residues: 268 loop : -0.11 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 119 TYR 0.016 0.001 TYR A 704 PHE 0.011 0.001 PHE A 434 TRP 0.009 0.001 TRP A 413 HIS 0.004 0.001 HIS A 848 Details of bonding type rmsd covalent geometry : bond 0.00310 (13618) covalent geometry : angle 0.51224 (18384) hydrogen bonds : bond 0.04217 ( 597) hydrogen bonds : angle 4.39365 ( 1689) metal coordination : bond 0.01201 ( 7) metal coordination : angle 2.91213 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 177 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 400 VAL cc_start: 0.7685 (OUTLIER) cc_final: 0.7481 (t) REVERT: A 421 ARG cc_start: 0.7316 (mmp80) cc_final: 0.7102 (tpp-160) REVERT: A 613 MET cc_start: 0.8703 (mtm) cc_final: 0.8485 (mtt) REVERT: A 649 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7442 (mp0) REVERT: A 720 ASP cc_start: 0.8462 (m-30) cc_final: 0.7974 (t0) REVERT: B 229 ARG cc_start: 0.7163 (ptt90) cc_final: 0.6760 (ttp-110) REVERT: B 479 GLN cc_start: 0.7858 (tp40) cc_final: 0.7369 (mp10) REVERT: B 482 GLU cc_start: 0.7605 (mm-30) cc_final: 0.7043 (tm-30) REVERT: B 564 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8331 (tp) REVERT: B 642 ASP cc_start: 0.7192 (m-30) cc_final: 0.6952 (m-30) REVERT: B 737 ILE cc_start: 0.8370 (OUTLIER) cc_final: 0.8100 (mt) REVERT: B 807 LYS cc_start: 0.8339 (pttt) cc_final: 0.7834 (ptpt) outliers start: 33 outliers final: 14 residues processed: 196 average time/residue: 0.6990 time to fit residues: 147.3623 Evaluate side-chains 188 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 273 LYS Chi-restraints excluded: chain B residue 477 ARG Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 564 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 858 SER Chi-restraints excluded: chain B residue 861 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 92 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 119 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS A 706 GLN B 318 ASN B 420 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.157742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.117489 restraints weight = 13830.613| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 2.16 r_work: 0.3029 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 13625 Z= 0.220 Angle : 0.579 6.272 18387 Z= 0.300 Chirality : 0.045 0.153 2018 Planarity : 0.005 0.038 2362 Dihedral : 4.476 19.567 1824 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.50 % Allowed : 13.33 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.20), residues: 1638 helix: 1.34 (0.20), residues: 660 sheet: 0.09 (0.32), residues: 256 loop : -0.17 (0.22), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 291 TYR 0.014 0.001 TYR B 234 PHE 0.012 0.002 PHE A 585 TRP 0.009 0.002 TRP B 332 HIS 0.004 0.001 HIS A 848 Details of bonding type rmsd covalent geometry : bond 0.00545 (13618) covalent geometry : angle 0.57883 (18384) hydrogen bonds : bond 0.04948 ( 597) hydrogen bonds : angle 4.43614 ( 1689) metal coordination : bond 0.00563 ( 7) metal coordination : angle 2.17286 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.585 Fit side-chains revert: symmetry clash REVERT: A 400 VAL cc_start: 0.7773 (OUTLIER) cc_final: 0.7483 (t) REVERT: A 421 ARG cc_start: 0.7379 (mmp80) cc_final: 0.7135 (tpp-160) REVERT: A 613 MET cc_start: 0.8816 (mtm) cc_final: 0.8603 (mtt) REVERT: A 649 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7428 (mp0) REVERT: A 720 ASP cc_start: 0.8505 (m-30) cc_final: 0.7993 (t0) REVERT: B 101 ARG cc_start: 0.8720 (mmm160) cc_final: 0.8507 (mtt-85) REVERT: B 229 ARG cc_start: 0.7091 (ptt90) cc_final: 0.6803 (ttp-110) REVERT: B 482 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7071 (tm-30) REVERT: B 642 ASP cc_start: 0.7213 (m-30) cc_final: 0.6956 (m-30) REVERT: B 807 LYS cc_start: 0.8429 (pttt) cc_final: 0.7914 (ptpt) outliers start: 37 outliers final: 18 residues processed: 193 average time/residue: 0.6992 time to fit residues: 145.4888 Evaluate side-chains 186 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 166 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 477 ARG Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 858 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 149 optimal weight: 3.9990 chunk 163 optimal weight: 0.5980 chunk 101 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 122 optimal weight: 0.9990 chunk 136 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 88 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS A 706 GLN B 420 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.160321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.120045 restraints weight = 13785.916| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.20 r_work: 0.3052 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 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 0.045 13625 Z= 0.139 Angle : 0.514 5.214 18387 Z= 0.268 Chirality : 0.042 0.157 2018 Planarity : 0.004 0.034 2362 Dihedral : 4.264 18.881 1824 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.10 % Allowed : 13.94 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.21), residues: 1638 helix: 1.54 (0.20), residues: 662 sheet: 0.18 (0.33), residues: 254 loop : -0.14 (0.23), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 119 TYR 0.017 0.001 TYR A 704 PHE 0.012 0.001 PHE A 705 TRP 0.008 0.001 TRP A 413 HIS 0.005 0.001 HIS A 848 Details of bonding type rmsd covalent geometry : bond 0.00332 (13618) covalent geometry : angle 0.51345 (18384) hydrogen bonds : bond 0.04222 ( 597) hydrogen bonds : angle 4.31542 ( 1689) metal coordination : bond 0.00846 ( 7) metal coordination : angle 2.34341 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 421 ARG cc_start: 0.7307 (mmp80) cc_final: 0.7041 (tpp-160) REVERT: A 613 MET cc_start: 0.8680 (mtm) cc_final: 0.8479 (mtt) REVERT: A 649 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7323 (mp0) REVERT: A 690 ARG cc_start: 0.7268 (mpt180) cc_final: 0.7067 (mmt180) REVERT: A 720 ASP cc_start: 0.8424 (m-30) cc_final: 0.7883 (t0) REVERT: B 101 ARG cc_start: 0.8639 (mmm160) cc_final: 0.8411 (mtt-85) REVERT: B 229 ARG cc_start: 0.7045 (ptt90) cc_final: 0.6721 (ttp-110) REVERT: B 275 GLU cc_start: 0.7656 (mt-10) cc_final: 0.7423 (mt-10) REVERT: B 397 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8306 (mp) REVERT: B 479 GLN cc_start: 0.7877 (tp40) cc_final: 0.7307 (mp10) REVERT: B 482 GLU cc_start: 0.7449 (mm-30) cc_final: 0.6803 (tm-30) REVERT: B 642 ASP cc_start: 0.7157 (m-30) cc_final: 0.6890 (m-30) REVERT: B 737 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7958 (mt) REVERT: B 807 LYS cc_start: 0.8245 (pttt) cc_final: 0.7725 (ptpt) outliers start: 31 outliers final: 16 residues processed: 194 average time/residue: 0.7136 time to fit residues: 149.1417 Evaluate side-chains 191 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 172 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 477 ARG Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 737 ILE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 72 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 115 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 88 optimal weight: 0.0870 chunk 111 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 127 optimal weight: 0.0970 chunk 89 optimal weight: 1.9990 overall best weight: 0.5156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 GLN ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS A 706 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.161699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.121858 restraints weight = 13756.280| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.18 r_work: 0.3073 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13625 Z= 0.112 Angle : 0.494 5.786 18387 Z= 0.256 Chirality : 0.041 0.156 2018 Planarity : 0.004 0.032 2362 Dihedral : 4.089 19.083 1824 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.56 % Allowed : 14.82 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.02 (0.21), residues: 1638 helix: 1.71 (0.20), residues: 662 sheet: 0.24 (0.32), residues: 270 loop : -0.04 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 643 TYR 0.013 0.001 TYR A 704 PHE 0.012 0.001 PHE A 705 TRP 0.008 0.001 TRP A 413 HIS 0.005 0.001 HIS A 848 Details of bonding type rmsd covalent geometry : bond 0.00260 (13618) covalent geometry : angle 0.49343 (18384) hydrogen bonds : bond 0.03860 ( 597) hydrogen bonds : angle 4.21861 ( 1689) metal coordination : bond 0.00936 ( 7) metal coordination : angle 2.15907 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 175 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 421 ARG cc_start: 0.7283 (mmp80) cc_final: 0.7014 (tpp-160) REVERT: A 649 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: A 720 ASP cc_start: 0.8351 (m-30) cc_final: 0.7871 (t0) REVERT: B 101 ARG cc_start: 0.8636 (mmm160) cc_final: 0.8408 (mtt-85) REVERT: B 229 ARG cc_start: 0.7194 (ptt90) cc_final: 0.6789 (ttp-110) REVERT: B 275 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7416 (mt-10) REVERT: B 345 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7592 (pm20) REVERT: B 397 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8318 (mp) REVERT: B 479 GLN cc_start: 0.7856 (tp40) cc_final: 0.7286 (mp10) REVERT: B 482 GLU cc_start: 0.7408 (mm-30) cc_final: 0.6711 (tm-30) REVERT: B 613 MET cc_start: 0.8392 (mtm) cc_final: 0.8174 (mtm) REVERT: B 642 ASP cc_start: 0.7181 (m-30) cc_final: 0.6946 (m-30) REVERT: B 690 ARG cc_start: 0.7187 (ptp90) cc_final: 0.6961 (mtm-85) REVERT: B 807 LYS cc_start: 0.8186 (pttt) cc_final: 0.7695 (ptpt) REVERT: B 808 ASP cc_start: 0.8762 (m-30) cc_final: 0.8420 (m-30) outliers start: 23 outliers final: 14 residues processed: 190 average time/residue: 0.6900 time to fit residues: 141.0415 Evaluate side-chains 188 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 171 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 477 ARG Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 92 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 157 optimal weight: 3.9990 chunk 81 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS A 706 GLN B 420 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.158518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.118642 restraints weight = 13853.558| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.16 r_work: 0.3036 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 13625 Z= 0.198 Angle : 0.562 8.607 18387 Z= 0.290 Chirality : 0.044 0.154 2018 Planarity : 0.004 0.035 2362 Dihedral : 4.322 18.898 1824 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.03 % Allowed : 14.34 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.21), residues: 1638 helix: 1.55 (0.20), residues: 660 sheet: 0.14 (0.32), residues: 254 loop : -0.11 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 291 TYR 0.013 0.001 TYR B 234 PHE 0.013 0.002 PHE B 435 TRP 0.008 0.001 TRP B 332 HIS 0.005 0.001 HIS A 848 Details of bonding type rmsd covalent geometry : bond 0.00489 (13618) covalent geometry : angle 0.56133 (18384) hydrogen bonds : bond 0.04695 ( 597) hydrogen bonds : angle 4.35517 ( 1689) metal coordination : bond 0.00428 ( 7) metal coordination : angle 1.81301 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 175 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 313 CYS cc_start: 0.8545 (t) cc_final: 0.8001 (m) REVERT: A 649 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7412 (mp0) REVERT: A 720 ASP cc_start: 0.8446 (m-30) cc_final: 0.7917 (t0) REVERT: A 807 LYS cc_start: 0.8481 (ptmm) cc_final: 0.8189 (ptpp) REVERT: B 73 MET cc_start: 0.8996 (OUTLIER) cc_final: 0.8726 (ttm) REVERT: B 101 ARG cc_start: 0.8682 (mmm160) cc_final: 0.8458 (mtt-85) REVERT: B 229 ARG cc_start: 0.7255 (ptt90) cc_final: 0.6789 (ttp-110) REVERT: B 273 LYS cc_start: 0.7182 (tppt) cc_final: 0.6652 (tppp) REVERT: B 275 GLU cc_start: 0.7705 (mt-10) cc_final: 0.7473 (mt-10) REVERT: B 313 CYS cc_start: 0.8529 (OUTLIER) cc_final: 0.7971 (m) REVERT: B 345 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7781 (pm20) REVERT: B 397 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8381 (mp) REVERT: B 479 GLN cc_start: 0.7883 (tp40) cc_final: 0.7331 (mp10) REVERT: B 482 GLU cc_start: 0.7526 (mm-30) cc_final: 0.6895 (tm-30) REVERT: B 642 ASP cc_start: 0.7152 (m-30) cc_final: 0.6885 (m-30) REVERT: B 690 ARG cc_start: 0.7264 (ptp90) cc_final: 0.7014 (mtm-85) REVERT: B 807 LYS cc_start: 0.8322 (pttt) cc_final: 0.7824 (ptpt) outliers start: 30 outliers final: 19 residues processed: 196 average time/residue: 0.6960 time to fit residues: 146.9428 Evaluate side-chains 199 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 488 THR Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain B residue 10 VAL Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 477 ARG Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 858 SER Chi-restraints excluded: chain B residue 881 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 39 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 3 optimal weight: 0.7980 chunk 154 optimal weight: 0.4980 chunk 19 optimal weight: 0.0970 chunk 31 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 152 optimal weight: 0.9980 chunk 155 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS A 706 GLN B 420 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.161306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.121779 restraints weight = 13816.680| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.37 r_work: 0.3083 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 13625 Z= 0.107 Angle : 0.486 5.620 18387 Z= 0.254 Chirality : 0.041 0.158 2018 Planarity : 0.004 0.033 2362 Dihedral : 4.041 19.548 1824 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.08 % Allowed : 15.49 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.01 (0.21), residues: 1638 helix: 1.72 (0.20), residues: 662 sheet: 0.09 (0.32), residues: 260 loop : 0.00 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 119 TYR 0.014 0.001 TYR A 704 PHE 0.012 0.001 PHE B 435 TRP 0.009 0.001 TRP A 413 HIS 0.006 0.001 HIS A 848 Details of bonding type rmsd covalent geometry : bond 0.00248 (13618) covalent geometry : angle 0.48561 (18384) hydrogen bonds : bond 0.03796 ( 597) hydrogen bonds : angle 4.22847 ( 1689) metal coordination : bond 0.00951 ( 7) metal coordination : angle 2.17931 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3276 Ramachandran restraints generated. 1638 Oldfield, 0 Emsley, 1638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 177 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 313 CYS cc_start: 0.8489 (t) cc_final: 0.7935 (m) REVERT: A 336 ASP cc_start: 0.8403 (m-30) cc_final: 0.8114 (t0) REVERT: A 649 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7431 (mp0) REVERT: A 720 ASP cc_start: 0.8409 (m-30) cc_final: 0.7953 (t0) REVERT: B 73 MET cc_start: 0.8945 (OUTLIER) cc_final: 0.8740 (ttm) REVERT: B 229 ARG cc_start: 0.7261 (ptt90) cc_final: 0.6800 (ttp-110) REVERT: B 273 LYS cc_start: 0.7139 (tppt) cc_final: 0.6603 (tppp) REVERT: B 275 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7479 (mt-10) REVERT: B 313 CYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8034 (m) REVERT: B 345 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7782 (pm20) REVERT: B 397 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8453 (mp) REVERT: B 479 GLN cc_start: 0.7819 (tp40) cc_final: 0.7353 (mp10) REVERT: B 482 GLU cc_start: 0.7531 (mm-30) cc_final: 0.6907 (tm-30) REVERT: B 618 ASN cc_start: 0.7371 (t0) cc_final: 0.7053 (t0) REVERT: B 642 ASP cc_start: 0.7224 (m-30) cc_final: 0.7000 (m-30) REVERT: B 690 ARG cc_start: 0.7308 (ptp90) cc_final: 0.7068 (mtp180) REVERT: B 807 LYS cc_start: 0.8311 (pttt) cc_final: 0.7850 (ptpt) REVERT: B 808 ASP cc_start: 0.8814 (m-30) cc_final: 0.8492 (m-30) outliers start: 16 outliers final: 9 residues processed: 185 average time/residue: 0.7362 time to fit residues: 146.2478 Evaluate side-chains 184 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 313 CYS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 477 ARG Chi-restraints excluded: chain B residue 711 ASP Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 135 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 80 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 11 optimal weight: 0.1980 chunk 150 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN A 479 GLN A 618 ASN ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS A 706 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.161754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.121813 restraints weight = 13759.493| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.20 r_work: 0.3068 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13625 Z= 0.121 Angle : 0.498 9.146 18387 Z= 0.257 Chirality : 0.042 0.157 2018 Planarity : 0.004 0.033 2362 Dihedral : 4.011 19.032 1824 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.49 % Allowed : 15.09 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % 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: 1.06 (0.21), residues: 1638 helix: 1.76 (0.20), residues: 662 sheet: 0.14 (0.32), residues: 260 loop : 0.01 (0.23), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 689 TYR 0.014 0.001 TYR A 629 PHE 0.012 0.001 PHE B 435 TRP 0.007 0.001 TRP A 413 HIS 0.005 0.001 HIS A 848 Details of bonding type rmsd covalent geometry : bond 0.00289 (13618) covalent geometry : angle 0.49704 (18384) hydrogen bonds : bond 0.03880 ( 597) hydrogen bonds : angle 4.19462 ( 1689) metal coordination : bond 0.00710 ( 7) metal coordination : angle 1.87472 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4901.33 seconds wall clock time: 84 minutes 5.06 seconds (5045.06 seconds total)