Starting phenix.real_space_refine on Thu Jul 31 09:51:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zel_14690/07_2025/7zel_14690.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zel_14690/07_2025/7zel_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zel_14690/07_2025/7zel_14690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zel_14690/07_2025/7zel_14690.map" model { file = "/net/cci-nas-00/data/ceres_data/7zel_14690/07_2025/7zel_14690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zel_14690/07_2025/7zel_14690.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 8.00, per 1000 atoms: 0.60 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: 2.86 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.67 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: 4.56 Time building geometry restraints manager: 3.45 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: 0.06 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: 1.370 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: 0.500 Check model and map are aligned: 0.090 Set scattering table: 0.140 Process input model: 33.810 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.440 ------------------------------------------------------------------------------- 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 : 4.89 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (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 TRP 0.007 0.001 TRP A 898 HIS 0.004 0.001 HIS B 420 PHE 0.023 0.001 PHE B 218 TYR 0.010 0.001 TYR A 234 ARG 0.006 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.24332 ( 597) hydrogen bonds : angle 7.10496 ( 1689) metal coordination : bond 0.01017 ( 7) metal coordination : angle 1.80519 ( 3) covalent geometry : bond 0.00348 (13618) covalent geometry : angle 0.56889 (18384) *********************** 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 : 1.519 Fit side-chains revert: symmetry clash REVERT: A 73 MET cc_start: 0.8533 (ttp) cc_final: 0.8271 (ttp) REVERT: A 256 GLU cc_start: 0.7021 (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: 0.8151 (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: 1.6875 time to fit residues: 375.7189 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 : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 138 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 0.0030 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 128 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 overall best weight: 0.6392 ------------------------------------------------------------------------------- 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 663 GLN A 706 GLN B 69 HIS B 222 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.163196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.123894 restraints weight = 13677.191| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.28 r_work: 0.3100 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13625 Z= 0.133 Angle : 0.533 5.778 18387 Z= 0.281 Chirality : 0.043 0.155 2018 Planarity : 0.004 0.040 2362 Dihedral : 4.194 17.940 1824 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.42 % Allowed : 7.04 % Favored : 91.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.20), residues: 1638 helix: 1.11 (0.20), residues: 672 sheet: 0.80 (0.31), residues: 272 loop : 0.15 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.003 0.001 HIS B 420 PHE 0.017 0.001 PHE B 218 TYR 0.014 0.001 TYR B 309 ARG 0.009 0.001 ARG A 119 Details of bonding type rmsd hydrogen bonds : bond 0.04963 ( 597) hydrogen bonds : angle 4.73512 ( 1689) metal coordination : bond 0.01110 ( 7) metal coordination : angle 2.75597 ( 3) covalent geometry : bond 0.00302 (13618) covalent geometry : angle 0.53223 (18384) *********************** 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 200 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 1.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7802 (mt-10) REVERT: A 38 GLN cc_start: 0.7915 (OUTLIER) cc_final: 0.7626 (tt0) REVERT: A 256 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6693 (pt0) REVERT: A 337 LYS cc_start: 0.8371 (OUTLIER) cc_final: 0.8090 (tptt) REVERT: A 617 ARG cc_start: 0.7048 (ttt-90) cc_final: 0.6799 (ttp-110) REVERT: A 720 ASP cc_start: 0.8448 (m-30) cc_final: 0.7870 (t0) REVERT: A 830 MET cc_start: 0.7315 (tpp) cc_final: 0.7013 (tpt) REVERT: A 858 SER cc_start: 0.8373 (m) cc_final: 0.8009 (m) REVERT: B 229 ARG cc_start: 0.6857 (ptt90) cc_final: 0.6461 (ttp-110) REVERT: B 291 ARG cc_start: 0.6941 (pmm-80) cc_final: 0.6578 (mmp80) REVERT: B 345 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7607 (pm20) REVERT: B 686 SER cc_start: 0.8222 (t) cc_final: 0.8012 (p) REVERT: B 807 LYS cc_start: 0.8068 (pttt) cc_final: 0.7645 (ptpt) outliers start: 21 outliers final: 6 residues processed: 191 average time/residue: 1.7884 time to fit residues: 367.0585 Evaluate side-chains 168 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 158 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 706 GLN Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 345 GLU Chi-restraints excluded: chain B residue 477 ARG Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 776 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 45 optimal weight: 0.7980 chunk 155 optimal weight: 0.0980 chunk 68 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 138 optimal weight: 0.5980 chunk 25 optimal weight: 4.9990 chunk 149 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 432 GLN ** A 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 661 HIS A 706 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 = 0.3754 r_free = 0.3754 target = 0.160620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.122391 restraints weight = 13865.735| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.21 r_work: 0.3036 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13625 Z= 0.145 Angle : 0.512 5.051 18387 Z= 0.267 Chirality : 0.043 0.154 2018 Planarity : 0.004 0.034 2362 Dihedral : 4.154 17.663 1824 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.17 % Allowed : 9.07 % Favored : 88.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.20), residues: 1638 helix: 1.41 (0.20), residues: 674 sheet: 0.76 (0.31), residues: 266 loop : 0.12 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 332 HIS 0.004 0.001 HIS A 420 PHE 0.015 0.001 PHE A 218 TYR 0.012 0.001 TYR A 704 ARG 0.005 0.000 ARG A 119 Details of bonding type rmsd hydrogen bonds : bond 0.04614 ( 597) hydrogen bonds : angle 4.47523 ( 1689) metal coordination : bond 0.00718 ( 7) metal coordination : angle 2.19019 ( 3) covalent geometry : bond 0.00348 (13618) covalent geometry : angle 0.51175 (18384) *********************** 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 202 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 170 time to evaluate : 1.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7748 (mt-10) REVERT: A 38 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7688 (tt0) REVERT: A 617 ARG cc_start: 0.7139 (ttt-90) cc_final: 0.6793 (ttp-110) REVERT: A 649 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: A 720 ASP cc_start: 0.8336 (m-30) cc_final: 0.7886 (t0) REVERT: A 858 SER cc_start: 0.8370 (m) cc_final: 0.7975 (m) REVERT: A 885 LEU cc_start: 0.8330 (OUTLIER) cc_final: 0.8108 (tp) REVERT: B 229 ARG cc_start: 0.7027 (ptt90) cc_final: 0.6563 (ttp-110) REVERT: B 273 LYS cc_start: 0.7045 (tppp) cc_final: 0.6687 (tppp) REVERT: B 345 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7745 (pm20) REVERT: B 479 GLN cc_start: 0.7925 (tp40) cc_final: 0.7318 (mp10) REVERT: B 711 ASP cc_start: 0.6603 (t0) cc_final: 0.6187 (t0) REVERT: B 807 LYS cc_start: 0.8137 (pttt) cc_final: 0.7797 (ptpt) REVERT: B 808 ASP cc_start: 0.8747 (m-30) cc_final: 0.8382 (m-30) REVERT: B 840 ASP cc_start: 0.7906 (p0) cc_final: 0.7702 (p0) outliers start: 32 outliers final: 12 residues processed: 193 average time/residue: 1.5410 time to fit residues: 320.7229 Evaluate side-chains 184 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 1.409 ------------------------------------------------------------------------------- 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 340 CYS Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 345 GLU 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 594 GLU Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 14 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 133 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 102 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 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 = 0.161279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.122857 restraints weight = 13763.728| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.08 r_work: 0.3050 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13625 Z= 0.119 Angle : 0.484 5.089 18387 Z= 0.252 Chirality : 0.042 0.157 2018 Planarity : 0.004 0.030 2362 Dihedral : 4.023 17.709 1824 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.84 % Allowed : 10.22 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.21), residues: 1638 helix: 1.68 (0.20), residues: 674 sheet: 0.64 (0.32), residues: 270 loop : 0.16 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.005 0.001 HIS A 848 PHE 0.021 0.001 PHE B 218 TYR 0.011 0.001 TYR B 234 ARG 0.006 0.000 ARG A 643 Details of bonding type rmsd hydrogen bonds : bond 0.04040 ( 597) hydrogen bonds : angle 4.28670 ( 1689) metal coordination : bond 0.00770 ( 7) metal coordination : angle 2.01424 ( 3) covalent geometry : bond 0.00279 (13618) covalent geometry : angle 0.48298 (18384) *********************** 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 219 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 177 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7661 (tt0) REVERT: A 613 MET cc_start: 0.8631 (mtm) cc_final: 0.8419 (mtt) REVERT: A 617 ARG cc_start: 0.7210 (ttt-90) cc_final: 0.6867 (ttp-110) REVERT: A 649 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7242 (mp0) REVERT: A 720 ASP cc_start: 0.8309 (m-30) cc_final: 0.7870 (t0) REVERT: A 858 SER cc_start: 0.8357 (m) cc_final: 0.7959 (m) REVERT: B 91 GLN cc_start: 0.8317 (tt0) cc_final: 0.8102 (pt0) REVERT: B 229 ARG cc_start: 0.6948 (ptt90) cc_final: 0.6536 (ttp-110) REVERT: B 273 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6714 (tppp) REVERT: B 275 GLU cc_start: 0.7716 (mt-10) cc_final: 0.7455 (mt-10) REVERT: B 337 LYS cc_start: 0.8339 (mmmt) cc_final: 0.8127 (mmmt) REVERT: B 482 GLU cc_start: 0.7401 (mm-30) cc_final: 0.6795 (tm-30) REVERT: B 590 ARG cc_start: 0.8158 (ttt-90) cc_final: 0.7866 (ttm-80) REVERT: B 711 ASP cc_start: 0.6546 (t0) cc_final: 0.6166 (t0) REVERT: B 807 LYS cc_start: 0.8123 (pttt) cc_final: 0.7695 (ptpt) REVERT: B 808 ASP cc_start: 0.8760 (m-30) cc_final: 0.8373 (m-30) outliers start: 42 outliers final: 12 residues processed: 204 average time/residue: 1.4603 time to fit residues: 321.4226 Evaluate side-chains 187 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 172 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 748 ILE 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 408 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 881 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 137 optimal weight: 5.9990 chunk 148 optimal weight: 0.3980 chunk 118 optimal weight: 0.7980 chunk 101 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 47 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 162 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 overall best weight: 0.2980 ------------------------------------------------------------------------------- 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 A 661 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.163152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.125017 restraints weight = 13874.635| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.19 r_work: 0.3079 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 13625 Z= 0.095 Angle : 0.462 5.403 18387 Z= 0.239 Chirality : 0.041 0.157 2018 Planarity : 0.004 0.035 2362 Dihedral : 3.832 17.238 1824 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.83 % Allowed : 11.43 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.21), residues: 1638 helix: 1.88 (0.20), residues: 674 sheet: 0.63 (0.32), residues: 270 loop : 0.22 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.005 0.001 HIS A 848 PHE 0.011 0.001 PHE A 223 TYR 0.010 0.001 TYR A 704 ARG 0.010 0.000 ARG A 119 Details of bonding type rmsd hydrogen bonds : bond 0.03583 ( 597) hydrogen bonds : angle 4.16781 ( 1689) metal coordination : bond 0.00900 ( 7) metal coordination : angle 1.96502 ( 3) covalent geometry : bond 0.00210 (13618) covalent geometry : angle 0.46136 (18384) *********************** 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 211 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 617 ARG cc_start: 0.7192 (ttt-90) cc_final: 0.6824 (ttp-110) REVERT: A 649 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7225 (mp0) REVERT: A 689 ARG cc_start: 0.7138 (mtm-85) cc_final: 0.6891 (mtm-85) REVERT: A 720 ASP cc_start: 0.8309 (m-30) cc_final: 0.7827 (t0) REVERT: A 858 SER cc_start: 0.8449 (m) cc_final: 0.8153 (m) REVERT: B 47 MET cc_start: 0.9051 (mmp) cc_final: 0.8729 (mmp) REVERT: B 91 GLN cc_start: 0.8306 (tt0) cc_final: 0.8099 (pt0) REVERT: B 229 ARG cc_start: 0.6965 (ptt90) cc_final: 0.6545 (ttp-110) REVERT: B 275 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7438 (mt-10) REVERT: B 345 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7253 (mp0) REVERT: B 397 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8288 (mp) REVERT: B 479 GLN cc_start: 0.7858 (tp40) cc_final: 0.7237 (mp10) REVERT: B 482 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6726 (tm-30) REVERT: B 516 CYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8512 (m) REVERT: B 590 ARG cc_start: 0.8153 (ttt-90) cc_final: 0.7872 (ttm-80) REVERT: B 618 ASN cc_start: 0.7443 (t0) cc_final: 0.7137 (t0) REVERT: B 643 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7423 (mtp-110) REVERT: B 690 ARG cc_start: 0.7256 (ptp90) cc_final: 0.7039 (mtm-85) REVERT: B 711 ASP cc_start: 0.6452 (t0) cc_final: 0.6162 (t0) REVERT: B 807 LYS cc_start: 0.8125 (pttt) cc_final: 0.7689 (ptpt) REVERT: B 808 ASP cc_start: 0.8695 (m-30) cc_final: 0.8226 (m-30) outliers start: 27 outliers final: 12 residues processed: 200 average time/residue: 1.4791 time to fit residues: 320.0637 Evaluate side-chains 185 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 169 time to evaluate : 1.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 517 LEU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 102 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 516 CYS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 689 ARG 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 120 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.160212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.121792 restraints weight = 14005.249| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 2.30 r_work: 0.3037 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13625 Z= 0.157 Angle : 0.510 5.312 18387 Z= 0.264 Chirality : 0.043 0.155 2018 Planarity : 0.004 0.031 2362 Dihedral : 4.020 16.602 1824 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.03 % Allowed : 11.84 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.21), residues: 1638 helix: 1.76 (0.20), residues: 674 sheet: 0.57 (0.32), residues: 270 loop : 0.13 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 332 HIS 0.006 0.001 HIS A 848 PHE 0.010 0.001 PHE A 585 TYR 0.011 0.001 TYR B 234 ARG 0.008 0.001 ARG A 119 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 597) hydrogen bonds : angle 4.21166 ( 1689) metal coordination : bond 0.00263 ( 7) metal coordination : angle 1.39168 ( 3) covalent geometry : bond 0.00384 (13618) covalent geometry : angle 0.51022 (18384) *********************** 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 207 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 1.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: A 73 MET cc_start: 0.8855 (ttp) cc_final: 0.8613 (ttp) REVERT: A 617 ARG cc_start: 0.7193 (ttt-90) cc_final: 0.6767 (ttp-110) REVERT: A 649 GLU cc_start: 0.7975 (OUTLIER) cc_final: 0.7270 (mp0) REVERT: A 720 ASP cc_start: 0.8317 (m-30) cc_final: 0.7873 (t0) REVERT: A 858 SER cc_start: 0.8359 (m) cc_final: 0.7960 (m) REVERT: B 13 SER cc_start: 0.7427 (m) cc_final: 0.6996 (t) REVERT: B 91 GLN cc_start: 0.8331 (tt0) cc_final: 0.8103 (pt0) REVERT: B 229 ARG cc_start: 0.7121 (ptt90) cc_final: 0.6704 (ttp-110) REVERT: B 275 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7438 (mt-10) REVERT: B 397 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8309 (mp) REVERT: B 482 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6735 (tm-30) REVERT: B 590 ARG cc_start: 0.8150 (ttt-90) cc_final: 0.7866 (ttm-80) REVERT: B 643 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7371 (mtp-110) REVERT: B 690 ARG cc_start: 0.7163 (ptp90) cc_final: 0.6889 (mtp180) REVERT: B 711 ASP cc_start: 0.6546 (t0) cc_final: 0.6217 (t0) REVERT: B 807 LYS cc_start: 0.8157 (pttt) cc_final: 0.7722 (ptpt) REVERT: B 808 ASP cc_start: 0.8738 (m-30) cc_final: 0.8247 (m-30) outliers start: 30 outliers final: 14 residues processed: 197 average time/residue: 1.6898 time to fit residues: 360.6508 Evaluate side-chains 191 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 748 ILE 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 397 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 689 ARG Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 881 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 22 optimal weight: 8.9990 chunk 156 optimal weight: 0.0370 chunk 43 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 64 optimal weight: 0.0050 chunk 86 optimal weight: 0.0980 chunk 74 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 overall best weight: 0.3872 ------------------------------------------------------------------------------- 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 661 HIS A 706 GLN B 318 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.162452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.124254 restraints weight = 13811.344| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 2.14 r_work: 0.3072 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13625 Z= 0.098 Angle : 0.461 5.916 18387 Z= 0.239 Chirality : 0.041 0.156 2018 Planarity : 0.004 0.030 2362 Dihedral : 3.829 17.067 1824 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.89 % Allowed : 12.52 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.21), residues: 1638 helix: 1.95 (0.20), residues: 674 sheet: 0.51 (0.32), residues: 270 loop : 0.19 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.005 0.001 HIS A 848 PHE 0.013 0.001 PHE A 218 TYR 0.010 0.001 TYR B 486 ARG 0.008 0.000 ARG A 119 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 597) hydrogen bonds : angle 4.09937 ( 1689) metal coordination : bond 0.00805 ( 7) metal coordination : angle 1.80991 ( 3) covalent geometry : bond 0.00223 (13618) covalent geometry : angle 0.46089 (18384) *********************** 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 207 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 179 time to evaluate : 2.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7586 (tt0) REVERT: A 421 ARG cc_start: 0.7286 (tpp-160) cc_final: 0.7038 (mmt180) REVERT: A 617 ARG cc_start: 0.7210 (ttt-90) cc_final: 0.6801 (ttp-110) REVERT: A 649 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7274 (mp0) REVERT: A 720 ASP cc_start: 0.8290 (m-30) cc_final: 0.7850 (t0) REVERT: A 858 SER cc_start: 0.8453 (m) cc_final: 0.8155 (m) REVERT: B 13 SER cc_start: 0.7121 (m) cc_final: 0.6729 (t) REVERT: B 229 ARG cc_start: 0.7177 (ptt90) cc_final: 0.6792 (ttp-110) REVERT: B 273 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6697 (tppp) REVERT: B 275 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7443 (mt-10) REVERT: B 397 LEU cc_start: 0.8554 (OUTLIER) cc_final: 0.8289 (mp) REVERT: B 479 GLN cc_start: 0.7848 (tp40) cc_final: 0.7332 (mp10) REVERT: B 482 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6672 (tm-30) REVERT: B 590 ARG cc_start: 0.8158 (ttt-90) cc_final: 0.7886 (ttm-80) REVERT: B 643 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7408 (mtp-110) REVERT: B 807 LYS cc_start: 0.8143 (pttt) cc_final: 0.7682 (ptpt) REVERT: B 808 ASP cc_start: 0.8678 (m-30) cc_final: 0.8215 (m-30) outliers start: 28 outliers final: 13 residues processed: 193 average time/residue: 1.7581 time to fit residues: 367.8698 Evaluate side-chains 195 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 178 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 73 MET Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 273 LYS 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 675 THR Chi-restraints excluded: chain B residue 689 ARG 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 43 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 125 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 111 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 33 optimal weight: 0.0170 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 661 HIS A 706 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.161789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.123860 restraints weight = 13865.858| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.17 r_work: 0.3050 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13625 Z= 0.111 Angle : 0.478 8.885 18387 Z= 0.245 Chirality : 0.041 0.157 2018 Planarity : 0.004 0.030 2362 Dihedral : 3.822 16.402 1824 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.83 % Allowed : 12.79 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.21), residues: 1638 helix: 1.95 (0.20), residues: 674 sheet: 0.52 (0.32), residues: 270 loop : 0.19 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 332 HIS 0.005 0.001 HIS A 848 PHE 0.010 0.001 PHE B 435 TYR 0.009 0.001 TYR B 486 ARG 0.006 0.000 ARG A 643 Details of bonding type rmsd hydrogen bonds : bond 0.03709 ( 597) hydrogen bonds : angle 4.09320 ( 1689) metal coordination : bond 0.00522 ( 7) metal coordination : angle 1.38803 ( 3) covalent geometry : bond 0.00262 (13618) covalent geometry : angle 0.47732 (18384) *********************** 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 208 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 181 time to evaluate : 2.000 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7924 (OUTLIER) cc_final: 0.7595 (tt0) REVERT: A 617 ARG cc_start: 0.7241 (ttt-90) cc_final: 0.6809 (ttp-110) REVERT: A 649 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7285 (mp0) REVERT: A 720 ASP cc_start: 0.8311 (m-30) cc_final: 0.7866 (t0) REVERT: A 858 SER cc_start: 0.8395 (m) cc_final: 0.8091 (m) REVERT: B 13 SER cc_start: 0.7313 (m) cc_final: 0.6921 (t) REVERT: B 101 ARG cc_start: 0.8559 (mmm160) cc_final: 0.8323 (mtt-85) REVERT: B 229 ARG cc_start: 0.7179 (ptt90) cc_final: 0.6765 (ttp-110) REVERT: B 273 LYS cc_start: 0.6940 (OUTLIER) cc_final: 0.6706 (tppp) REVERT: B 275 GLU cc_start: 0.7658 (mt-10) cc_final: 0.7442 (mt-10) REVERT: B 345 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7665 (pm20) REVERT: B 397 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8320 (mp) REVERT: B 482 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6681 (tm-30) REVERT: B 590 ARG cc_start: 0.8136 (ttt-90) cc_final: 0.7882 (ttm-80) REVERT: B 618 ASN cc_start: 0.7283 (t0) cc_final: 0.7014 (t0) REVERT: B 643 ARG cc_start: 0.7735 (mtp85) cc_final: 0.7343 (mtp-110) REVERT: B 645 ILE cc_start: 0.8255 (OUTLIER) cc_final: 0.8051 (pt) REVERT: B 781 LYS cc_start: 0.7809 (pttt) cc_final: 0.7563 (pttm) REVERT: B 807 LYS cc_start: 0.8153 (pttt) cc_final: 0.7679 (ptpt) REVERT: B 808 ASP cc_start: 0.8688 (m-30) cc_final: 0.8239 (m-30) outliers start: 27 outliers final: 11 residues processed: 198 average time/residue: 1.4670 time to fit residues: 317.5792 Evaluate side-chains 192 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 175 time to evaluate : 1.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 748 ILE 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 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 516 CYS Chi-restraints excluded: chain B residue 645 ILE Chi-restraints excluded: chain B residue 675 THR 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 30 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 148 optimal weight: 0.1980 chunk 140 optimal weight: 1.9990 chunk 62 optimal weight: 0.0050 chunk 22 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 99 optimal weight: 0.0870 chunk 153 optimal weight: 0.9980 overall best weight: 0.6574 ------------------------------------------------------------------------------- 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 706 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.163184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.123316 restraints weight = 13818.291| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.16 r_work: 0.3106 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13625 Z= 0.118 Angle : 0.484 6.746 18387 Z= 0.249 Chirality : 0.042 0.156 2018 Planarity : 0.004 0.030 2362 Dihedral : 3.835 16.577 1824 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.62 % Allowed : 13.46 % Favored : 84.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.21), residues: 1638 helix: 1.94 (0.20), residues: 674 sheet: 0.49 (0.32), residues: 270 loop : 0.16 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 332 HIS 0.005 0.001 HIS A 848 PHE 0.009 0.001 PHE A 585 TYR 0.011 0.001 TYR A 629 ARG 0.005 0.000 ARG A 689 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 597) hydrogen bonds : angle 4.09656 ( 1689) metal coordination : bond 0.00494 ( 7) metal coordination : angle 1.45740 ( 3) covalent geometry : bond 0.00281 (13618) covalent geometry : angle 0.48405 (18384) *********************** 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 199 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 1.602 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7590 (tt0) REVERT: A 336 ASP cc_start: 0.8287 (m-30) cc_final: 0.7948 (t0) REVERT: A 617 ARG cc_start: 0.7258 (ttt-90) cc_final: 0.6831 (ttp-110) REVERT: A 649 GLU cc_start: 0.8000 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: A 689 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6951 (mtm-85) REVERT: A 720 ASP cc_start: 0.8340 (m-30) cc_final: 0.7895 (t0) REVERT: A 807 LYS cc_start: 0.8439 (ptpp) cc_final: 0.8182 (ptmm) REVERT: A 858 SER cc_start: 0.8449 (m) cc_final: 0.8163 (m) REVERT: B 13 SER cc_start: 0.7417 (m) cc_final: 0.7018 (t) REVERT: B 101 ARG cc_start: 0.8624 (mmm160) cc_final: 0.8348 (mtt-85) REVERT: B 229 ARG cc_start: 0.7229 (ptt90) cc_final: 0.6806 (ttp-110) REVERT: B 273 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6715 (tppp) REVERT: B 275 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7459 (mt-10) REVERT: B 345 GLU cc_start: 0.7978 (OUTLIER) cc_final: 0.7724 (pm20) REVERT: B 397 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8313 (mp) REVERT: B 479 GLN cc_start: 0.7638 (tp40) cc_final: 0.7244 (mp10) REVERT: B 482 GLU cc_start: 0.7412 (mm-30) cc_final: 0.6755 (tm-30) REVERT: B 590 ARG cc_start: 0.8160 (ttt-90) cc_final: 0.7902 (ttm-80) REVERT: B 618 ASN cc_start: 0.7306 (t0) cc_final: 0.7030 (t0) REVERT: B 643 ARG cc_start: 0.7692 (mtp85) cc_final: 0.7313 (mtp-110) REVERT: B 807 LYS cc_start: 0.8204 (pttt) cc_final: 0.7740 (ptpt) REVERT: B 808 ASP cc_start: 0.8671 (m-30) cc_final: 0.8225 (m-30) outliers start: 24 outliers final: 11 residues processed: 191 average time/residue: 1.4727 time to fit residues: 304.0884 Evaluate side-chains 191 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 174 time to evaluate : 1.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 689 ARG Chi-restraints excluded: chain A residue 748 ILE 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 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 516 CYS Chi-restraints excluded: chain B residue 675 THR 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 154 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 102 optimal weight: 0.0570 chunk 28 optimal weight: 0.9990 chunk 143 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 HIS A 706 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.162103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.122217 restraints weight = 13721.133| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.11 r_work: 0.3102 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2289 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= 0.123 Angle : 0.493 8.900 18387 Z= 0.253 Chirality : 0.042 0.156 2018 Planarity : 0.004 0.030 2362 Dihedral : 3.848 16.338 1824 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 1.42 % Allowed : 14.21 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.21), residues: 1638 helix: 1.91 (0.20), residues: 674 sheet: 0.46 (0.31), residues: 270 loop : 0.16 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 332 HIS 0.005 0.001 HIS A 848 PHE 0.009 0.001 PHE A 585 TYR 0.009 0.001 TYR B 234 ARG 0.006 0.000 ARG A 689 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 597) hydrogen bonds : angle 4.11618 ( 1689) metal coordination : bond 0.00470 ( 7) metal coordination : angle 1.39987 ( 3) covalent geometry : bond 0.00295 (13618) covalent geometry : angle 0.49302 (18384) ********************** 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 199 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 1.608 Fit side-chains revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7862 (OUTLIER) cc_final: 0.7536 (tt0) REVERT: A 313 CYS cc_start: 0.8485 (t) cc_final: 0.7759 (m) REVERT: A 336 ASP cc_start: 0.8291 (m-30) cc_final: 0.7962 (t0) REVERT: A 617 ARG cc_start: 0.7174 (ttt-90) cc_final: 0.6685 (ttp-110) REVERT: A 649 GLU cc_start: 0.7924 (OUTLIER) cc_final: 0.7247 (mp0) REVERT: A 689 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.6854 (mtm-85) REVERT: A 720 ASP cc_start: 0.8298 (m-30) cc_final: 0.7841 (t0) REVERT: A 778 ARG cc_start: 0.7719 (mtt-85) cc_final: 0.7400 (mmt-90) REVERT: A 858 SER cc_start: 0.8381 (m) cc_final: 0.8091 (m) REVERT: B 13 SER cc_start: 0.7572 (m) cc_final: 0.7144 (t) REVERT: B 101 ARG cc_start: 0.8587 (mmm160) cc_final: 0.8297 (mtt-85) REVERT: B 229 ARG cc_start: 0.7265 (ptt90) cc_final: 0.6807 (ttp-110) REVERT: B 273 LYS cc_start: 0.6916 (OUTLIER) cc_final: 0.6643 (tppp) REVERT: B 275 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7330 (mt-10) REVERT: B 345 GLU cc_start: 0.7850 (OUTLIER) cc_final: 0.7606 (pm20) REVERT: B 397 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8222 (mp) REVERT: B 479 GLN cc_start: 0.7645 (tp40) cc_final: 0.7221 (mp10) REVERT: B 482 GLU cc_start: 0.7330 (mm-30) cc_final: 0.6652 (tm-30) REVERT: B 590 ARG cc_start: 0.8108 (ttt-90) cc_final: 0.7828 (ttm-80) REVERT: B 618 ASN cc_start: 0.7370 (t0) cc_final: 0.7064 (t0) REVERT: B 643 ARG cc_start: 0.7635 (mtp85) cc_final: 0.7272 (mtp-110) REVERT: B 781 LYS cc_start: 0.7811 (pttt) cc_final: 0.7588 (pttm) REVERT: B 807 LYS cc_start: 0.8122 (pttt) cc_final: 0.7631 (ptpt) REVERT: B 808 ASP cc_start: 0.8646 (m-30) cc_final: 0.8186 (m-30) outliers start: 21 outliers final: 10 residues processed: 193 average time/residue: 1.5159 time to fit residues: 315.9364 Evaluate side-chains 188 residues out of total 1478 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 1.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 689 ARG Chi-restraints excluded: chain A residue 748 ILE 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 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 516 CYS 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 52 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 159 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 661 HIS A 706 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.161545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.121247 restraints weight = 13857.127| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.20 r_work: 0.3072 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 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 : 0.004 0.049 13625 Z= 0.152 Angle : 0.519 8.043 18387 Z= 0.267 Chirality : 0.043 0.153 2018 Planarity : 0.004 0.030 2362 Dihedral : 3.998 16.416 1824 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 1.29 % Allowed : 14.34 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.21), residues: 1638 helix: 1.91 (0.20), residues: 662 sheet: 0.45 (0.31), residues: 272 loop : 0.07 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 332 HIS 0.007 0.001 HIS A 848 PHE 0.016 0.001 PHE B 435 TYR 0.011 0.001 TYR A 582 ARG 0.006 0.001 ARG A 689 Details of bonding type rmsd hydrogen bonds : bond 0.04164 ( 597) hydrogen bonds : angle 4.18295 ( 1689) metal coordination : bond 0.00267 ( 7) metal coordination : angle 1.27427 ( 3) covalent geometry : bond 0.00371 (13618) covalent geometry : angle 0.51915 (18384) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11231.53 seconds wall clock time: 197 minutes 51.30 seconds (11871.30 seconds total)