Starting phenix.real_space_refine on Thu Sep 26 14:31:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zel_14690/09_2024/7zel_14690.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zel_14690/09_2024/7zel_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zel_14690/09_2024/7zel_14690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zel_14690/09_2024/7zel_14690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zel_14690/09_2024/7zel_14690.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zel_14690/09_2024/7zel_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-5461/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: 8.58, per 1000 atoms: 0.64 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: 3.19 Conformation dependent library (CDL) restraints added in 1.7 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: 1.71 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: 5.21 Time building geometry restraints manager: 3.78 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: 0.00 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: 9.460 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.970 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:12.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.330 ------------------------------------------------------------------------------- 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 13618 Z= 0.225 Angle : 0.569 5.607 18384 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 1.431 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: 1.6677 time to fit residues: 371.8844 Evaluate side-chains 156 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.604 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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 13618 Z= 0.194 Angle : 0.532 5.778 18384 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 *********************** 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 fitting. rotamer outliers: 21 poor density : 179 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7380 (mt-10) REVERT: A 38 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7670 (tt0) REVERT: A 337 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7986 (tptt) REVERT: A 720 ASP cc_start: 0.8084 (m-30) cc_final: 0.7865 (t0) REVERT: A 858 SER cc_start: 0.8409 (m) cc_final: 0.8005 (m) REVERT: B 807 LYS cc_start: 0.8192 (pttt) cc_final: 0.7856 (ptpt) outliers start: 21 outliers final: 6 residues processed: 191 average time/residue: 1.5624 time to fit residues: 320.5944 Evaluate side-chains 165 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 156 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 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 82 optimal weight: 2.9990 chunk 46 optimal weight: 0.0370 chunk 123 optimal weight: 2.9990 chunk 101 optimal weight: 0.0050 chunk 41 optimal weight: 0.0870 chunk 149 optimal weight: 6.9990 chunk 161 optimal weight: 4.9990 chunk 132 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 119 optimal weight: 0.2980 overall best weight: 0.2050 ------------------------------------------------------------------------------- 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 A 661 HIS B 663 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13618 Z= 0.126 Angle : 0.458 5.043 18384 Z= 0.240 Chirality : 0.041 0.156 2018 Planarity : 0.004 0.035 2362 Dihedral : 3.899 17.811 1824 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.62 % Allowed : 9.20 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.30 (0.21), residues: 1638 helix: 1.61 (0.20), residues: 674 sheet: 0.77 (0.31), residues: 274 loop : 0.28 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.003 0.001 HIS A 420 PHE 0.013 0.001 PHE B 218 TYR 0.015 0.001 TYR A 704 ARG 0.008 0.000 ARG B 229 *********************** 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 204 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 180 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7275 (mt-10) REVERT: A 649 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7066 (mp0) REVERT: A 858 SER cc_start: 0.8424 (m) cc_final: 0.8010 (m) REVERT: B 275 GLU cc_start: 0.7560 (mt-10) cc_final: 0.7284 (mt-10) REVERT: B 479 GLN cc_start: 0.7743 (tp40) cc_final: 0.7436 (mp10) REVERT: B 808 ASP cc_start: 0.8357 (m-30) cc_final: 0.8052 (m-30) outliers start: 24 outliers final: 4 residues processed: 196 average time/residue: 1.4721 time to fit residues: 311.7275 Evaluate side-chains 170 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 164 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 617 ARG 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 147 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 158 optimal weight: 8.9990 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN A 661 HIS A 706 GLN B 580 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.091 13618 Z= 0.503 Angle : 0.668 7.430 18384 Z= 0.345 Chirality : 0.050 0.151 2018 Planarity : 0.005 0.049 2362 Dihedral : 4.617 21.072 1824 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.25 % Allowed : 9.54 % Favored : 87.21 % 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: 0.77 (0.20), residues: 1638 helix: 1.24 (0.20), residues: 660 sheet: 0.54 (0.31), residues: 268 loop : -0.09 (0.22), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 332 HIS 0.006 0.002 HIS B 709 PHE 0.016 0.002 PHE B 320 TYR 0.017 0.002 TYR B 234 ARG 0.011 0.001 ARG A 135 *********************** 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 fitting. rotamer outliers: 48 poor density : 171 time to evaluate : 1.601 Fit side-chains revert: symmetry clash REVERT: A 649 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7030 (mp0) REVERT: A 807 LYS cc_start: 0.8767 (ptpp) cc_final: 0.8385 (ptmt) REVERT: A 858 SER cc_start: 0.8384 (m) cc_final: 0.8020 (m) REVERT: A 885 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8363 (tp) REVERT: B 345 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7835 (pm20) REVERT: B 748 ILE cc_start: 0.8301 (OUTLIER) cc_final: 0.8095 (mm) REVERT: B 807 LYS cc_start: 0.8460 (pttt) cc_final: 0.8008 (ptpt) outliers start: 48 outliers final: 17 residues processed: 203 average time/residue: 1.5280 time to fit residues: 335.4165 Evaluate side-chains 188 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 167 time to evaluate : 1.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 340 CYS Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 426 LEU Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 720 ASP Chi-restraints excluded: chain A residue 877 ILE 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 516 CYS Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 748 ILE Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 858 SER Chi-restraints excluded: chain B residue 881 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 0.5980 chunk 89 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 135 optimal weight: 1.9990 chunk 109 optimal weight: 10.0000 chunk 0 optimal weight: 1.9990 chunk 80 optimal weight: 0.4980 chunk 142 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 13618 Z= 0.183 Angle : 0.507 6.270 18384 Z= 0.266 Chirality : 0.042 0.154 2018 Planarity : 0.004 0.036 2362 Dihedral : 4.201 17.813 1824 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.10 % Allowed : 12.11 % Favored : 85.79 % 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: 1.01 (0.21), residues: 1638 helix: 1.53 (0.20), residues: 674 sheet: 0.42 (0.32), residues: 270 loop : 0.03 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.004 0.001 HIS A 848 PHE 0.012 0.001 PHE A 223 TYR 0.017 0.001 TYR A 704 ARG 0.011 0.000 ARG A 119 *********************** 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 213 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 182 time to evaluate : 1.408 Fit side-chains revert: symmetry clash REVERT: A 613 MET cc_start: 0.8789 (mtm) cc_final: 0.8565 (mtt) REVERT: A 649 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.7124 (mp0) REVERT: A 858 SER cc_start: 0.8391 (m) cc_final: 0.7960 (m) REVERT: B 479 GLN cc_start: 0.7723 (tp40) cc_final: 0.7431 (mp10) REVERT: B 643 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7601 (mtp-110) REVERT: B 807 LYS cc_start: 0.8310 (pttt) cc_final: 0.7902 (ptpt) REVERT: B 808 ASP cc_start: 0.8506 (m-30) cc_final: 0.8181 (m-30) outliers start: 31 outliers final: 11 residues processed: 200 average time/residue: 1.4460 time to fit residues: 312.6795 Evaluate side-chains 188 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 176 time to evaluate : 1.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 617 ARG Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 836 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 2.9990 chunk 142 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 158 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN A 661 HIS A 706 GLN B 318 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 13618 Z= 0.372 Angle : 0.590 7.062 18384 Z= 0.306 Chirality : 0.046 0.152 2018 Planarity : 0.005 0.039 2362 Dihedral : 4.424 18.774 1824 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.50 % Allowed : 12.86 % Favored : 84.64 % 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: 0.81 (0.20), residues: 1638 helix: 1.35 (0.20), residues: 672 sheet: 0.35 (0.32), residues: 266 loop : -0.07 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 332 HIS 0.007 0.001 HIS A 848 PHE 0.016 0.002 PHE A 705 TYR 0.014 0.002 TYR B 234 ARG 0.008 0.001 ARG B 229 *********************** 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 209 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 172 time to evaluate : 1.585 Fit side-chains revert: symmetry clash REVERT: A 649 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7119 (mp0) REVERT: A 689 ARG cc_start: 0.7396 (mtm-85) cc_final: 0.7127 (mtm-85) REVERT: A 711 ASP cc_start: 0.7651 (m-30) cc_final: 0.7390 (m-30) REVERT: A 858 SER cc_start: 0.8434 (m) cc_final: 0.8059 (m) REVERT: B 275 GLU cc_start: 0.7528 (mt-10) cc_final: 0.7287 (mt-10) REVERT: B 643 ARG cc_start: 0.7888 (mtp85) cc_final: 0.7613 (mtp-110) REVERT: B 807 LYS cc_start: 0.8407 (pttt) cc_final: 0.7946 (ptpt) outliers start: 37 outliers final: 17 residues processed: 196 average time/residue: 1.4571 time to fit residues: 308.6485 Evaluate side-chains 185 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 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 152 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 115 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 158 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 96 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 GLN A 479 GLN A 661 HIS A 706 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13618 Z= 0.201 Angle : 0.505 6.320 18384 Z= 0.263 Chirality : 0.042 0.155 2018 Planarity : 0.004 0.033 2362 Dihedral : 4.171 17.287 1824 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.83 % Allowed : 13.94 % Favored : 84.24 % 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: 1.01 (0.21), residues: 1638 helix: 1.60 (0.20), residues: 674 sheet: 0.29 (0.32), residues: 270 loop : 0.02 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.005 0.001 HIS A 848 PHE 0.012 0.001 PHE A 705 TYR 0.015 0.001 TYR A 704 ARG 0.009 0.000 ARG B 229 *********************** 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 196 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 169 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: A 613 MET cc_start: 0.8782 (mtm) cc_final: 0.8525 (mtt) REVERT: A 649 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: A 689 ARG cc_start: 0.7375 (mtm-85) cc_final: 0.7113 (mtm-85) REVERT: A 711 ASP cc_start: 0.7698 (m-30) cc_final: 0.7444 (m-30) REVERT: A 858 SER cc_start: 0.8416 (m) cc_final: 0.7982 (m) REVERT: B 275 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7286 (mt-10) REVERT: B 397 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8554 (mp) REVERT: B 643 ARG cc_start: 0.7891 (mtp85) cc_final: 0.7628 (mtp-110) REVERT: B 807 LYS cc_start: 0.8316 (pttt) cc_final: 0.7913 (ptpt) REVERT: B 808 ASP cc_start: 0.8488 (m-30) cc_final: 0.8168 (m-30) outliers start: 27 outliers final: 12 residues processed: 187 average time/residue: 1.5250 time to fit residues: 309.4666 Evaluate side-chains 181 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 167 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 408 THR Chi-restraints excluded: chain B residue 477 ARG Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 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 97 optimal weight: 7.9990 chunk 63 optimal weight: 3.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 107 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 479 GLN A 661 HIS A 706 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13618 Z= 0.332 Angle : 0.572 8.293 18384 Z= 0.295 Chirality : 0.045 0.154 2018 Planarity : 0.004 0.046 2362 Dihedral : 4.345 17.800 1824 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.23 % Allowed : 13.94 % Favored : 83.83 % 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: 0.85 (0.20), residues: 1638 helix: 1.46 (0.20), residues: 672 sheet: 0.21 (0.33), residues: 254 loop : -0.08 (0.22), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 332 HIS 0.005 0.001 HIS A 848 PHE 0.018 0.002 PHE A 705 TYR 0.013 0.001 TYR B 234 ARG 0.011 0.001 ARG B 229 *********************** 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 203 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 170 time to evaluate : 1.538 Fit side-chains revert: symmetry clash REVERT: A 613 MET cc_start: 0.8851 (mtm) cc_final: 0.8613 (mtt) REVERT: A 649 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7142 (mp0) REVERT: A 711 ASP cc_start: 0.7727 (m-30) cc_final: 0.7472 (m-30) REVERT: A 858 SER cc_start: 0.8443 (m) cc_final: 0.8048 (m) REVERT: A 885 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8352 (tp) REVERT: B 275 GLU cc_start: 0.7506 (mt-10) cc_final: 0.7274 (mt-10) REVERT: B 479 GLN cc_start: 0.7667 (tp40) cc_final: 0.7423 (mp10) REVERT: B 643 ARG cc_start: 0.7902 (mtp85) cc_final: 0.7641 (mtp-110) REVERT: B 690 ARG cc_start: 0.7321 (ptp90) cc_final: 0.7082 (mtp180) REVERT: B 807 LYS cc_start: 0.8384 (pttt) cc_final: 0.7934 (ptpt) outliers start: 33 outliers final: 20 residues processed: 192 average time/residue: 1.4438 time to fit residues: 300.0966 Evaluate side-chains 190 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 168 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 776 THR Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 13 SER Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 124 ARG 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 488 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 612 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 2.9990 chunk 151 optimal weight: 0.4980 chunk 138 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 64 optimal weight: 0.4980 chunk 115 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 133 optimal weight: 2.9990 chunk 139 optimal weight: 0.9980 chunk 146 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13618 Z= 0.183 Angle : 0.498 6.765 18384 Z= 0.260 Chirality : 0.042 0.157 2018 Planarity : 0.004 0.038 2362 Dihedral : 4.115 17.153 1824 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.42 % Allowed : 15.02 % Favored : 83.56 % 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: 1.03 (0.21), residues: 1638 helix: 1.64 (0.20), residues: 674 sheet: 0.23 (0.32), residues: 270 loop : 0.02 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 413 HIS 0.004 0.001 HIS A 848 PHE 0.014 0.001 PHE B 435 TYR 0.012 0.001 TYR A 704 ARG 0.010 0.000 ARG B 229 *********************** 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 195 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 174 time to evaluate : 1.509 Fit side-chains revert: symmetry clash REVERT: A 613 MET cc_start: 0.8764 (mtm) cc_final: 0.8541 (mtt) REVERT: A 649 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7168 (mp0) REVERT: A 711 ASP cc_start: 0.7666 (m-30) cc_final: 0.7391 (m-30) REVERT: A 858 SER cc_start: 0.8421 (m) cc_final: 0.7986 (m) REVERT: B 124 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7417 (ttp80) REVERT: B 275 GLU cc_start: 0.7494 (mt-10) cc_final: 0.7282 (mt-10) REVERT: B 479 GLN cc_start: 0.7665 (tp40) cc_final: 0.7404 (mp10) REVERT: B 643 ARG cc_start: 0.7898 (mtp85) cc_final: 0.7643 (mtp-110) REVERT: B 807 LYS cc_start: 0.8305 (pttt) cc_final: 0.7907 (ptpt) REVERT: B 808 ASP cc_start: 0.8456 (m-30) cc_final: 0.8145 (m-30) outliers start: 21 outliers final: 14 residues processed: 186 average time/residue: 1.5255 time to fit residues: 306.2396 Evaluate side-chains 181 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 165 time to evaluate : 1.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 418 SER Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 124 ARG 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 776 THR Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 881 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 1.9990 chunk 155 optimal weight: 0.0020 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 108 optimal weight: 0.0970 chunk 163 optimal weight: 0.3980 chunk 150 optimal weight: 0.0010 chunk 130 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 100 optimal weight: 4.9990 chunk 79 optimal weight: 0.5980 overall best weight: 0.2192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 GLN A 661 HIS A 706 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13618 Z= 0.133 Angle : 0.472 9.278 18384 Z= 0.244 Chirality : 0.041 0.161 2018 Planarity : 0.004 0.051 2362 Dihedral : 3.875 16.687 1824 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.95 % Allowed : 15.43 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.21), residues: 1638 helix: 1.82 (0.20), residues: 674 sheet: 0.32 (0.32), residues: 270 loop : 0.12 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 413 HIS 0.005 0.000 HIS A 848 PHE 0.015 0.001 PHE B 435 TYR 0.017 0.001 TYR A 704 ARG 0.013 0.000 ARG B 229 ********************** 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 188 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 174 time to evaluate : 1.514 Fit side-chains revert: symmetry clash REVERT: A 613 MET cc_start: 0.8688 (mtm) cc_final: 0.8457 (mtp) REVERT: A 649 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7170 (mp0) REVERT: A 711 ASP cc_start: 0.7641 (m-30) cc_final: 0.7359 (m-30) REVERT: A 858 SER cc_start: 0.8436 (m) cc_final: 0.8134 (m) REVERT: B 124 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7423 (ttp80) REVERT: B 275 GLU cc_start: 0.7490 (mt-10) cc_final: 0.7266 (mt-10) REVERT: B 479 GLN cc_start: 0.7651 (tp40) cc_final: 0.7382 (mp10) REVERT: B 618 ASN cc_start: 0.7418 (t0) cc_final: 0.7091 (t0) REVERT: B 643 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7651 (mtp-110) REVERT: B 807 LYS cc_start: 0.8323 (pttt) cc_final: 0.8073 (ptpt) REVERT: B 808 ASP cc_start: 0.8322 (m-30) cc_final: 0.7966 (m-30) outliers start: 14 outliers final: 8 residues processed: 183 average time/residue: 1.4470 time to fit residues: 286.2009 Evaluate side-chains 176 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 166 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 124 ARG 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 836 VAL Chi-restraints excluded: chain B residue 881 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 2.9990 chunk 138 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 119 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 GLN A 479 GLN A 661 HIS A 706 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.159462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.119356 restraints weight = 13826.148| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.22 r_work: 0.3047 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 13618 Z= 0.301 Angle : 0.551 6.702 18384 Z= 0.285 Chirality : 0.044 0.155 2018 Planarity : 0.004 0.048 2362 Dihedral : 4.202 16.966 1824 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.22 % Allowed : 15.02 % Favored : 83.76 % 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: 1.02 (0.21), residues: 1638 helix: 1.63 (0.20), residues: 672 sheet: 0.20 (0.32), residues: 262 loop : 0.05 (0.23), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 332 HIS 0.005 0.001 HIS A 848 PHE 0.011 0.002 PHE A 896 TYR 0.011 0.001 TYR B 582 ARG 0.012 0.001 ARG B 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5431.15 seconds wall clock time: 95 minutes 37.27 seconds (5737.27 seconds total)