Starting phenix.real_space_refine on Mon Apr 8 11:30:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zel_14690/04_2024/7zel_14690.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zel_14690/04_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_14690/04_2024/7zel_14690.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zel_14690/04_2024/7zel_14690.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zel_14690/04_2024/7zel_14690.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zel_14690/04_2024/7zel_14690.pdb" } 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 Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 6.94, per 1000 atoms: 0.52 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 - 3.50 Amino acid : False - 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: 5.37 Conformation dependent library (CDL) restraints added in 2.5 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: 1.80 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: 5.13 Time building geometry restraints manager: 5.65 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: 98.82 - 105.87: 344 105.87 - 112.92: 7226 112.92 - 119.98: 4665 119.98 - 127.03: 6006 127.03 - 134.08: 143 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 2.440 nonbonded pdb=" OE1 GLU A 95 " pdb=" OG SER A 538 " model vdw 2.233 2.440 nonbonded pdb=" NH2 ARG B 732 " pdb=" OE2 GLU B 861 " model vdw 2.255 2.520 nonbonded pdb=" O LEU B 718 " pdb=" NH2 ARG B 724 " model vdw 2.258 2.520 ... (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 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: 1.690 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: 7.500 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 41.470 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 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:12.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.820 ------------------------------------------------------------------------------- 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 : 1.602 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: 1.7818 time to fit residues: 396.5105 Evaluate side-chains 156 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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: 0.0870 chunk 124 optimal weight: 0.9990 chunk 68 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 1.9990 overall best weight: 1.2166 ------------------------------------------------------------------------------- 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 ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 774 GLN B 69 HIS B 222 HIS ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13618 Z= 0.281 Angle : 0.560 6.183 18384 Z= 0.294 Chirality : 0.044 0.153 2018 Planarity : 0.005 0.042 2362 Dihedral : 4.338 19.071 1824 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.42 % Allowed : 7.71 % Favored : 90.87 % 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: 1.00 (0.20), residues: 666 sheet: 0.82 (0.31), residues: 274 loop : 0.04 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.005 0.001 HIS A 420 PHE 0.019 0.002 PHE A 218 TYR 0.013 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 191 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 170 time to evaluate : 1.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.7363 (mt-10) REVERT: A 38 GLN cc_start: 0.7952 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: A 649 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.6989 (mp0) REVERT: A 858 SER cc_start: 0.8359 (m) cc_final: 0.7991 (m) REVERT: B 807 LYS cc_start: 0.8296 (pttt) cc_final: 0.7895 (ptpt) outliers start: 21 outliers final: 7 residues processed: 182 average time/residue: 1.6703 time to fit residues: 326.2622 Evaluate side-chains 163 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 GLU Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain 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 516 CYS Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 861 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 101 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 149 optimal weight: 0.0070 chunk 161 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 overall best weight: 0.8802 ------------------------------------------------------------------------------- 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 ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 663 GLN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 880 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13618 Z= 0.217 Angle : 0.506 5.030 18384 Z= 0.265 Chirality : 0.042 0.154 2018 Planarity : 0.004 0.037 2362 Dihedral : 4.173 16.882 1824 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.30 % Allowed : 9.61 % Favored : 88.09 % 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: 1.00 (0.20), residues: 1638 helix: 1.38 (0.20), residues: 672 sheet: 0.74 (0.31), residues: 272 loop : 0.03 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 413 HIS 0.004 0.001 HIS A 420 PHE 0.015 0.001 PHE B 218 TYR 0.013 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: 34 poor density : 170 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7634 (tt0) REVERT: A 643 ARG cc_start: 0.7832 (mmm-85) cc_final: 0.7607 (mmm-85) REVERT: A 649 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: A 858 SER cc_start: 0.8317 (m) cc_final: 0.7920 (m) REVERT: B 273 LYS cc_start: 0.7171 (tppp) cc_final: 0.6830 (tppp) REVERT: B 337 LYS cc_start: 0.8139 (mmmt) cc_final: 0.7914 (mmmt) REVERT: B 807 LYS cc_start: 0.8226 (pttt) cc_final: 0.7949 (ptpt) outliers start: 34 outliers final: 11 residues processed: 192 average time/residue: 1.5324 time to fit residues: 317.7296 Evaluate side-chains 175 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 162 time to evaluate : 1.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 GLN Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 720 ASP 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 675 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 858 SER Chi-restraints excluded: chain B residue 861 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 0.1980 chunk 149 optimal weight: 3.9990 chunk 158 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 141 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 420 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 13618 Z= 0.382 Angle : 0.589 6.946 18384 Z= 0.306 Chirality : 0.046 0.153 2018 Planarity : 0.005 0.043 2362 Dihedral : 4.455 19.389 1824 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.04 % Allowed : 10.35 % Favored : 86.60 % 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: 0.83 (0.20), residues: 1638 helix: 1.28 (0.20), residues: 670 sheet: 0.64 (0.32), residues: 270 loop : -0.10 (0.22), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 332 HIS 0.005 0.001 HIS B 420 PHE 0.016 0.002 PHE B 218 TYR 0.015 0.002 TYR B 234 ARG 0.008 0.001 ARG B 229 *********************** 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 211 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 166 time to evaluate : 1.421 Fit side-chains revert: symmetry clash REVERT: A 400 VAL cc_start: 0.8122 (OUTLIER) cc_final: 0.7734 (t) REVERT: A 478 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7121 (pt0) REVERT: A 613 MET cc_start: 0.8802 (mtm) cc_final: 0.8589 (mtt) REVERT: A 649 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7113 (mp0) REVERT: A 689 ARG cc_start: 0.7353 (mtm-85) cc_final: 0.7147 (mtm-85) REVERT: A 807 LYS cc_start: 0.8654 (ptpp) cc_final: 0.8379 (ptmt) REVERT: A 885 LEU cc_start: 0.8607 (OUTLIER) cc_final: 0.8369 (tp) REVERT: B 273 LYS cc_start: 0.7150 (tppp) cc_final: 0.6828 (tppp) REVERT: B 748 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.8086 (mm) REVERT: B 807 LYS cc_start: 0.8412 (pttt) cc_final: 0.7967 (ptpt) outliers start: 45 outliers final: 18 residues processed: 191 average time/residue: 1.5458 time to fit residues: 319.2871 Evaluate side-chains 188 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain A residue 748 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 477 ARG Chi-restraints excluded: chain B residue 488 THR Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 686 SER Chi-restraints excluded: chain B residue 688 THR 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: 0.9980 chunk 65 optimal weight: 1.9990 chunk 135 optimal weight: 0.3980 chunk 109 optimal weight: 9.9990 chunk 0 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 142 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 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 ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13618 Z= 0.180 Angle : 0.481 5.068 18384 Z= 0.251 Chirality : 0.042 0.155 2018 Planarity : 0.004 0.034 2362 Dihedral : 4.126 16.710 1824 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.17 % Allowed : 12.18 % Favored : 85.66 % 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 (0.21), residues: 1638 helix: 1.60 (0.20), residues: 672 sheet: 0.64 (0.32), residues: 272 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 0.011 0.001 PHE A 585 TYR 0.018 0.001 TYR A 704 ARG 0.008 0.000 ARG B 229 *********************** 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 206 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 174 time to evaluate : 1.567 Fit side-chains revert: symmetry clash REVERT: A 400 VAL cc_start: 0.8071 (OUTLIER) cc_final: 0.7843 (t) REVERT: A 478 GLU cc_start: 0.7329 (OUTLIER) cc_final: 0.7085 (pt0) REVERT: A 613 MET cc_start: 0.8780 (mtm) cc_final: 0.8572 (mtt) REVERT: A 649 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7098 (mp0) REVERT: B 13 SER cc_start: 0.7046 (m) cc_final: 0.6729 (t) REVERT: B 47 MET cc_start: 0.8590 (mmp) cc_final: 0.8202 (mmt) REVERT: B 273 LYS cc_start: 0.7016 (tppp) cc_final: 0.6815 (tppp) REVERT: B 397 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8558 (mp) REVERT: B 643 ARG cc_start: 0.7901 (mtp85) cc_final: 0.7609 (mtp-110) REVERT: B 807 LYS cc_start: 0.8311 (pttt) cc_final: 0.8023 (ptpt) REVERT: B 808 ASP cc_start: 0.8510 (m-30) cc_final: 0.8196 (m-30) outliers start: 32 outliers final: 13 residues processed: 190 average time/residue: 1.5213 time to fit residues: 312.3512 Evaluate side-chains 185 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 1.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 711 ASP 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 397 LEU Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 675 THR Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 858 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 158 optimal weight: 0.0570 chunk 131 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- 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 ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 318 ASN ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2004 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= 0.223 Angle : 0.498 5.765 18384 Z= 0.259 Chirality : 0.042 0.156 2018 Planarity : 0.004 0.035 2362 Dihedral : 4.114 16.688 1824 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.23 % Allowed : 12.38 % 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: 1.12 (0.21), residues: 1638 helix: 1.66 (0.20), residues: 672 sheet: 0.61 (0.32), residues: 272 loop : -0.02 (0.23), 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 0.011 0.001 PHE A 585 TYR 0.011 0.001 TYR B 234 ARG 0.009 0.000 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 204 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 171 time to evaluate : 1.529 Fit side-chains REVERT: A 400 VAL cc_start: 0.7981 (OUTLIER) cc_final: 0.7743 (t) REVERT: A 478 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7134 (pt0) REVERT: A 649 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7032 (mp0) REVERT: B 13 SER cc_start: 0.7218 (m) cc_final: 0.6947 (t) REVERT: B 47 MET cc_start: 0.8637 (mmp) cc_final: 0.8252 (mmt) REVERT: B 101 ARG cc_start: 0.8328 (mmm160) cc_final: 0.8109 (mtt-85) REVERT: B 273 LYS cc_start: 0.6981 (tppp) cc_final: 0.6770 (tppp) REVERT: B 275 GLU cc_start: 0.7456 (mt-10) cc_final: 0.7204 (mt-10) REVERT: B 397 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8548 (mp) REVERT: B 643 ARG cc_start: 0.7918 (mtp85) cc_final: 0.7633 (mtp-110) REVERT: B 703 ASP cc_start: 0.8452 (t0) cc_final: 0.8251 (t70) REVERT: B 807 LYS cc_start: 0.8344 (pttt) cc_final: 0.7919 (ptpt) outliers start: 33 outliers final: 14 residues processed: 190 average time/residue: 1.6228 time to fit residues: 333.6463 Evaluate side-chains 186 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 168 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 477 ARG Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 676 GLU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 711 ASP Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 858 SER Chi-restraints excluded: chain B residue 861 GLU 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: 0.8980 chunk 17 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 115 optimal weight: 0.4980 chunk 89 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 158 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 96 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2065 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= 0.209 Angle : 0.489 6.024 18384 Z= 0.254 Chirality : 0.042 0.156 2018 Planarity : 0.004 0.035 2362 Dihedral : 4.074 16.546 1824 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.89 % Allowed : 13.13 % Favored : 84.98 % 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: 1.15 (0.21), residues: 1638 helix: 1.72 (0.20), residues: 672 sheet: 0.58 (0.32), residues: 272 loop : -0.02 (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 0.011 0.001 PHE A 218 TYR 0.018 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 200 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 1.705 Fit side-chains revert: symmetry clash REVERT: A 478 GLU cc_start: 0.7334 (OUTLIER) cc_final: 0.7096 (pt0) REVERT: A 643 ARG cc_start: 0.7759 (mmm-85) cc_final: 0.7537 (mmm-85) REVERT: A 649 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7092 (mp0) REVERT: B 13 SER cc_start: 0.7152 (m) cc_final: 0.6844 (t) REVERT: B 101 ARG cc_start: 0.8327 (mmm160) cc_final: 0.8120 (mtt-85) REVERT: B 275 GLU cc_start: 0.7448 (mt-10) cc_final: 0.7224 (mt-10) REVERT: B 397 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8557 (mp) REVERT: B 643 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7623 (mtp-110) REVERT: B 703 ASP cc_start: 0.8451 (t0) cc_final: 0.8248 (t70) REVERT: B 807 LYS cc_start: 0.8335 (pttt) cc_final: 0.7936 (ptpt) REVERT: B 808 ASP cc_start: 0.8504 (m-30) cc_final: 0.8186 (m-30) outliers start: 28 outliers final: 15 residues processed: 189 average time/residue: 1.5620 time to fit residues: 318.8304 Evaluate side-chains 185 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 1.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 241 THR 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 711 ASP Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 397 LEU Chi-restraints excluded: chain B residue 477 ARG Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 688 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 97 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 124 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13618 Z= 0.286 Angle : 0.531 8.492 18384 Z= 0.273 Chirality : 0.044 0.153 2018 Planarity : 0.004 0.035 2362 Dihedral : 4.188 16.806 1824 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.30 % Allowed : 13.06 % 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: 1.03 (0.21), residues: 1638 helix: 1.61 (0.20), residues: 670 sheet: 0.43 (0.33), residues: 262 loop : -0.03 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 332 HIS 0.007 0.001 HIS A 848 PHE 0.014 0.002 PHE A 705 TYR 0.012 0.001 TYR B 234 ARG 0.009 0.000 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 204 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 170 time to evaluate : 1.211 Fit side-chains revert: symmetry clash REVERT: A 478 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7147 (pt0) REVERT: A 649 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7094 (mp0) REVERT: A 885 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8350 (tp) REVERT: B 13 SER cc_start: 0.7436 (m) cc_final: 0.7106 (t) REVERT: B 101 ARG cc_start: 0.8346 (mmm160) cc_final: 0.8136 (mtt-85) REVERT: B 275 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7225 (mt-10) REVERT: B 643 ARG cc_start: 0.7917 (mtp85) cc_final: 0.7624 (mtp-110) REVERT: B 807 LYS cc_start: 0.8380 (pttt) cc_final: 0.7947 (ptpt) outliers start: 34 outliers final: 14 residues processed: 195 average time/residue: 1.2279 time to fit residues: 258.7043 Evaluate side-chains 188 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 171 time to evaluate : 1.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 241 THR 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 711 ASP Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain B residue 11 GLU Chi-restraints excluded: chain B residue 102 CYS Chi-restraints excluded: chain B residue 477 ARG Chi-restraints excluded: chain B residue 516 CYS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 776 THR Chi-restraints excluded: chain B residue 836 VAL Chi-restraints excluded: chain B residue 858 SER Chi-restraints excluded: chain B residue 881 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 1.9990 chunk 151 optimal weight: 0.9980 chunk 138 optimal weight: 0.5980 chunk 147 optimal weight: 1.9990 chunk 88 optimal weight: 0.2980 chunk 64 optimal weight: 0.0870 chunk 115 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 133 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 146 optimal weight: 0.3980 overall best weight: 0.4358 ------------------------------------------------------------------------------- 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 ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 733 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.2223 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= 0.151 Angle : 0.461 5.114 18384 Z= 0.241 Chirality : 0.041 0.158 2018 Planarity : 0.004 0.037 2362 Dihedral : 3.884 16.289 1824 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.95 % Allowed : 14.55 % Favored : 84.51 % 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: 1.81 (0.20), residues: 672 sheet: 0.59 (0.32), residues: 272 loop : 0.05 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 413 HIS 0.006 0.001 HIS A 848 PHE 0.012 0.001 PHE B 435 TYR 0.011 0.001 TYR B 486 ARG 0.011 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 188 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 174 time to evaluate : 1.580 Fit side-chains revert: symmetry clash REVERT: A 478 GLU cc_start: 0.7200 (OUTLIER) cc_final: 0.6909 (pt0) REVERT: A 613 MET cc_start: 0.8657 (mtm) cc_final: 0.8401 (mtt) REVERT: A 649 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7150 (mp0) REVERT: B 13 SER cc_start: 0.6928 (m) cc_final: 0.6625 (t) REVERT: B 101 ARG cc_start: 0.8334 (mmm160) cc_final: 0.8132 (mtt-85) REVERT: B 275 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7204 (mt-10) REVERT: B 618 ASN cc_start: 0.7344 (t0) cc_final: 0.7067 (t0) REVERT: B 643 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7631 (mtp-110) REVERT: B 690 ARG cc_start: 0.7304 (ptp90) cc_final: 0.7009 (mtp180) REVERT: B 807 LYS cc_start: 0.8340 (pttt) cc_final: 0.7991 (ptpt) REVERT: B 808 ASP cc_start: 0.8388 (m-30) cc_final: 0.8040 (m-30) outliers start: 14 outliers final: 8 residues processed: 182 average time/residue: 1.5505 time to fit residues: 304.7504 Evaluate side-chains 175 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 165 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 711 ASP 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 836 VAL Chi-restraints excluded: chain B residue 858 SER 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: 0.0070 chunk 95 optimal weight: 0.8980 chunk 73 optimal weight: 0.0870 chunk 108 optimal weight: 0.9990 chunk 163 optimal weight: 2.9990 chunk 150 optimal weight: 0.4980 chunk 130 optimal weight: 0.7980 chunk 13 optimal weight: 0.0980 chunk 100 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 overall best weight: 0.2976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 663 GLN A 706 GLN ** A 733 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13618 Z= 0.131 Angle : 0.460 8.830 18384 Z= 0.236 Chirality : 0.041 0.161 2018 Planarity : 0.004 0.041 2362 Dihedral : 3.755 15.699 1824 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.88 % Allowed : 14.88 % 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: 1.40 (0.21), residues: 1638 helix: 1.93 (0.20), residues: 672 sheet: 0.70 (0.32), residues: 268 loop : 0.12 (0.23), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 413 HIS 0.006 0.001 HIS A 848 PHE 0.013 0.001 PHE B 435 TYR 0.010 0.001 TYR B 486 ARG 0.010 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 184 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 1.418 Fit side-chains REVERT: A 241 THR cc_start: 0.8134 (OUTLIER) cc_final: 0.7782 (m) REVERT: A 478 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6902 (pt0) REVERT: A 613 MET cc_start: 0.8717 (mtm) cc_final: 0.8471 (mtt) REVERT: A 649 GLU cc_start: 0.7748 (OUTLIER) cc_final: 0.7173 (mp0) REVERT: A 778 ARG cc_start: 0.7581 (mmt-90) cc_final: 0.7363 (mmt-90) REVERT: B 13 SER cc_start: 0.6950 (m) cc_final: 0.6663 (t) REVERT: B 275 GLU cc_start: 0.7408 (mt-10) cc_final: 0.7166 (mt-10) REVERT: B 618 ASN cc_start: 0.7386 (t0) cc_final: 0.7108 (t0) REVERT: B 643 ARG cc_start: 0.7883 (mtp85) cc_final: 0.7614 (mtp-110) REVERT: B 807 LYS cc_start: 0.8328 (pttt) cc_final: 0.7985 (ptpt) REVERT: B 808 ASP cc_start: 0.8315 (m-30) cc_final: 0.7958 (m-30) outliers start: 13 outliers final: 8 residues processed: 177 average time/residue: 1.5717 time to fit residues: 302.0648 Evaluate side-chains 177 residues out of total 1478 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 166 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 241 THR Chi-restraints excluded: chain A residue 478 GLU Chi-restraints excluded: chain A residue 649 GLU Chi-restraints excluded: chain A residue 706 GLN Chi-restraints excluded: chain A residue 711 ASP 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 836 VAL Chi-restraints excluded: chain B residue 858 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 3.9990 chunk 138 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 133 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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 ** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.159277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.118704 restraints weight = 13791.089| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.16 r_work: 0.3041 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13618 Z= 0.321 Angle : 0.559 6.159 18384 Z= 0.288 Chirality : 0.045 0.174 2018 Planarity : 0.005 0.054 2362 Dihedral : 4.163 16.473 1824 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.08 % Allowed : 14.88 % Favored : 84.03 % 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: 1.09 (0.21), residues: 1638 helix: 1.65 (0.20), residues: 672 sheet: 0.50 (0.33), residues: 258 loop : -0.00 (0.23), residues: 708 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 0.018 0.002 PHE A 705 TYR 0.012 0.001 TYR B 582 ARG 0.013 0.001 ARG B 229 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5418.90 seconds wall clock time: 99 minutes 38.40 seconds (5978.40 seconds total)