Starting phenix.real_space_refine on Sat Aug 23 18:15:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uyc_42799/08_2025/8uyc_42799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uyc_42799/08_2025/8uyc_42799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8uyc_42799/08_2025/8uyc_42799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uyc_42799/08_2025/8uyc_42799.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8uyc_42799/08_2025/8uyc_42799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uyc_42799/08_2025/8uyc_42799.map" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.039 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: 5 Type Number sf(0) Gaussians Mg 6 5.21 5 S 76 5.16 5 C 8850 2.51 5 N 2356 2.21 5 O 2528 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13816 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 6905 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 43, 'TRANS': 854} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'GLN:plan1': 5, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "B" Number of atoms: 6905 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 6905 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 43, 'TRANS': 854} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 4, 'GLN:plan1': 5, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 56 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.24, per 1000 atoms: 0.23 Number of scatterers: 13816 At special positions: 0 Unit cell: (113.71, 115.37, 130.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 Mg 6 11.99 O 2528 8.00 N 2356 7.00 C 8850 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: 1.18 Conformation dependent library (CDL) restraints added in 645.1 milliseconds Enol-peptide restraints added in 1.2 microseconds 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3384 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 10 sheets defined 58.0% alpha, 16.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 30 through 34 removed outlier: 3.559A pdb=" N VAL A 34 " --> pdb=" O ASN A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 47 removed outlier: 3.827A pdb=" N VAL A 47 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 57 removed outlier: 3.875A pdb=" N TRP A 54 " --> pdb=" O GLU A 50 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 99 through 113 Processing helix chain 'A' and resid 120 through 153 removed outlier: 3.862A pdb=" N VAL A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 179 No H-bonds generated for 'chain 'A' and resid 177 through 179' Processing helix chain 'A' and resid 232 through 236 Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 262 through 267 Processing helix chain 'A' and resid 279 through 311 Proline residue: A 301 - end of helix Processing helix chain 'A' and resid 313 through 327 removed outlier: 3.973A pdb=" N GLY A 327 " --> pdb=" O SER A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 331 removed outlier: 6.232A pdb=" N GLU A 331 " --> pdb=" O LEU A 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 328 through 331' Processing helix chain 'A' and resid 332 through 350 removed outlier: 3.627A pdb=" N THR A 338 " --> pdb=" O PRO A 334 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ALA A 342 " --> pdb=" O THR A 338 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARG A 343 " --> pdb=" O SER A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 367 removed outlier: 4.066A pdb=" N GLN A 362 " --> pdb=" O LEU A 358 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN A 363 " --> pdb=" O ASP A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 378 removed outlier: 4.172A pdb=" N THR A 377 " --> pdb=" O ASP A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 409 removed outlier: 3.680A pdb=" N LEU A 400 " --> pdb=" O SER A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 425 Processing helix chain 'A' and resid 426 through 437 Processing helix chain 'A' and resid 471 through 477 removed outlier: 3.590A pdb=" N VAL A 477 " --> pdb=" O GLU A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 491 through 508 Processing helix chain 'A' and resid 528 through 532 Processing helix chain 'A' and resid 550 through 562 Processing helix chain 'A' and resid 572 through 584 Processing helix chain 'A' and resid 594 through 596 No H-bonds generated for 'chain 'A' and resid 594 through 596' Processing helix chain 'A' and resid 600 through 608 Processing helix chain 'A' and resid 618 through 629 Processing helix chain 'A' and resid 642 through 644 No H-bonds generated for 'chain 'A' and resid 642 through 644' Processing helix chain 'A' and resid 645 through 652 Processing helix chain 'A' and resid 662 through 668 Processing helix chain 'A' and resid 677 through 717 removed outlier: 3.507A pdb=" N LEU A 681 " --> pdb=" O SER A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 726 through 742 Processing helix chain 'A' and resid 743 through 747 Processing helix chain 'A' and resid 762 through 773 removed outlier: 4.270A pdb=" N GLY A 766 " --> pdb=" O PRO A 762 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG A 767 " --> pdb=" O ALA A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 789 removed outlier: 4.121A pdb=" N PHE A 779 " --> pdb=" O ILE A 775 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP A 780 " --> pdb=" O SER A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 797 No H-bonds generated for 'chain 'A' and resid 795 through 797' Processing helix chain 'A' and resid 798 through 822 removed outlier: 3.617A pdb=" N PHE A 802 " --> pdb=" O THR A 798 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N VAL A 809 " --> pdb=" O GLY A 805 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N VAL A 818 " --> pdb=" O GLN A 814 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N HIS A 819 " --> pdb=" O THR A 815 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET A 820 " --> pdb=" O LEU A 816 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 854 Proline residue: A 852 - end of helix Processing helix chain 'A' and resid 855 through 860 removed outlier: 4.413A pdb=" N TYR A 859 " --> pdb=" O PRO A 855 " (cutoff:3.500A) Processing helix chain 'A' and resid 868 through 895 removed outlier: 4.140A pdb=" N TRP A 872 " --> pdb=" O SER A 868 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N GLY A 889 " --> pdb=" O GLN A 885 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE A 890 " --> pdb=" O LEU A 886 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N TYR A 891 " --> pdb=" O VAL A 887 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 10 Processing helix chain 'B' and resid 30 through 34 removed outlier: 3.556A pdb=" N VAL B 34 " --> pdb=" O ASN B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 47 removed outlier: 3.824A pdb=" N VAL B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 57 removed outlier: 3.875A pdb=" N TRP B 54 " --> pdb=" O GLU B 50 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS B 55 " --> pdb=" O GLU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 Processing helix chain 'B' and resid 88 through 98 Processing helix chain 'B' and resid 99 through 113 Processing helix chain 'B' and resid 120 through 153 removed outlier: 3.863A pdb=" N VAL B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 179 No H-bonds generated for 'chain 'B' and resid 177 through 179' Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 262 through 267 Processing helix chain 'B' and resid 279 through 311 Proline residue: B 301 - end of helix Processing helix chain 'B' and resid 313 through 327 removed outlier: 3.973A pdb=" N GLY B 327 " --> pdb=" O SER B 323 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 331 removed outlier: 6.237A pdb=" N GLU B 331 " --> pdb=" O LEU B 328 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 328 through 331' Processing helix chain 'B' and resid 332 through 350 removed outlier: 3.631A pdb=" N THR B 338 " --> pdb=" O PRO B 334 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ALA B 342 " --> pdb=" O THR B 338 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ARG B 343 " --> pdb=" O SER B 339 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 367 removed outlier: 4.067A pdb=" N GLN B 362 " --> pdb=" O LEU B 358 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN B 363 " --> pdb=" O ASP B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 378 removed outlier: 4.176A pdb=" N THR B 377 " --> pdb=" O ASP B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 409 removed outlier: 3.680A pdb=" N LEU B 400 " --> pdb=" O SER B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 415 through 425 Processing helix chain 'B' and resid 426 through 437 Processing helix chain 'B' and resid 471 through 477 removed outlier: 3.585A pdb=" N VAL B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 508 Processing helix chain 'B' and resid 528 through 532 Processing helix chain 'B' and resid 550 through 562 Processing helix chain 'B' and resid 572 through 584 Processing helix chain 'B' and resid 594 through 596 No H-bonds generated for 'chain 'B' and resid 594 through 596' Processing helix chain 'B' and resid 600 through 608 Processing helix chain 'B' and resid 618 through 629 Processing helix chain 'B' and resid 642 through 644 No H-bonds generated for 'chain 'B' and resid 642 through 644' Processing helix chain 'B' and resid 645 through 652 Processing helix chain 'B' and resid 662 through 668 Processing helix chain 'B' and resid 677 through 717 removed outlier: 3.504A pdb=" N LEU B 681 " --> pdb=" O SER B 677 " (cutoff:3.500A) Processing helix chain 'B' and resid 726 through 742 Processing helix chain 'B' and resid 743 through 747 Processing helix chain 'B' and resid 762 through 789 removed outlier: 4.276A pdb=" N GLY B 766 " --> pdb=" O PRO B 762 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG B 767 " --> pdb=" O ALA B 763 " (cutoff:3.500A) Proline residue: B 774 - end of helix removed outlier: 3.726A pdb=" N PHE B 779 " --> pdb=" O ILE B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 797 No H-bonds generated for 'chain 'B' and resid 795 through 797' Processing helix chain 'B' and resid 798 through 822 removed outlier: 3.622A pdb=" N PHE B 802 " --> pdb=" O THR B 798 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL B 809 " --> pdb=" O GLY B 805 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 818 " --> pdb=" O GLN B 814 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N HIS B 819 " --> pdb=" O THR B 815 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET B 820 " --> pdb=" O LEU B 816 " (cutoff:3.500A) Processing helix chain 'B' and resid 834 through 854 Proline residue: B 852 - end of helix Processing helix chain 'B' and resid 855 through 860 removed outlier: 4.410A pdb=" N TYR B 859 " --> pdb=" O PRO B 855 " (cutoff:3.500A) Processing helix chain 'B' and resid 868 through 895 removed outlier: 4.116A pdb=" N TRP B 872 " --> pdb=" O SER B 868 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N GLY B 889 " --> pdb=" O GLN B 885 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N PHE B 890 " --> pdb=" O LEU B 886 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR B 891 " --> pdb=" O VAL B 887 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 175 removed outlier: 4.756A pdb=" N THR A 158 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N VAL A 246 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE A 206 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N SER A 248 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP A 204 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR A 250 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA A 202 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN A 252 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LEU A 205 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 172 through 175 removed outlier: 4.756A pdb=" N THR A 158 " --> pdb=" O LYS A 186 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N VAL A 246 " --> pdb=" O PHE A 206 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N PHE A 206 " --> pdb=" O VAL A 246 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N SER A 248 " --> pdb=" O ASP A 204 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASP A 204 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N THR A 250 " --> pdb=" O ALA A 202 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N ALA A 202 " --> pdb=" O THR A 250 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN A 252 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 197 " --> pdb=" O CYS A 240 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 353 through 355 removed outlier: 6.592A pdb=" N GLY A 655 " --> pdb=" O ILE A 671 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N LEU A 673 " --> pdb=" O GLY A 655 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N SER A 657 " --> pdb=" O LEU A 673 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL A 636 " --> pdb=" O ILE A 654 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N ILE A 656 " --> pdb=" O VAL A 636 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N PHE A 638 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL A 658 " --> pdb=" O PHE A 638 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE A 369 " --> pdb=" O GLY A 637 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N MET A 639 " --> pdb=" O ILE A 369 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N CYS A 371 " --> pdb=" O MET A 639 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU A 370 " --> pdb=" O LYS A 566 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N LEU A 568 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N THR A 372 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N PHE A 614 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ILE A 567 " --> pdb=" O PHE A 614 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL A 591 " --> pdb=" O ALA A 615 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 389 removed outlier: 8.809A pdb=" N LEU A 535 " --> pdb=" O TYR A 519 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N TYR A 519 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N LEU A 537 " --> pdb=" O THR A 517 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR A 517 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY A 539 " --> pdb=" O VAL A 515 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA A 457 " --> pdb=" O LYS A 439 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N LYS A 439 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 389 removed outlier: 5.157A pdb=" N CYS A 478 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU A 537 " --> pdb=" O CYS A 478 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N GLN A 480 " --> pdb=" O LEU A 537 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N GLY A 539 " --> pdb=" O GLN A 480 " (cutoff:3.500A) removed outlier: 9.138A pdb=" N ARG A 482 " --> pdb=" O GLY A 539 " (cutoff:3.500A) removed outlier: 12.564A pdb=" N ILE A 541 " --> pdb=" O ARG A 482 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 172 through 175 removed outlier: 4.757A pdb=" N THR B 158 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 246 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL B 207 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER B 248 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU B 205 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N MET B 254 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE B 199 " --> pdb=" O MET B 254 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU B 205 " --> pdb=" O LYS B 221 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 172 through 175 removed outlier: 4.757A pdb=" N THR B 158 " --> pdb=" O LYS B 186 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 246 " --> pdb=" O VAL B 207 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL B 207 " --> pdb=" O VAL B 246 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER B 248 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU B 205 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N MET B 254 " --> pdb=" O ILE B 199 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N ILE B 199 " --> pdb=" O MET B 254 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 197 " --> pdb=" O CYS B 240 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 353 through 355 removed outlier: 6.592A pdb=" N GLY B 655 " --> pdb=" O ILE B 671 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU B 673 " --> pdb=" O GLY B 655 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER B 657 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N VAL B 636 " --> pdb=" O ILE B 654 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N ILE B 656 " --> pdb=" O VAL B 636 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N PHE B 638 " --> pdb=" O ILE B 656 " (cutoff:3.500A) removed outlier: 8.432A pdb=" N VAL B 658 " --> pdb=" O PHE B 638 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE B 369 " --> pdb=" O GLY B 637 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N MET B 639 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N CYS B 371 " --> pdb=" O MET B 639 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N LEU B 370 " --> pdb=" O LYS B 566 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU B 568 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N THR B 372 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N PHE B 614 " --> pdb=" O VAL B 565 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE B 567 " --> pdb=" O PHE B 614 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N VAL B 591 " --> pdb=" O ALA B 615 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 385 through 389 removed outlier: 3.855A pdb=" N LEU B 385 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N LEU B 535 " --> pdb=" O TYR B 519 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N TYR B 519 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N LEU B 537 " --> pdb=" O THR B 517 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N THR B 517 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY B 539 " --> pdb=" O VAL B 515 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ALA B 457 " --> pdb=" O LYS B 439 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N LYS B 439 " --> pdb=" O ALA B 457 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 385 through 389 removed outlier: 3.855A pdb=" N LEU B 385 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N CYS B 478 " --> pdb=" O LEU B 535 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU B 537 " --> pdb=" O CYS B 478 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N GLN B 480 " --> pdb=" O LEU B 537 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY B 539 " --> pdb=" O GLN B 480 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N ARG B 482 " --> pdb=" O GLY B 539 " (cutoff:3.500A) removed outlier: 12.564A pdb=" N ILE B 541 " --> pdb=" O ARG B 482 " (cutoff:3.500A) 789 hydrogen bonds defined for protein. 2295 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.78 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2434 1.32 - 1.44: 3391 1.44 - 1.57: 8141 1.57 - 1.69: 0 1.69 - 1.81: 132 Bond restraints: 14098 Sorted by residual: bond pdb=" C GLN A 380 " pdb=" O GLN A 380 " ideal model delta sigma weight residual 1.234 1.202 0.032 1.35e-02 5.49e+03 5.79e+00 bond pdb=" CA GLN A 380 " pdb=" C GLN A 380 " ideal model delta sigma weight residual 1.528 1.500 0.027 1.37e-02 5.33e+03 3.99e+00 bond pdb=" C LEU B 333 " pdb=" N PRO B 334 " ideal model delta sigma weight residual 1.335 1.354 -0.019 1.28e-02 6.10e+03 2.25e+00 bond pdb=" C LEU A 333 " pdb=" N PRO A 334 " ideal model delta sigma weight residual 1.335 1.353 -0.018 1.28e-02 6.10e+03 2.08e+00 bond pdb=" CA GLN A 380 " pdb=" CB GLN A 380 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.61e-02 3.86e+03 1.75e+00 ... (remaining 14093 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 18800 1.53 - 3.05: 332 3.05 - 4.58: 56 4.58 - 6.10: 12 6.10 - 7.63: 2 Bond angle restraints: 19202 Sorted by residual: angle pdb=" N ILE B 775 " pdb=" CA ILE B 775 " pdb=" C ILE B 775 " ideal model delta sigma weight residual 110.42 108.01 2.41 9.60e-01 1.09e+00 6.33e+00 angle pdb=" C MET A 335 " pdb=" N ILE A 336 " pdb=" CA ILE A 336 " ideal model delta sigma weight residual 120.77 123.99 -3.22 1.31e+00 5.83e-01 6.04e+00 angle pdb=" N PHE A 119 " pdb=" CA PHE A 119 " pdb=" C PHE A 119 " ideal model delta sigma weight residual 113.72 110.01 3.71 1.52e+00 4.33e-01 5.95e+00 angle pdb=" N THR A 372 " pdb=" CA THR A 372 " pdb=" C THR A 372 " ideal model delta sigma weight residual 108.34 111.51 -3.17 1.31e+00 5.83e-01 5.85e+00 angle pdb=" N PHE B 119 " pdb=" CA PHE B 119 " pdb=" C PHE B 119 " ideal model delta sigma weight residual 113.72 110.10 3.62 1.52e+00 4.33e-01 5.68e+00 ... (remaining 19197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 7730 16.74 - 33.48: 606 33.48 - 50.22: 108 50.22 - 66.96: 26 66.96 - 83.70: 8 Dihedral angle restraints: 8478 sinusoidal: 3272 harmonic: 5206 Sorted by residual: dihedral pdb=" CG ARG B 690 " pdb=" CD ARG B 690 " pdb=" NE ARG B 690 " pdb=" CZ ARG B 690 " ideal model delta sinusoidal sigma weight residual 90.00 134.76 -44.76 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG A 690 " pdb=" CD ARG A 690 " pdb=" NE ARG A 690 " pdb=" CZ ARG A 690 " ideal model delta sinusoidal sigma weight residual 90.00 134.72 -44.72 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG A 11 " pdb=" CD ARG A 11 " pdb=" NE ARG A 11 " pdb=" CZ ARG A 11 " ideal model delta sinusoidal sigma weight residual -90.00 -128.05 38.05 2 1.50e+01 4.44e-03 8.10e+00 ... (remaining 8475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1399 0.027 - 0.054: 509 0.054 - 0.081: 220 0.081 - 0.108: 110 0.108 - 0.134: 36 Chirality restraints: 2274 Sorted by residual: chirality pdb=" CA GLU B 70 " pdb=" N GLU B 70 " pdb=" C GLU B 70 " pdb=" CB GLU B 70 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE B 671 " pdb=" N ILE B 671 " pdb=" C ILE B 671 " pdb=" CB ILE B 671 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 chirality pdb=" CA ILE A 671 " pdb=" N ILE A 671 " pdb=" C ILE A 671 " pdb=" CB ILE A 671 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 2271 not shown) Planarity restraints: 2446 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 744 " 0.030 5.00e-02 4.00e+02 4.63e-02 3.43e+00 pdb=" N PRO A 745 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 745 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 745 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 744 " -0.029 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO B 745 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 745 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 745 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 21 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.67e+00 pdb=" N PRO A 22 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 22 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 22 " 0.023 5.00e-02 4.00e+02 ... (remaining 2443 not shown) Histogram of nonbonded interaction distances: 2.02 - 2.59: 115 2.59 - 3.17: 11796 3.17 - 3.75: 21872 3.75 - 4.32: 29010 4.32 - 4.90: 49473 Nonbonded interactions: 112266 Sorted by model distance: nonbonded pdb=" OD1 ASN A 709 " pdb="MG MG A1001 " model vdw 2.016 2.170 nonbonded pdb=" OD1 ASN B 709 " pdb="MG MG B1001 " model vdw 2.017 2.170 nonbonded pdb=" OD1 ASP B 191 " pdb="MG MG B1002 " model vdw 2.157 2.170 nonbonded pdb=" OD1 ASP B 441 " pdb="MG MG B1003 " model vdw 2.158 2.170 nonbonded pdb=" OD1 ASP A 441 " pdb="MG MG A1003 " model vdw 2.158 2.170 ... (remaining 112261 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: 0.03 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.760 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: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.240 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 : 0.002 0.032 14098 Z= 0.120 Angle : 0.523 7.625 19202 Z= 0.298 Chirality : 0.039 0.134 2274 Planarity : 0.004 0.046 2446 Dihedral : 12.750 83.697 5094 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.21), residues: 1792 helix: 1.64 (0.18), residues: 914 sheet: -0.19 (0.35), residues: 188 loop : -0.21 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 650 TYR 0.008 0.001 TYR A 698 PHE 0.012 0.001 PHE B 264 TRP 0.005 0.001 TRP A 760 HIS 0.001 0.000 HIS B 230 Details of bonding type rmsd covalent geometry : bond 0.00220 (14098) covalent geometry : angle 0.52265 (19202) hydrogen bonds : bond 0.14007 ( 755) hydrogen bonds : angle 5.66441 ( 2295) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8780 (mt) cc_final: 0.8542 (mp) REVERT: A 372 THR cc_start: 0.9121 (p) cc_final: 0.8889 (t) REVERT: A 545 ASP cc_start: 0.8044 (t0) cc_final: 0.7174 (p0) REVERT: A 737 TYR cc_start: 0.8011 (t80) cc_final: 0.7773 (t80) REVERT: A 856 LEU cc_start: 0.7865 (mt) cc_final: 0.7650 (mt) REVERT: B 322 LEU cc_start: 0.8381 (tp) cc_final: 0.8163 (tp) REVERT: B 372 THR cc_start: 0.9091 (p) cc_final: 0.8858 (t) REVERT: B 545 ASP cc_start: 0.8094 (t0) cc_final: 0.7191 (p0) REVERT: B 814 GLN cc_start: 0.7559 (tt0) cc_final: 0.7283 (mm-40) REVERT: B 881 MET cc_start: 0.7502 (mtp) cc_final: 0.6850 (ppp) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.1229 time to fit residues: 62.0376 Evaluate side-chains 164 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 0.0000 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN A 733 GLN ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 741 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.102516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.082070 restraints weight = 32416.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084364 restraints weight = 18704.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.085861 restraints weight = 13226.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.086775 restraints weight = 10643.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.087434 restraints weight = 9335.689| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14098 Z= 0.133 Angle : 0.539 8.565 19202 Z= 0.281 Chirality : 0.042 0.149 2274 Planarity : 0.005 0.052 2446 Dihedral : 3.900 29.636 1906 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.10 % Allowed : 9.50 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.30 (0.20), residues: 1792 helix: 1.79 (0.18), residues: 946 sheet: -0.06 (0.34), residues: 208 loop : -0.14 (0.25), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 616 TYR 0.020 0.002 TYR A 698 PHE 0.012 0.001 PHE A 364 TRP 0.013 0.001 TRP B 806 HIS 0.009 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00303 (14098) covalent geometry : angle 0.53865 (19202) hydrogen bonds : bond 0.03943 ( 755) hydrogen bonds : angle 4.29453 ( 2295) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 178 time to evaluate : 0.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8791 (mt) cc_final: 0.8571 (mp) REVERT: A 339 SER cc_start: 0.8809 (p) cc_final: 0.8584 (p) REVERT: A 545 ASP cc_start: 0.8036 (t0) cc_final: 0.6946 (p0) REVERT: A 843 ILE cc_start: 0.8590 (mm) cc_final: 0.8201 (mt) REVERT: A 856 LEU cc_start: 0.8021 (mt) cc_final: 0.7656 (mt) REVERT: B 322 LEU cc_start: 0.8415 (tp) cc_final: 0.8127 (tp) REVERT: B 339 SER cc_start: 0.8790 (p) cc_final: 0.8578 (p) REVERT: B 545 ASP cc_start: 0.8023 (t0) cc_final: 0.6990 (p0) REVERT: B 741 GLN cc_start: 0.8003 (OUTLIER) cc_final: 0.7635 (mm-40) REVERT: B 881 MET cc_start: 0.7491 (mtp) cc_final: 0.6778 (ppp) outliers start: 31 outliers final: 22 residues processed: 201 average time/residue: 0.0928 time to fit residues: 30.6237 Evaluate side-chains 174 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 741 GLN Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 846 ILE Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 27 optimal weight: 8.9990 chunk 55 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 125 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 733 GLN ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.102738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.082196 restraints weight = 32317.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084489 restraints weight = 18669.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.085979 restraints weight = 13190.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.086787 restraints weight = 10626.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.087535 restraints weight = 9386.571| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 14098 Z= 0.112 Angle : 0.507 7.893 19202 Z= 0.261 Chirality : 0.041 0.213 2274 Planarity : 0.005 0.054 2446 Dihedral : 3.806 27.028 1906 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.97 % Allowed : 11.74 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.21), residues: 1792 helix: 1.93 (0.18), residues: 944 sheet: -0.20 (0.33), residues: 216 loop : -0.14 (0.25), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 507 TYR 0.019 0.001 TYR A 698 PHE 0.011 0.001 PHE B 364 TRP 0.008 0.001 TRP B 806 HIS 0.005 0.001 HIS A 76 Details of bonding type rmsd covalent geometry : bond 0.00250 (14098) covalent geometry : angle 0.50658 (19202) hydrogen bonds : bond 0.03632 ( 755) hydrogen bonds : angle 4.02737 ( 2295) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.549 Fit side-chains revert: symmetry clash REVERT: A 339 SER cc_start: 0.8921 (p) cc_final: 0.8664 (p) REVERT: A 545 ASP cc_start: 0.8037 (t0) cc_final: 0.7674 (t70) REVERT: A 814 GLN cc_start: 0.7707 (mm-40) cc_final: 0.7427 (mm110) REVERT: B 322 LEU cc_start: 0.8476 (tp) cc_final: 0.8231 (tp) REVERT: B 339 SER cc_start: 0.8927 (p) cc_final: 0.8655 (p) REVERT: B 545 ASP cc_start: 0.8023 (t0) cc_final: 0.7134 (p0) REVERT: B 881 MET cc_start: 0.7368 (mtp) cc_final: 0.6734 (ppp) outliers start: 29 outliers final: 20 residues processed: 187 average time/residue: 0.0943 time to fit residues: 29.3159 Evaluate side-chains 165 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 145 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 324 VAL Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 324 VAL Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 88 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 142 optimal weight: 0.0570 chunk 169 optimal weight: 3.9990 chunk 136 optimal weight: 0.1980 chunk 151 optimal weight: 0.3980 chunk 87 optimal weight: 0.9990 chunk 116 optimal weight: 6.9990 chunk 121 optimal weight: 4.9990 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 472 GLN ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 GLN B 803 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.103713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.083192 restraints weight = 32160.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.085501 restraints weight = 18518.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087061 restraints weight = 13016.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.087992 restraints weight = 10418.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.088511 restraints weight = 9125.258| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14098 Z= 0.096 Angle : 0.482 7.510 19202 Z= 0.247 Chirality : 0.041 0.178 2274 Planarity : 0.004 0.056 2446 Dihedral : 3.693 27.975 1906 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.44 % Allowed : 13.16 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.21), residues: 1792 helix: 2.07 (0.18), residues: 938 sheet: -0.01 (0.37), residues: 188 loop : -0.09 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 507 TYR 0.018 0.001 TYR A 698 PHE 0.012 0.001 PHE B 364 TRP 0.011 0.001 TRP A 806 HIS 0.003 0.001 HIS A 388 Details of bonding type rmsd covalent geometry : bond 0.00207 (14098) covalent geometry : angle 0.48157 (19202) hydrogen bonds : bond 0.03352 ( 755) hydrogen bonds : angle 3.84197 ( 2295) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: A 116 GLU cc_start: 0.5731 (tp30) cc_final: 0.5332 (tp30) REVERT: A 339 SER cc_start: 0.8952 (p) cc_final: 0.8685 (p) REVERT: A 545 ASP cc_start: 0.8002 (t0) cc_final: 0.7619 (t70) REVERT: B 339 SER cc_start: 0.8946 (p) cc_final: 0.8655 (p) REVERT: B 545 ASP cc_start: 0.8035 (t0) cc_final: 0.7689 (t70) REVERT: B 881 MET cc_start: 0.7374 (mtp) cc_final: 0.6727 (ppp) outliers start: 36 outliers final: 18 residues processed: 186 average time/residue: 0.0897 time to fit residues: 27.8064 Evaluate side-chains 167 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 172 optimal weight: 9.9990 chunk 46 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 72 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 122 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 755 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.099217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.078595 restraints weight = 32717.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.080735 restraints weight = 19128.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.082018 restraints weight = 13662.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.083011 restraints weight = 11186.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.083462 restraints weight = 9806.259| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 14098 Z= 0.181 Angle : 0.552 8.433 19202 Z= 0.286 Chirality : 0.043 0.156 2274 Planarity : 0.005 0.053 2446 Dihedral : 3.956 27.466 1906 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.71 % Allowed : 14.31 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.21), residues: 1792 helix: 1.88 (0.18), residues: 936 sheet: -0.04 (0.37), residues: 186 loop : -0.19 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 482 TYR 0.022 0.002 TYR A 698 PHE 0.015 0.002 PHE B 101 TRP 0.012 0.001 TRP B 806 HIS 0.004 0.001 HIS B 401 Details of bonding type rmsd covalent geometry : bond 0.00427 (14098) covalent geometry : angle 0.55217 (19202) hydrogen bonds : bond 0.04008 ( 755) hydrogen bonds : angle 4.08731 ( 2295) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 0.555 Fit side-chains REVERT: A 116 GLU cc_start: 0.5798 (tp30) cc_final: 0.5426 (tp30) REVERT: A 339 SER cc_start: 0.8908 (p) cc_final: 0.8605 (p) REVERT: A 545 ASP cc_start: 0.8015 (t0) cc_final: 0.7661 (t70) REVERT: A 695 MET cc_start: 0.9199 (ttp) cc_final: 0.8791 (ttm) REVERT: B 339 SER cc_start: 0.8918 (p) cc_final: 0.8609 (p) REVERT: B 545 ASP cc_start: 0.8050 (t0) cc_final: 0.7745 (t70) REVERT: B 695 MET cc_start: 0.9188 (ttp) cc_final: 0.8784 (ttm) REVERT: B 881 MET cc_start: 0.7387 (mtp) cc_final: 0.6743 (ppp) outliers start: 40 outliers final: 25 residues processed: 177 average time/residue: 0.0902 time to fit residues: 26.3902 Evaluate side-chains 168 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 143 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 120 optimal weight: 2.9990 chunk 174 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 139 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 755 GLN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.099354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.078811 restraints weight = 32612.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.080975 restraints weight = 19081.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.082247 restraints weight = 13626.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.083230 restraints weight = 11170.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.083681 restraints weight = 9802.704| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 14098 Z= 0.159 Angle : 0.546 13.307 19202 Z= 0.278 Chirality : 0.043 0.202 2274 Planarity : 0.005 0.052 2446 Dihedral : 3.966 28.174 1906 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.37 % Allowed : 15.81 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.34 (0.21), residues: 1792 helix: 1.81 (0.18), residues: 948 sheet: 0.01 (0.38), residues: 182 loop : -0.11 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 616 TYR 0.020 0.002 TYR A 698 PHE 0.012 0.002 PHE B 364 TRP 0.011 0.001 TRP A 806 HIS 0.003 0.001 HIS A 729 Details of bonding type rmsd covalent geometry : bond 0.00370 (14098) covalent geometry : angle 0.54590 (19202) hydrogen bonds : bond 0.03842 ( 755) hydrogen bonds : angle 4.05985 ( 2295) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 143 time to evaluate : 0.603 Fit side-chains REVERT: A 116 GLU cc_start: 0.5849 (tp30) cc_final: 0.5471 (tp30) REVERT: A 339 SER cc_start: 0.8914 (p) cc_final: 0.8653 (p) REVERT: A 545 ASP cc_start: 0.8034 (t0) cc_final: 0.7732 (t70) REVERT: A 695 MET cc_start: 0.9187 (ttp) cc_final: 0.8774 (ttm) REVERT: A 865 LEU cc_start: 0.7989 (tp) cc_final: 0.7770 (tp) REVERT: B 339 SER cc_start: 0.8921 (p) cc_final: 0.8657 (p) REVERT: B 545 ASP cc_start: 0.8081 (t0) cc_final: 0.7806 (t70) REVERT: B 881 MET cc_start: 0.7376 (mtp) cc_final: 0.6754 (ppp) outliers start: 35 outliers final: 27 residues processed: 172 average time/residue: 0.0916 time to fit residues: 26.1543 Evaluate side-chains 167 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 140 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 653 ASP Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 653 ASP Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 167 optimal weight: 5.9990 chunk 33 optimal weight: 0.3980 chunk 139 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 141 optimal weight: 7.9990 chunk 16 optimal weight: 0.0970 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.100763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.080310 restraints weight = 32356.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.082543 restraints weight = 18869.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.083994 restraints weight = 13419.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.084785 restraints weight = 10871.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.085417 restraints weight = 9614.034| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14098 Z= 0.113 Angle : 0.515 12.383 19202 Z= 0.259 Chirality : 0.041 0.210 2274 Planarity : 0.004 0.052 2446 Dihedral : 3.847 27.092 1906 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.44 % Allowed : 16.55 % Favored : 81.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.21), residues: 1792 helix: 2.01 (0.18), residues: 936 sheet: 0.20 (0.39), residues: 166 loop : -0.12 (0.25), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 616 TYR 0.018 0.002 TYR B 869 PHE 0.012 0.001 PHE B 364 TRP 0.008 0.001 TRP B 806 HIS 0.003 0.001 HIS B 729 Details of bonding type rmsd covalent geometry : bond 0.00256 (14098) covalent geometry : angle 0.51546 (19202) hydrogen bonds : bond 0.03548 ( 755) hydrogen bonds : angle 3.92404 ( 2295) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 147 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 116 GLU cc_start: 0.5845 (tp30) cc_final: 0.5459 (tp30) REVERT: A 339 SER cc_start: 0.8913 (p) cc_final: 0.8645 (p) REVERT: A 545 ASP cc_start: 0.8069 (t0) cc_final: 0.7794 (t70) REVERT: A 695 MET cc_start: 0.9180 (ttp) cc_final: 0.8766 (ttm) REVERT: B 339 SER cc_start: 0.8911 (p) cc_final: 0.8651 (p) REVERT: B 545 ASP cc_start: 0.8031 (t0) cc_final: 0.7743 (t70) REVERT: B 695 MET cc_start: 0.9173 (ttp) cc_final: 0.8770 (ttm) REVERT: B 881 MET cc_start: 0.7316 (mtp) cc_final: 0.6680 (ppp) outliers start: 36 outliers final: 26 residues processed: 177 average time/residue: 0.0827 time to fit residues: 24.3693 Evaluate side-chains 168 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 41 optimal weight: 0.3980 chunk 87 optimal weight: 0.9980 chunk 147 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 158 optimal weight: 1.9990 chunk 88 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 168 optimal weight: 4.9990 chunk 127 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 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 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.101241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.080840 restraints weight = 32244.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.083047 restraints weight = 18908.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.084482 restraints weight = 13504.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.085410 restraints weight = 10952.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.085818 restraints weight = 9635.593| |-----------------------------------------------------------------------------| r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.3291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14098 Z= 0.113 Angle : 0.504 6.978 19202 Z= 0.258 Chirality : 0.042 0.215 2274 Planarity : 0.004 0.052 2446 Dihedral : 3.812 27.124 1906 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.37 % Allowed : 16.96 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.21), residues: 1792 helix: 2.05 (0.18), residues: 938 sheet: 0.19 (0.39), residues: 168 loop : -0.12 (0.25), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 507 TYR 0.018 0.001 TYR A 869 PHE 0.012 0.001 PHE B 802 TRP 0.042 0.001 TRP B 806 HIS 0.002 0.001 HIS A 729 Details of bonding type rmsd covalent geometry : bond 0.00255 (14098) covalent geometry : angle 0.50361 (19202) hydrogen bonds : bond 0.03521 ( 755) hydrogen bonds : angle 3.89817 ( 2295) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.560 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.5831 (tp30) cc_final: 0.5429 (tp30) REVERT: A 339 SER cc_start: 0.8919 (p) cc_final: 0.8635 (p) REVERT: A 545 ASP cc_start: 0.8035 (t0) cc_final: 0.7769 (t70) REVERT: A 695 MET cc_start: 0.9171 (ttp) cc_final: 0.8755 (ttm) REVERT: B 339 SER cc_start: 0.8907 (p) cc_final: 0.8630 (p) REVERT: B 545 ASP cc_start: 0.8018 (t0) cc_final: 0.7786 (t70) REVERT: B 582 GLU cc_start: 0.7252 (tp30) cc_final: 0.7012 (tp30) REVERT: B 695 MET cc_start: 0.9172 (ttp) cc_final: 0.8774 (ttm) REVERT: B 881 MET cc_start: 0.7248 (mtp) cc_final: 0.6672 (ppp) outliers start: 35 outliers final: 30 residues processed: 178 average time/residue: 0.0885 time to fit residues: 25.9513 Evaluate side-chains 170 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 70 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 67 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 75 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 54 optimal weight: 0.9980 chunk 110 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.101201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.080976 restraints weight = 32376.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.083163 restraints weight = 19022.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084594 restraints weight = 13579.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.085399 restraints weight = 11022.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.085650 restraints weight = 9744.953| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14098 Z= 0.117 Angle : 0.517 7.861 19202 Z= 0.262 Chirality : 0.042 0.206 2274 Planarity : 0.004 0.051 2446 Dihedral : 3.813 26.996 1906 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.31 % Allowed : 17.64 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.21), residues: 1792 helix: 2.07 (0.18), residues: 938 sheet: -0.03 (0.37), residues: 188 loop : -0.07 (0.25), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 11 TYR 0.033 0.002 TYR B 869 PHE 0.013 0.001 PHE B 364 TRP 0.016 0.001 TRP B 806 HIS 0.002 0.001 HIS A 729 Details of bonding type rmsd covalent geometry : bond 0.00268 (14098) covalent geometry : angle 0.51750 (19202) hydrogen bonds : bond 0.03514 ( 755) hydrogen bonds : angle 3.89785 ( 2295) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 143 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 116 GLU cc_start: 0.5858 (tp30) cc_final: 0.5463 (tp30) REVERT: A 339 SER cc_start: 0.8899 (p) cc_final: 0.8626 (p) REVERT: A 545 ASP cc_start: 0.8019 (t0) cc_final: 0.7771 (t70) REVERT: A 695 MET cc_start: 0.9163 (ttp) cc_final: 0.8747 (ttm) REVERT: B 339 SER cc_start: 0.8909 (p) cc_final: 0.8634 (p) REVERT: B 545 ASP cc_start: 0.8014 (t0) cc_final: 0.7786 (t70) REVERT: B 695 MET cc_start: 0.9165 (ttp) cc_final: 0.8761 (ttm) REVERT: B 820 MET cc_start: 0.7793 (mmm) cc_final: 0.6947 (tmm) outliers start: 34 outliers final: 31 residues processed: 170 average time/residue: 0.0797 time to fit residues: 22.6444 Evaluate side-chains 171 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 51 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 95 optimal weight: 0.0000 chunk 91 optimal weight: 0.2980 chunk 138 optimal weight: 0.0670 chunk 174 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 3 optimal weight: 0.0980 chunk 139 optimal weight: 0.4980 chunk 48 optimal weight: 0.2980 overall best weight: 0.1522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 734 ASN A 803 GLN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.104195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.084138 restraints weight = 32054.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.086360 restraints weight = 18803.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.087836 restraints weight = 13381.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.088769 restraints weight = 10764.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.089386 restraints weight = 9414.362| |-----------------------------------------------------------------------------| r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14098 Z= 0.095 Angle : 0.515 13.871 19202 Z= 0.256 Chirality : 0.041 0.202 2274 Planarity : 0.004 0.052 2446 Dihedral : 3.695 26.158 1906 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.56 % Allowed : 18.66 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.21), residues: 1792 helix: 2.21 (0.18), residues: 938 sheet: 0.02 (0.37), residues: 188 loop : -0.15 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 11 TYR 0.031 0.001 TYR B 869 PHE 0.013 0.001 PHE B 364 TRP 0.013 0.001 TRP B 806 HIS 0.008 0.001 HIS B 819 Details of bonding type rmsd covalent geometry : bond 0.00202 (14098) covalent geometry : angle 0.51454 (19202) hydrogen bonds : bond 0.03170 ( 755) hydrogen bonds : angle 3.76112 ( 2295) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3584 Ramachandran restraints generated. 1792 Oldfield, 0 Emsley, 1792 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: A 116 GLU cc_start: 0.5729 (tp30) cc_final: 0.5332 (tp30) REVERT: A 339 SER cc_start: 0.8947 (p) cc_final: 0.8725 (p) REVERT: A 679 MET cc_start: 0.6538 (tpt) cc_final: 0.6336 (tpt) REVERT: B 339 SER cc_start: 0.8922 (p) cc_final: 0.8681 (p) REVERT: B 856 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7789 (mt) outliers start: 23 outliers final: 20 residues processed: 180 average time/residue: 0.0815 time to fit residues: 24.4084 Evaluate side-chains 166 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 145 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 MET Chi-restraints excluded: chain B residue 299 MET Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 26 optimal weight: 0.3980 chunk 140 optimal weight: 0.6980 chunk 155 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 154 optimal weight: 0.7980 chunk 127 optimal weight: 0.8980 chunk 7 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 129 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 741 GLN B 741 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.102752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.082834 restraints weight = 32374.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.085086 restraints weight = 18686.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.086590 restraints weight = 13157.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.087550 restraints weight = 10568.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.088047 restraints weight = 9228.344| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.3556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14098 Z= 0.117 Angle : 0.572 13.278 19202 Z= 0.277 Chirality : 0.046 0.683 2274 Planarity : 0.004 0.050 2446 Dihedral : 3.803 26.526 1906 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.17 % Allowed : 18.93 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.57 (0.21), residues: 1792 helix: 2.13 (0.18), residues: 938 sheet: -0.13 (0.37), residues: 192 loop : -0.13 (0.25), residues: 662 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 11 TYR 0.036 0.001 TYR B 869 PHE 0.012 0.001 PHE A 807 TRP 0.014 0.001 TRP B 806 HIS 0.002 0.001 HIS B 388 Details of bonding type rmsd covalent geometry : bond 0.00270 (14098) covalent geometry : angle 0.57180 (19202) hydrogen bonds : bond 0.03385 ( 755) hydrogen bonds : angle 3.83201 ( 2295) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2248.71 seconds wall clock time: 39 minutes 51.97 seconds (2391.97 seconds total)