Starting phenix.real_space_refine on Sun Jan 19 14:25:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uyc_42799/01_2025/8uyc_42799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uyc_42799/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8uyc_42799/01_2025/8uyc_42799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uyc_42799/01_2025/8uyc_42799.map" model { file = "/net/cci-nas-00/data/ceres_data/8uyc_42799/01_2025/8uyc_42799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uyc_42799/01_2025/8uyc_42799.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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, 'ASN:plan1': 1, 'GLN:plan1': 5, '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, 'ASN:plan1': 1, 'GLN:plan1': 5, '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: 9.66, per 1000 atoms: 0.70 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: 3.72 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.78 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: 5.35 Time building geometry restraints manager: 4.16 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: 0.07 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: 3.710 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: 0.020 Extract box with map and model: 0.590 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 35.380 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.000 ------------------------------------------------------------------------------- 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= 0.144 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 : 7.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (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 TRP 0.005 0.001 TRP A 760 HIS 0.001 0.000 HIS B 230 PHE 0.012 0.001 PHE B 264 TYR 0.008 0.001 TYR A 698 ARG 0.003 0.000 ARG A 650 *********************** 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 : 1.579 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: 0.2713 time to fit residues: 135.7297 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 : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 74 optimal weight: 0.0870 chunk 46 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 72 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 overall best weight: 1.9564 ------------------------------------------------------------------------------- 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 ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.099203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.078610 restraints weight = 32366.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.080732 restraints weight = 18795.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.082157 restraints weight = 13453.180| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 14098 Z= 0.325 Angle : 0.612 9.734 19202 Z= 0.319 Chirality : 0.045 0.159 2274 Planarity : 0.005 0.050 2446 Dihedral : 4.178 29.691 1906 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.78 % Allowed : 9.84 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.20), residues: 1792 helix: 1.58 (0.18), residues: 944 sheet: -0.21 (0.34), residues: 208 loop : -0.26 (0.25), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 806 HIS 0.011 0.002 HIS B 76 PHE 0.015 0.002 PHE B 614 TYR 0.031 0.002 TYR A 698 ARG 0.006 0.001 ARG A 616 *********************** 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 217 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 176 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8745 (mt) cc_final: 0.8495 (mp) REVERT: A 339 SER cc_start: 0.8789 (p) cc_final: 0.8560 (p) REVERT: A 545 ASP cc_start: 0.8111 (t0) cc_final: 0.7037 (p0) REVERT: A 737 TYR cc_start: 0.8320 (t80) cc_final: 0.8117 (t80) REVERT: A 856 LEU cc_start: 0.8166 (mt) cc_final: 0.7793 (mt) REVERT: B 339 SER cc_start: 0.8773 (p) cc_final: 0.8547 (p) REVERT: B 545 ASP cc_start: 0.8119 (t0) cc_final: 0.7079 (p0) REVERT: B 843 ILE cc_start: 0.8620 (mm) cc_final: 0.8311 (mt) REVERT: B 881 MET cc_start: 0.7550 (mtp) cc_final: 0.6790 (ppp) outliers start: 41 outliers final: 26 residues processed: 204 average time/residue: 0.1955 time to fit residues: 64.9269 Evaluate side-chains 177 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.572 ------------------------------------------------------------------------------- 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 262 THR Chi-restraints excluded: chain A residue 326 VAL 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 795 THR Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 262 THR 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 710 VAL Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 817 ILE 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 89 optimal weight: 10.0000 chunk 32 optimal weight: 0.5980 chunk 118 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 105 optimal weight: 8.9990 chunk 170 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 70 optimal weight: 0.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 472 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 = 0.3426 r_free = 0.3426 target = 0.099582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.078751 restraints weight = 32485.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.080938 restraints weight = 18968.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.082368 restraints weight = 13581.838| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 14098 Z= 0.235 Angle : 0.536 8.425 19202 Z= 0.278 Chirality : 0.042 0.149 2274 Planarity : 0.005 0.052 2446 Dihedral : 4.076 27.492 1906 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.24 % Allowed : 13.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.20), residues: 1792 helix: 1.74 (0.18), residues: 944 sheet: -0.28 (0.33), residues: 212 loop : -0.23 (0.25), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 760 HIS 0.005 0.001 HIS B 76 PHE 0.013 0.002 PHE A 364 TYR 0.022 0.001 TYR A 698 ARG 0.004 0.000 ARG A 507 *********************** 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 192 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8726 (mt) cc_final: 0.8461 (mp) REVERT: A 339 SER cc_start: 0.8914 (p) cc_final: 0.8699 (p) REVERT: A 545 ASP cc_start: 0.8021 (t0) cc_final: 0.7623 (t70) REVERT: A 737 TYR cc_start: 0.8235 (t80) cc_final: 0.7913 (t80) REVERT: A 843 ILE cc_start: 0.8684 (mm) cc_final: 0.8351 (mt) REVERT: A 856 LEU cc_start: 0.8117 (mt) cc_final: 0.7803 (mt) REVERT: B 339 SER cc_start: 0.8902 (p) cc_final: 0.8628 (p) REVERT: B 545 ASP cc_start: 0.8015 (t0) cc_final: 0.7628 (t70) REVERT: B 843 ILE cc_start: 0.8671 (mm) cc_final: 0.8365 (mt) REVERT: B 881 MET cc_start: 0.7535 (mtp) cc_final: 0.6778 (ppp) outliers start: 33 outliers final: 23 residues processed: 187 average time/residue: 0.2119 time to fit residues: 63.9309 Evaluate side-chains 182 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 159 time to evaluate : 1.545 ------------------------------------------------------------------------------- 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 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 817 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 322 LEU 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 712 SER Chi-restraints excluded: chain B residue 735 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 79 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 104 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 472 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.100128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.079391 restraints weight = 32285.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.081608 restraints weight = 18811.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.083074 restraints weight = 13376.927| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 14098 Z= 0.200 Angle : 0.515 8.076 19202 Z= 0.266 Chirality : 0.042 0.209 2274 Planarity : 0.005 0.053 2446 Dihedral : 3.966 28.620 1906 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.71 % Allowed : 14.25 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.21), residues: 1792 helix: 1.95 (0.18), residues: 930 sheet: -0.16 (0.33), residues: 208 loop : -0.21 (0.25), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 806 HIS 0.003 0.001 HIS A 76 PHE 0.013 0.001 PHE A 364 TYR 0.020 0.001 TYR A 698 ARG 0.002 0.000 ARG A 616 *********************** 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 203 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 1.699 Fit side-chains REVERT: A 108 LEU cc_start: 0.8699 (mt) cc_final: 0.8471 (mp) REVERT: A 339 SER cc_start: 0.8941 (p) cc_final: 0.8667 (p) REVERT: A 545 ASP cc_start: 0.8057 (t0) cc_final: 0.7702 (t70) REVERT: A 695 MET cc_start: 0.9190 (ttp) cc_final: 0.8758 (ttm) REVERT: A 737 TYR cc_start: 0.8224 (t80) cc_final: 0.7815 (t80) REVERT: A 843 ILE cc_start: 0.8663 (mm) cc_final: 0.8375 (mt) REVERT: B 339 SER cc_start: 0.8931 (p) cc_final: 0.8694 (p) REVERT: B 545 ASP cc_start: 0.8051 (t0) cc_final: 0.7702 (t70) REVERT: B 843 ILE cc_start: 0.8682 (mm) cc_final: 0.8367 (mt) REVERT: B 881 MET cc_start: 0.7448 (mtp) cc_final: 0.6741 (ppp) outliers start: 40 outliers final: 27 residues processed: 196 average time/residue: 0.2011 time to fit residues: 64.1590 Evaluate side-chains 168 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 1.641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU 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 322 LEU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 350 LYS 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 735 LEU 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 112 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 322 LEU 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 817 ILE Chi-restraints excluded: chain B residue 826 VAL 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 51 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 19 optimal weight: 0.7980 chunk 47 optimal weight: 0.0020 chunk 84 optimal weight: 0.7980 chunk 173 optimal weight: 0.9980 chunk 136 optimal weight: 0.0370 chunk 41 optimal weight: 0.4980 chunk 62 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 overall best weight: 0.4266 ------------------------------------------------------------------------------- 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 = 0.3467 r_free = 0.3467 target = 0.102117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.081634 restraints weight = 32197.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.083894 restraints weight = 18718.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.085396 restraints weight = 13271.777| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14098 Z= 0.141 Angle : 0.488 7.261 19202 Z= 0.251 Chirality : 0.041 0.209 2274 Planarity : 0.004 0.053 2446 Dihedral : 3.871 27.325 1906 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.31 % Allowed : 15.47 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.21), residues: 1792 helix: 2.14 (0.18), residues: 920 sheet: -0.02 (0.36), residues: 188 loop : -0.24 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 806 HIS 0.003 0.001 HIS A 388 PHE 0.016 0.001 PHE B 101 TYR 0.017 0.001 TYR B 869 ARG 0.003 0.000 ARG A 507 *********************** 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 189 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 1.551 Fit side-chains REVERT: A 339 SER cc_start: 0.8942 (p) cc_final: 0.8723 (p) REVERT: A 545 ASP cc_start: 0.7998 (t0) cc_final: 0.7681 (t70) REVERT: A 737 TYR cc_start: 0.8033 (t80) cc_final: 0.7757 (t80) REVERT: A 843 ILE cc_start: 0.8637 (mm) cc_final: 0.8268 (mt) REVERT: B 296 MET cc_start: 0.9226 (ttp) cc_final: 0.9002 (ttp) REVERT: B 339 SER cc_start: 0.8932 (p) cc_final: 0.8706 (p) REVERT: B 545 ASP cc_start: 0.7956 (t0) cc_final: 0.7632 (t70) REVERT: B 843 ILE cc_start: 0.8658 (mm) cc_final: 0.8313 (mt) REVERT: B 881 MET cc_start: 0.7396 (mtp) cc_final: 0.6752 (ppp) outliers start: 34 outliers final: 22 residues processed: 182 average time/residue: 0.1976 time to fit residues: 59.1196 Evaluate side-chains 159 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 137 time to evaluate : 1.553 ------------------------------------------------------------------------------- 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 187 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 730 LEU 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 254 MET Chi-restraints excluded: chain B residue 322 LEU 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 730 LEU Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 826 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 171 optimal weight: 0.7980 chunk 139 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 101 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 35 optimal weight: 0.0070 chunk 93 optimal weight: 7.9990 chunk 165 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 52 optimal weight: 7.9990 chunk 118 optimal weight: 1.9990 overall best weight: 2.1604 ------------------------------------------------------------------------------- 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 209 GLN A 755 GLN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 741 GLN B 755 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.097404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.076676 restraints weight = 33194.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.078779 restraints weight = 19584.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.080169 restraints weight = 14081.170| |-----------------------------------------------------------------------------| r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 14098 Z= 0.344 Angle : 0.597 9.813 19202 Z= 0.311 Chirality : 0.045 0.195 2274 Planarity : 0.005 0.049 2446 Dihedral : 4.204 28.699 1906 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 2.99 % Allowed : 15.88 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.20), residues: 1792 helix: 1.72 (0.18), residues: 938 sheet: 0.02 (0.37), residues: 182 loop : -0.23 (0.24), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 760 HIS 0.004 0.001 HIS A 41 PHE 0.020 0.002 PHE B 101 TYR 0.019 0.002 TYR A 698 ARG 0.003 0.000 ARG B 8 *********************** 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 190 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 1.709 Fit side-chains REVERT: A 339 SER cc_start: 0.8899 (p) cc_final: 0.8608 (p) REVERT: A 545 ASP cc_start: 0.8147 (t0) cc_final: 0.7825 (t70) REVERT: A 589 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7701 (pm20) REVERT: A 695 MET cc_start: 0.9163 (ttp) cc_final: 0.8727 (ttm) REVERT: A 737 TYR cc_start: 0.8475 (t80) cc_final: 0.7829 (t80) REVERT: B 339 SER cc_start: 0.8892 (p) cc_final: 0.8575 (p) REVERT: B 368 ASP cc_start: 0.8936 (p0) cc_final: 0.8666 (p0) REVERT: B 545 ASP cc_start: 0.8137 (t0) cc_final: 0.7815 (t70) REVERT: B 589 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7730 (pm20) REVERT: B 695 MET cc_start: 0.9147 (ttp) cc_final: 0.8713 (ttm) REVERT: B 737 TYR cc_start: 0.8223 (t80) cc_final: 0.7687 (t80) REVERT: B 881 MET cc_start: 0.7435 (mtp) cc_final: 0.6816 (ppp) outliers start: 44 outliers final: 30 residues processed: 182 average time/residue: 0.2205 time to fit residues: 63.3039 Evaluate side-chains 168 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 1.622 ------------------------------------------------------------------------------- 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 187 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 589 GLU 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 713 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 846 ILE Chi-restraints excluded: chain A residue 856 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 322 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 589 GLU 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 730 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 817 ILE 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 142 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 116 optimal weight: 9.9990 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.097923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.077281 restraints weight = 32965.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.079419 restraints weight = 19374.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.080787 restraints weight = 13880.727| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14098 Z= 0.288 Angle : 0.562 8.184 19202 Z= 0.292 Chirality : 0.043 0.176 2274 Planarity : 0.005 0.049 2446 Dihedral : 4.192 28.358 1906 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.78 % Allowed : 16.28 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.20), residues: 1792 helix: 1.74 (0.18), residues: 940 sheet: 0.01 (0.38), residues: 182 loop : -0.25 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 760 HIS 0.003 0.001 HIS A 581 PHE 0.029 0.002 PHE B 101 TYR 0.019 0.002 TYR B 869 ARG 0.005 0.000 ARG B 141 *********************** 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 184 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 143 time to evaluate : 1.521 Fit side-chains REVERT: A 339 SER cc_start: 0.8886 (p) cc_final: 0.8599 (p) REVERT: A 545 ASP cc_start: 0.8115 (t0) cc_final: 0.7839 (t70) REVERT: A 589 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7674 (pm20) REVERT: A 695 MET cc_start: 0.9168 (ttp) cc_final: 0.8731 (ttm) REVERT: A 820 MET cc_start: 0.7872 (mmm) cc_final: 0.7341 (tmm) REVERT: B 339 SER cc_start: 0.8881 (p) cc_final: 0.8597 (p) REVERT: B 368 ASP cc_start: 0.8923 (p0) cc_final: 0.8711 (p0) REVERT: B 545 ASP cc_start: 0.8141 (t0) cc_final: 0.7901 (t70) REVERT: B 589 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7772 (pm20) REVERT: B 695 MET cc_start: 0.9140 (ttp) cc_final: 0.8711 (ttm) REVERT: B 737 TYR cc_start: 0.8277 (t80) cc_final: 0.7796 (t80) REVERT: B 881 MET cc_start: 0.7417 (mtp) cc_final: 0.6714 (ppp) outliers start: 41 outliers final: 33 residues processed: 180 average time/residue: 0.2013 time to fit residues: 58.5216 Evaluate side-chains 170 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 135 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 124 ILE 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 349 SER Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 589 GLU 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 713 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 124 ILE Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 589 GLU 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 730 LEU Chi-restraints excluded: chain B residue 795 THR Chi-restraints excluded: chain B residue 817 ILE 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 36 optimal weight: 2.9990 chunk 128 optimal weight: 0.1980 chunk 110 optimal weight: 2.9990 chunk 156 optimal weight: 0.8980 chunk 152 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 114 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 108 optimal weight: 0.7980 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 = 0.3437 r_free = 0.3437 target = 0.100248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.079489 restraints weight = 32588.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.081720 restraints weight = 19120.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.083182 restraints weight = 13686.336| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14098 Z= 0.173 Angle : 0.519 7.234 19202 Z= 0.265 Chirality : 0.041 0.165 2274 Planarity : 0.005 0.050 2446 Dihedral : 4.000 27.637 1906 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.37 % Allowed : 16.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.21), residues: 1792 helix: 1.96 (0.18), residues: 940 sheet: 0.14 (0.40), residues: 166 loop : -0.16 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 806 HIS 0.002 0.001 HIS B 581 PHE 0.021 0.001 PHE B 101 TYR 0.020 0.001 TYR A 869 ARG 0.005 0.000 ARG A 141 *********************** 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 181 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.506 Fit side-chains revert: symmetry clash REVERT: A 339 SER cc_start: 0.8896 (p) cc_final: 0.8617 (p) REVERT: A 545 ASP cc_start: 0.8143 (t0) cc_final: 0.7857 (t70) REVERT: A 695 MET cc_start: 0.9161 (ttp) cc_final: 0.8730 (ttm) REVERT: A 730 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8569 (tt) REVERT: B 339 SER cc_start: 0.8892 (p) cc_final: 0.8606 (p) REVERT: B 545 ASP cc_start: 0.8080 (t0) cc_final: 0.7830 (t70) REVERT: B 695 MET cc_start: 0.9154 (ttp) cc_final: 0.8726 (ttm) REVERT: B 881 MET cc_start: 0.7394 (mtp) cc_final: 0.6815 (ppp) outliers start: 35 outliers final: 23 residues processed: 176 average time/residue: 0.2086 time to fit residues: 59.1403 Evaluate side-chains 164 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.658 ------------------------------------------------------------------------------- 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 187 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 856 LEU 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 322 LEU Chi-restraints excluded: chain B residue 350 LYS 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 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 83 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 0.4980 chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 0.0970 chunk 17 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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** ** 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 = 0.3438 r_free = 0.3438 target = 0.100302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.079801 restraints weight = 32271.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.081915 restraints weight = 19296.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.083315 restraints weight = 13989.108| |-----------------------------------------------------------------------------| r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14098 Z= 0.186 Angle : 0.534 7.633 19202 Z= 0.271 Chirality : 0.042 0.238 2274 Planarity : 0.005 0.049 2446 Dihedral : 3.975 27.362 1906 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.24 % Allowed : 16.89 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.21), residues: 1792 helix: 1.95 (0.18), residues: 940 sheet: 0.03 (0.38), residues: 170 loop : -0.14 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 806 HIS 0.002 0.001 HIS A 76 PHE 0.020 0.001 PHE B 101 TYR 0.032 0.001 TYR B 869 ARG 0.005 0.000 ARG B 141 *********************** 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 180 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 147 time to evaluate : 1.490 Fit side-chains REVERT: A 339 SER cc_start: 0.8885 (p) cc_final: 0.8585 (p) REVERT: A 545 ASP cc_start: 0.8083 (t0) cc_final: 0.7849 (t70) REVERT: A 695 MET cc_start: 0.9161 (ttp) cc_final: 0.8731 (ttm) REVERT: B 339 SER cc_start: 0.8878 (p) cc_final: 0.8582 (p) REVERT: B 545 ASP cc_start: 0.8092 (t0) cc_final: 0.7844 (t70) REVERT: B 695 MET cc_start: 0.9142 (ttp) cc_final: 0.8716 (ttm) REVERT: B 820 MET cc_start: 0.7855 (mmm) cc_final: 0.7380 (tmm) REVERT: B 881 MET cc_start: 0.7371 (mtp) cc_final: 0.6718 (ppp) outliers start: 33 outliers final: 27 residues processed: 172 average time/residue: 0.1988 time to fit residues: 55.2598 Evaluate side-chains 164 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 137 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 HIS 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 187 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 322 LEU 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 713 VAL Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain A residue 856 LEU 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 187 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 350 LYS 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 795 THR 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 43 optimal weight: 0.8980 chunk 165 optimal weight: 3.9990 chunk 1 optimal weight: 0.0970 chunk 106 optimal weight: 5.9990 chunk 128 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 157 optimal weight: 0.6980 chunk 174 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 741 GLN ** 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 = 0.3473 r_free = 0.3473 target = 0.102100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.081588 restraints weight = 32401.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.083799 restraints weight = 19239.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.085273 restraints weight = 13772.748| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 14098 Z= 0.151 Angle : 0.529 7.828 19202 Z= 0.264 Chirality : 0.042 0.235 2274 Planarity : 0.004 0.050 2446 Dihedral : 3.917 26.988 1906 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.63 % Allowed : 17.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.21), residues: 1792 helix: 2.08 (0.18), residues: 930 sheet: 0.05 (0.38), residues: 172 loop : -0.18 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 806 HIS 0.003 0.001 HIS A 388 PHE 0.017 0.001 PHE B 101 TYR 0.024 0.001 TYR A 869 ARG 0.005 0.000 ARG A 141 ********************** 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 174 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 150 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 339 SER cc_start: 0.8912 (p) cc_final: 0.8663 (p) REVERT: A 545 ASP cc_start: 0.8072 (t0) cc_final: 0.7846 (t70) REVERT: A 846 ILE cc_start: 0.8696 (mm) cc_final: 0.8415 (mt) REVERT: B 116 GLU cc_start: 0.5749 (tp30) cc_final: 0.5381 (tp30) REVERT: B 339 SER cc_start: 0.8895 (p) cc_final: 0.8648 (p) REVERT: B 881 MET cc_start: 0.7394 (mtp) cc_final: 0.6718 (ppp) outliers start: 24 outliers final: 20 residues processed: 167 average time/residue: 0.2006 time to fit residues: 54.3341 Evaluate side-chains 158 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 127 MET 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 589 GLU Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 712 SER 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 187 LEU Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 795 THR 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 163 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 138 optimal weight: 0.0060 chunk 1 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.4980 chunk 75 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.102810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.082258 restraints weight = 32645.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.084442 restraints weight = 19403.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.085917 restraints weight = 13885.288| |-----------------------------------------------------------------------------| r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14098 Z= 0.159 Angle : 0.545 7.961 19202 Z= 0.270 Chirality : 0.042 0.228 2274 Planarity : 0.005 0.050 2446 Dihedral : 3.897 26.489 1906 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.42 % Allowed : 18.25 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.21), residues: 1792 helix: 2.06 (0.18), residues: 932 sheet: 0.24 (0.38), residues: 168 loop : -0.22 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 806 HIS 0.003 0.001 HIS A 388 PHE 0.016 0.001 PHE B 101 TYR 0.035 0.001 TYR B 869 ARG 0.005 0.000 ARG A 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4070.35 seconds wall clock time: 74 minutes 13.92 seconds (4453.92 seconds total)