Starting phenix.real_space_refine on Mon Dec 30 19:51:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8uyc_42799/12_2024/8uyc_42799.cif Found real_map, /net/cci-nas-00/data/ceres_data/8uyc_42799/12_2024/8uyc_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_42799/12_2024/8uyc_42799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8uyc_42799/12_2024/8uyc_42799.map" model { file = "/net/cci-nas-00/data/ceres_data/8uyc_42799/12_2024/8uyc_42799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8uyc_42799/12_2024/8uyc_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 9.17, per 1000 atoms: 0.66 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: 3.10 Conformation dependent library (CDL) restraints added in 1.9 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: 1.86 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: 6.36 Time building geometry restraints manager: 3.69 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.840 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 35.840 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.850 ------------------------------------------------------------------------------- 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 : 1.653 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: 0.2689 time to fit residues: 135.7587 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 : 2.004 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 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 : 1.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8744 (mt) cc_final: 0.8492 (mp) REVERT: A 339 SER cc_start: 0.8803 (p) cc_final: 0.8568 (p) REVERT: A 545 ASP cc_start: 0.8117 (t0) cc_final: 0.7046 (p0) REVERT: A 737 TYR cc_start: 0.8311 (t80) cc_final: 0.8111 (t80) REVERT: A 856 LEU cc_start: 0.8157 (mt) cc_final: 0.7783 (mt) REVERT: B 339 SER cc_start: 0.8792 (p) cc_final: 0.8559 (p) REVERT: B 545 ASP cc_start: 0.8120 (t0) cc_final: 0.7084 (p0) REVERT: B 843 ILE cc_start: 0.8623 (mm) cc_final: 0.8317 (mt) REVERT: B 881 MET cc_start: 0.7511 (mtp) cc_final: 0.6787 (ppp) outliers start: 41 outliers final: 26 residues processed: 204 average time/residue: 0.2072 time to fit residues: 68.6884 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 : 1.583 ------------------------------------------------------------------------------- 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 50 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 110 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 161 optimal weight: 4.9990 chunk 174 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 160 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14098 Z= 0.184 Angle : 0.516 7.950 19202 Z= 0.266 Chirality : 0.041 0.142 2274 Planarity : 0.005 0.053 2446 Dihedral : 3.991 27.231 1906 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.97 % Allowed : 12.96 % Favored : 85.07 % 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: 1.23 (0.20), residues: 1792 helix: 1.80 (0.18), residues: 946 sheet: -0.23 (0.33), residues: 212 loop : -0.23 (0.25), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 806 HIS 0.005 0.001 HIS A 76 PHE 0.013 0.001 PHE A 364 TYR 0.020 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 189 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 160 time to evaluate : 1.681 Fit side-chains revert: symmetry clash REVERT: A 108 LEU cc_start: 0.8700 (mt) cc_final: 0.8470 (mp) REVERT: A 339 SER cc_start: 0.8930 (p) cc_final: 0.8713 (p) REVERT: A 545 ASP cc_start: 0.8046 (t0) cc_final: 0.7681 (t70) REVERT: A 843 ILE cc_start: 0.8657 (mm) cc_final: 0.8356 (mt) REVERT: B 127 MET cc_start: 0.7850 (ttm) cc_final: 0.7479 (ttm) REVERT: B 339 SER cc_start: 0.8914 (p) cc_final: 0.8639 (p) REVERT: B 545 ASP cc_start: 0.8029 (t0) cc_final: 0.7658 (t70) REVERT: B 843 ILE cc_start: 0.8614 (mm) cc_final: 0.8271 (mt) REVERT: B 881 MET cc_start: 0.7454 (mtp) cc_final: 0.6764 (ppp) outliers start: 29 outliers final: 21 residues processed: 185 average time/residue: 0.2087 time to fit residues: 62.4126 Evaluate side-chains 169 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.696 ------------------------------------------------------------------------------- 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 675 GLU Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 6.9990 chunk 121 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 154 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 HIS ** A 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 GLN A 472 GLN A 755 GLN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS ** B 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 GLN B 472 GLN B 741 GLN B 755 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 14098 Z= 0.387 Angle : 0.618 9.622 19202 Z= 0.322 Chirality : 0.045 0.234 2274 Planarity : 0.005 0.051 2446 Dihedral : 4.312 28.914 1906 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.73 % Allowed : 14.25 % Favored : 82.02 % 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: 1.02 (0.20), residues: 1792 helix: 1.59 (0.17), residues: 940 sheet: -0.26 (0.36), residues: 182 loop : -0.27 (0.25), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 760 HIS 0.004 0.001 HIS A 581 PHE 0.016 0.002 PHE B 101 TYR 0.024 0.002 TYR A 698 ARG 0.003 0.000 ARG B 8 *********************** 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 208 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 153 time to evaluate : 1.722 Fit side-chains REVERT: A 108 LEU cc_start: 0.8734 (mt) cc_final: 0.8462 (mp) REVERT: A 116 GLU cc_start: 0.5942 (tp30) cc_final: 0.5612 (tp30) REVERT: A 339 SER cc_start: 0.8907 (p) cc_final: 0.8661 (p) REVERT: A 545 ASP cc_start: 0.8120 (t0) cc_final: 0.7752 (t70) REVERT: B 323 SER cc_start: 0.8649 (t) cc_final: 0.8368 (p) REVERT: B 339 SER cc_start: 0.8893 (p) cc_final: 0.8622 (p) REVERT: B 545 ASP cc_start: 0.8121 (t0) cc_final: 0.7744 (t70) REVERT: B 737 TYR cc_start: 0.8239 (t80) cc_final: 0.7490 (t80) REVERT: B 741 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.7574 (mm-40) REVERT: B 881 MET cc_start: 0.7535 (mtp) cc_final: 0.6761 (ppp) outliers start: 55 outliers final: 30 residues processed: 200 average time/residue: 0.2067 time to fit residues: 66.6537 Evaluate side-chains 173 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 172 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 262 THR Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 710 VAL Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 846 ILE 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 262 THR Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 349 SER Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 710 VAL Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 741 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 128 optimal weight: 0.4980 chunk 70 optimal weight: 0.9980 chunk 146 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14098 Z= 0.176 Angle : 0.512 7.738 19202 Z= 0.265 Chirality : 0.041 0.176 2274 Planarity : 0.005 0.055 2446 Dihedral : 4.063 27.814 1906 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.31 % Allowed : 15.88 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.33 (0.21), residues: 1792 helix: 1.94 (0.18), residues: 930 sheet: -0.18 (0.36), residues: 190 loop : -0.24 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 806 HIS 0.003 0.001 HIS A 729 PHE 0.014 0.001 PHE A 364 TYR 0.018 0.001 TYR A 698 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 188 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 154 time to evaluate : 1.615 Fit side-chains REVERT: A 108 LEU cc_start: 0.8715 (mt) cc_final: 0.8427 (mp) REVERT: A 116 GLU cc_start: 0.5879 (tp30) cc_final: 0.5491 (tp30) REVERT: A 339 SER cc_start: 0.8938 (p) cc_final: 0.8667 (p) REVERT: A 545 ASP cc_start: 0.8016 (t0) cc_final: 0.7687 (t70) REVERT: A 695 MET cc_start: 0.9168 (ttp) cc_final: 0.8744 (ttm) REVERT: B 339 SER cc_start: 0.8933 (p) cc_final: 0.8647 (p) REVERT: B 545 ASP cc_start: 0.7994 (t0) cc_final: 0.7689 (t70) REVERT: B 695 MET cc_start: 0.9149 (ttp) cc_final: 0.8730 (ttm) REVERT: B 843 ILE cc_start: 0.8668 (mm) cc_final: 0.8361 (mt) REVERT: B 881 MET cc_start: 0.7425 (mtp) cc_final: 0.6795 (ppp) outliers start: 34 outliers final: 28 residues processed: 182 average time/residue: 0.2276 time to fit residues: 65.0128 Evaluate side-chains 170 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 1.711 ------------------------------------------------------------------------------- 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 187 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 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 817 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 0.0060 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 0.9980 chunk 42 optimal weight: 0.0970 chunk 172 optimal weight: 0.0870 chunk 142 optimal weight: 6.9990 chunk 79 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 166 optimal weight: 6.9990 overall best weight: 0.3972 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 ASN A 734 ASN ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3223 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= 0.141 Angle : 0.487 7.064 19202 Z= 0.250 Chirality : 0.040 0.145 2274 Planarity : 0.004 0.054 2446 Dihedral : 3.838 27.716 1906 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.10 % Allowed : 16.42 % Favored : 81.48 % 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: 2.11 (0.18), residues: 936 sheet: 0.02 (0.36), residues: 188 loop : -0.24 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 806 HIS 0.003 0.000 HIS B 388 PHE 0.011 0.001 PHE A 264 TYR 0.017 0.001 TYR A 869 ARG 0.005 0.000 ARG B 141 *********************** 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: 31 poor density : 159 time to evaluate : 1.625 Fit side-chains REVERT: A 116 GLU cc_start: 0.5848 (tp30) cc_final: 0.5447 (tp30) REVERT: A 296 MET cc_start: 0.9217 (ttp) cc_final: 0.8943 (ttp) REVERT: A 339 SER cc_start: 0.8934 (p) cc_final: 0.8684 (p) REVERT: A 545 ASP cc_start: 0.7975 (t0) cc_final: 0.7697 (t70) REVERT: A 679 MET cc_start: 0.6788 (tpt) cc_final: 0.6465 (tpt) REVERT: A 682 GLU cc_start: 0.7562 (tm-30) cc_final: 0.7253 (tm-30) REVERT: A 845 MET cc_start: 0.8020 (mtm) cc_final: 0.7789 (mtm) REVERT: B 339 SER cc_start: 0.8946 (p) cc_final: 0.8705 (p) REVERT: B 545 ASP cc_start: 0.7972 (t0) cc_final: 0.7712 (t70) REVERT: B 843 ILE cc_start: 0.8670 (mm) cc_final: 0.8334 (mt) REVERT: B 881 MET cc_start: 0.7318 (mtp) cc_final: 0.6727 (ppp) outliers start: 31 outliers final: 24 residues processed: 184 average time/residue: 0.2136 time to fit residues: 62.5873 Evaluate side-chains 162 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 138 time to evaluate : 1.624 ------------------------------------------------------------------------------- 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 126 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain 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 350 LYS Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 97 optimal weight: 0.0470 chunk 144 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 171 optimal weight: 6.9990 chunk 107 optimal weight: 0.3980 chunk 104 optimal weight: 0.9990 chunk 79 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.8884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3330 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= 0.179 Angle : 0.507 7.341 19202 Z= 0.260 Chirality : 0.041 0.209 2274 Planarity : 0.005 0.052 2446 Dihedral : 3.861 27.543 1906 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.71 % Allowed : 16.55 % Favored : 80.73 % 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: 1.53 (0.21), residues: 1792 helix: 2.09 (0.18), residues: 938 sheet: 0.26 (0.39), residues: 166 loop : -0.26 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 806 HIS 0.002 0.001 HIS A 729 PHE 0.012 0.001 PHE A 101 TYR 0.028 0.001 TYR B 869 ARG 0.005 0.000 ARG B 11 *********************** 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 187 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 147 time to evaluate : 1.691 Fit side-chains revert: symmetry clash REVERT: A 116 GLU cc_start: 0.5889 (tp30) cc_final: 0.5483 (tp30) REVERT: A 339 SER cc_start: 0.8922 (p) cc_final: 0.8677 (p) REVERT: A 545 ASP cc_start: 0.8034 (t0) cc_final: 0.7785 (t70) REVERT: B 116 GLU cc_start: 0.5806 (tp30) cc_final: 0.5434 (tp30) REVERT: B 339 SER cc_start: 0.8921 (p) cc_final: 0.8637 (p) REVERT: B 545 ASP cc_start: 0.8020 (t0) cc_final: 0.7768 (t70) REVERT: B 695 MET cc_start: 0.9164 (ttp) cc_final: 0.8759 (ttm) REVERT: B 881 MET cc_start: 0.7369 (mtp) cc_final: 0.6801 (ppp) outliers start: 40 outliers final: 28 residues processed: 180 average time/residue: 0.2133 time to fit residues: 62.0257 Evaluate side-chains 165 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 137 time to evaluate : 1.620 ------------------------------------------------------------------------------- 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 187 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 322 LEU Chi-restraints excluded: chain A residue 326 VAL Chi-restraints excluded: chain A residue 350 LYS Chi-restraints excluded: chain A residue 594 SER Chi-restraints excluded: chain A residue 675 GLU Chi-restraints excluded: chain A residue 712 SER Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 38 LEU Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 187 LEU Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 350 LYS Chi-restraints excluded: chain B residue 594 SER Chi-restraints excluded: chain B residue 675 GLU Chi-restraints excluded: chain B residue 712 SER Chi-restraints excluded: chain B residue 713 VAL Chi-restraints excluded: chain B residue 817 ILE Chi-restraints excluded: chain B residue 826 VAL Chi-restraints excluded: chain B residue 856 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 chunk 109 optimal weight: 3.9990 chunk 116 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 156 optimal weight: 0.6980 chunk 164 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 14098 Z= 0.161 Angle : 0.502 7.042 19202 Z= 0.255 Chirality : 0.041 0.214 2274 Planarity : 0.004 0.052 2446 Dihedral : 3.823 27.424 1906 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.31 % Allowed : 17.57 % Favored : 80.12 % 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: 1.57 (0.21), residues: 1792 helix: 2.12 (0.18), residues: 938 sheet: 0.18 (0.39), residues: 170 loop : -0.20 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 806 HIS 0.002 0.000 HIS B 388 PHE 0.012 0.001 PHE A 101 TYR 0.026 0.001 TYR B 869 ARG 0.004 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: 34 poor density : 147 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.5883 (tp30) cc_final: 0.5467 (tp30) REVERT: A 339 SER cc_start: 0.8946 (p) cc_final: 0.8710 (p) REVERT: A 545 ASP cc_start: 0.8056 (t0) cc_final: 0.7801 (t70) REVERT: B 116 GLU cc_start: 0.5784 (tp30) cc_final: 0.5415 (tp30) REVERT: B 339 SER cc_start: 0.8938 (p) cc_final: 0.8656 (p) REVERT: B 545 ASP cc_start: 0.8013 (t0) cc_final: 0.7744 (t70) REVERT: B 695 MET cc_start: 0.9154 (ttp) cc_final: 0.8742 (ttm) REVERT: B 881 MET cc_start: 0.7383 (mtp) cc_final: 0.6766 (ppp) outliers start: 34 outliers final: 26 residues processed: 175 average time/residue: 0.2205 time to fit residues: 62.4067 Evaluate side-chains 164 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 138 time to evaluate : 1.695 ------------------------------------------------------------------------------- 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 326 VAL 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 712 SER Chi-restraints excluded: chain A residue 817 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 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 712 SER 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 149 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 chunk 164 optimal weight: 0.0470 chunk 96 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 49 optimal weight: 0.5980 chunk 144 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 104 optimal weight: 4.9990 chunk 169 optimal weight: 3.9990 overall best weight: 1.5082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 GLN B 741 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3536 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= 0.253 Angle : 0.544 7.832 19202 Z= 0.278 Chirality : 0.043 0.237 2274 Planarity : 0.005 0.050 2446 Dihedral : 3.983 27.501 1906 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.10 % Allowed : 17.98 % Favored : 79.92 % 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: 1.93 (0.18), residues: 948 sheet: 0.24 (0.39), residues: 166 loop : -0.20 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 760 HIS 0.003 0.001 HIS A 401 PHE 0.012 0.001 PHE B 364 TYR 0.031 0.002 TYR B 869 ARG 0.003 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 171 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.5963 (tp30) cc_final: 0.5594 (tp30) REVERT: A 339 SER cc_start: 0.8931 (p) cc_final: 0.8644 (p) REVERT: A 368 ASP cc_start: 0.8879 (p0) cc_final: 0.8573 (p0) REVERT: A 545 ASP cc_start: 0.8177 (t0) cc_final: 0.7922 (t70) REVERT: A 695 MET cc_start: 0.9171 (ttp) cc_final: 0.8742 (ttm) REVERT: A 737 TYR cc_start: 0.8044 (t80) cc_final: 0.7667 (t80) REVERT: B 116 GLU cc_start: 0.5897 (tp30) cc_final: 0.5544 (tp30) REVERT: B 339 SER cc_start: 0.8918 (p) cc_final: 0.8629 (p) REVERT: B 545 ASP cc_start: 0.8089 (t0) cc_final: 0.7790 (t70) REVERT: B 695 MET cc_start: 0.9155 (ttp) cc_final: 0.8742 (ttm) REVERT: B 881 MET cc_start: 0.7424 (mtp) cc_final: 0.6783 (ppp) outliers start: 31 outliers final: 29 residues processed: 164 average time/residue: 0.2116 time to fit residues: 56.2383 Evaluate side-chains 169 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 140 time to evaluate : 1.645 ------------------------------------------------------------------------------- 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 326 VAL 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 817 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 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 712 SER 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 103 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 163 optimal weight: 0.6980 chunk 141 optimal weight: 0.0980 chunk 14 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 814 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.3583 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= 0.209 Angle : 0.531 7.315 19202 Z= 0.270 Chirality : 0.042 0.222 2274 Planarity : 0.004 0.050 2446 Dihedral : 3.977 27.497 1906 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.17 % Allowed : 18.05 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 946 sheet: 0.06 (0.38), residues: 170 loop : -0.15 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 806 HIS 0.002 0.001 HIS A 230 PHE 0.019 0.001 PHE A 101 TYR 0.035 0.002 TYR A 869 ARG 0.003 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 171 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 139 time to evaluate : 1.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 116 GLU cc_start: 0.5949 (tp30) cc_final: 0.5589 (tp30) REVERT: A 339 SER cc_start: 0.8911 (p) cc_final: 0.8617 (p) REVERT: A 545 ASP cc_start: 0.8156 (t0) cc_final: 0.7929 (t70) REVERT: A 695 MET cc_start: 0.9152 (ttp) cc_final: 0.8721 (ttm) REVERT: B 116 GLU cc_start: 0.5848 (tp30) cc_final: 0.5500 (tp30) REVERT: B 339 SER cc_start: 0.8902 (p) cc_final: 0.8601 (p) REVERT: B 545 ASP cc_start: 0.8079 (t0) cc_final: 0.7814 (t70) REVERT: B 695 MET cc_start: 0.9141 (ttp) cc_final: 0.8726 (ttm) REVERT: B 881 MET cc_start: 0.7400 (mtp) cc_final: 0.6784 (ppp) outliers start: 32 outliers final: 30 residues processed: 165 average time/residue: 0.2185 time to fit residues: 58.0580 Evaluate side-chains 166 residues out of total 1526 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 136 time to evaluate : 1.637 ------------------------------------------------------------------------------- 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 326 VAL 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 817 ILE Chi-restraints excluded: chain A residue 826 VAL Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 124 ILE 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 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 712 SER 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: 2.9990 chunk 130 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 141 optimal weight: 0.9990 chunk 59 optimal weight: 0.0270 chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 814 GLN ** 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 = 0.3444 r_free = 0.3444 target = 0.100577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.079624 restraints weight = 32552.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.081818 restraints weight = 19109.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.083290 restraints weight = 13649.647| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14098 Z= 0.186 Angle : 0.533 7.540 19202 Z= 0.268 Chirality : 0.042 0.222 2274 Planarity : 0.004 0.050 2446 Dihedral : 3.959 27.037 1906 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.37 % Allowed : 18.05 % Favored : 79.58 % 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: 2.00 (0.18), residues: 946 sheet: 0.07 (0.38), residues: 170 loop : -0.15 (0.25), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 806 HIS 0.002 0.001 HIS A 230 PHE 0.015 0.001 PHE A 101 TYR 0.027 0.001 TYR B 869 ARG 0.003 0.000 ARG A 141 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2860.59 seconds wall clock time: 54 minutes 10.18 seconds (3250.18 seconds total)