Starting phenix.real_space_refine on Fri Sep 27 17:01:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/09_2024/3j9p_6267.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/09_2024/3j9p_6267.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/09_2024/3j9p_6267.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/09_2024/3j9p_6267.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/09_2024/3j9p_6267.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j9p_6267/09_2024/3j9p_6267.cif" } resolution = 4.24 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 1.000 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: 4 Type Number sf(0) Gaussians S 120 5.16 5 C 11100 2.51 5 N 2844 2.21 5 O 2888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 16952 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 560, 4238 Classifications: {'peptide': 560} Incomplete info: {'truncation_to_alanine': 90} Link IDs: {'CIS': 22, 'PCIS': 1, 'PTRANS': 17, 'TRANS': 519} Chain breaks: 4 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 302 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 240 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 7, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 163 Restraints were copied for chains: C, B, D Time building chain proxies: 9.41, per 1000 atoms: 0.56 Number of scatterers: 16952 At special positions: 0 Unit cell: (115.482, 115.482, 142.225, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 120 16.00 O 2888 8.00 N 2844 7.00 C 11100 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: 4.71 Conformation dependent library (CDL) restraints added in 2.5 seconds 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4296 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 0 sheets defined 65.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'D' and resid 448 through 457 removed outlier: 3.976A pdb=" N PHE D 452 " --> pdb=" O SER D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 467 Processing helix chain 'D' and resid 484 through 492 removed outlier: 3.533A pdb=" N ALA D 490 " --> pdb=" O LEU D 486 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN D 492 " --> pdb=" O LEU D 488 " (cutoff:3.500A) Processing helix chain 'D' and resid 494 through 505 Processing helix chain 'D' and resid 516 through 522 removed outlier: 4.207A pdb=" N HIS D 520 " --> pdb=" O THR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 537 removed outlier: 3.740A pdb=" N LEU D 534 " --> pdb=" O MET D 530 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN D 537 " --> pdb=" O ILE D 533 " (cutoff:3.500A) Processing helix chain 'D' and resid 550 through 556 Processing helix chain 'D' and resid 560 through 569 removed outlier: 4.355A pdb=" N VAL D 564 " --> pdb=" O HIS D 560 " (cutoff:3.500A) Processing helix chain 'D' and resid 582 through 589 Processing helix chain 'D' and resid 592 through 602 removed outlier: 4.150A pdb=" N VAL D 596 " --> pdb=" O ARG D 592 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE D 600 " --> pdb=" O VAL D 596 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG D 601 " --> pdb=" O LEU D 597 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER D 602 " --> pdb=" O THR D 598 " (cutoff:3.500A) Processing helix chain 'D' and resid 620 through 627 Processing helix chain 'D' and resid 629 through 637 removed outlier: 3.575A pdb=" N CYS D 633 " --> pdb=" O TYR D 629 " (cutoff:3.500A) Processing helix chain 'D' and resid 684 through 691 Processing helix chain 'D' and resid 703 through 740 removed outlier: 3.763A pdb=" N TYR D 714 " --> pdb=" O LYS D 710 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET D 721 " --> pdb=" O ARG D 717 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY D 729 " --> pdb=" O SER D 725 " (cutoff:3.500A) Proline residue: D 732 - end of helix Processing helix chain 'D' and resid 766 through 783 removed outlier: 3.548A pdb=" N ILE D 770 " --> pdb=" O ASN D 766 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE D 782 " --> pdb=" O PHE D 778 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE D 783 " --> pdb=" O LEU D 779 " (cutoff:3.500A) Processing helix chain 'D' and resid 804 through 820 removed outlier: 3.753A pdb=" N TYR D 812 " --> pdb=" O GLU D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 821 through 823 No H-bonds generated for 'chain 'D' and resid 821 through 823' Processing helix chain 'D' and resid 828 through 850 removed outlier: 3.694A pdb=" N ALA D 836 " --> pdb=" O TRP D 832 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE D 837 " --> pdb=" O GLN D 833 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU D 848 " --> pdb=" O MET D 844 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR D 849 " --> pdb=" O ASN D 845 " (cutoff:3.500A) Processing helix chain 'D' and resid 858 through 892 removed outlier: 3.904A pdb=" N ARG D 872 " --> pdb=" O LYS D 868 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER D 873 " --> pdb=" O THR D 869 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU D 882 " --> pdb=" O ILE D 878 " (cutoff:3.500A) Processing helix chain 'D' and resid 900 through 913 removed outlier: 4.276A pdb=" N LEU D 913 " --> pdb=" O PHE D 909 " (cutoff:3.500A) Processing helix chain 'D' and resid 922 through 929 Processing helix chain 'D' and resid 933 through 948 removed outlier: 4.001A pdb=" N ALA D 939 " --> pdb=" O VAL D 935 " (cutoff:3.500A) Processing helix chain 'D' and resid 950 through 970 removed outlier: 3.965A pdb=" N HIS D 970 " --> pdb=" O ASP D 966 " (cutoff:3.500A) Processing helix chain 'D' and resid 970 through 988 removed outlier: 4.264A pdb=" N LYS D 974 " --> pdb=" O HIS D 970 " (cutoff:3.500A) Processing helix chain 'D' and resid 1040 through 1071 removed outlier: 4.217A pdb=" N ILE D1044 " --> pdb=" O LEU D1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR D1049 " --> pdb=" O LEU D1045 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG D1050 " --> pdb=" O LYS D1046 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS D1060 " --> pdb=" O PHE D1056 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN D1061 " --> pdb=" O LEU D1057 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D1071 " --> pdb=" O LEU D1067 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 457 removed outlier: 3.977A pdb=" N PHE A 452 " --> pdb=" O SER A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 458 through 467 Processing helix chain 'A' and resid 484 through 492 removed outlier: 3.533A pdb=" N ALA A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASN A 492 " --> pdb=" O LEU A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 516 through 522 removed outlier: 4.207A pdb=" N HIS A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 537 removed outlier: 3.740A pdb=" N LEU A 534 " --> pdb=" O MET A 530 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASN A 537 " --> pdb=" O ILE A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 556 Processing helix chain 'A' and resid 560 through 569 removed outlier: 4.356A pdb=" N VAL A 564 " --> pdb=" O HIS A 560 " (cutoff:3.500A) Processing helix chain 'A' and resid 582 through 589 Processing helix chain 'A' and resid 592 through 602 removed outlier: 4.150A pdb=" N VAL A 596 " --> pdb=" O ARG A 592 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG A 601 " --> pdb=" O LEU A 597 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER A 602 " --> pdb=" O THR A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 627 Processing helix chain 'A' and resid 629 through 637 removed outlier: 3.574A pdb=" N CYS A 633 " --> pdb=" O TYR A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 684 through 691 Processing helix chain 'A' and resid 703 through 740 removed outlier: 3.764A pdb=" N TYR A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 721 " --> pdb=" O ARG A 717 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY A 729 " --> pdb=" O SER A 725 " (cutoff:3.500A) Proline residue: A 732 - end of helix Processing helix chain 'A' and resid 766 through 783 removed outlier: 3.547A pdb=" N ILE A 770 " --> pdb=" O ASN A 766 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A 782 " --> pdb=" O PHE A 778 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE A 783 " --> pdb=" O LEU A 779 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 820 removed outlier: 3.752A pdb=" N TYR A 812 " --> pdb=" O GLU A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 821 through 823 No H-bonds generated for 'chain 'A' and resid 821 through 823' Processing helix chain 'A' and resid 828 through 850 removed outlier: 3.695A pdb=" N ALA A 836 " --> pdb=" O TRP A 832 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE A 837 " --> pdb=" O GLN A 833 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR A 849 " --> pdb=" O ASN A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 858 through 892 removed outlier: 3.904A pdb=" N ARG A 872 " --> pdb=" O LYS A 868 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N SER A 873 " --> pdb=" O THR A 869 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N LEU A 882 " --> pdb=" O ILE A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 900 through 913 removed outlier: 4.278A pdb=" N LEU A 913 " --> pdb=" O PHE A 909 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 929 Processing helix chain 'A' and resid 933 through 948 removed outlier: 4.003A pdb=" N ALA A 939 " --> pdb=" O VAL A 935 " (cutoff:3.500A) Processing helix chain 'A' and resid 950 through 970 removed outlier: 3.964A pdb=" N HIS A 970 " --> pdb=" O ASP A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 970 through 988 removed outlier: 4.264A pdb=" N LYS A 974 " --> pdb=" O HIS A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1071 removed outlier: 4.217A pdb=" N ILE A1044 " --> pdb=" O LEU A1040 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N TYR A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG A1050 " --> pdb=" O LYS A1046 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS A1060 " --> pdb=" O PHE A1056 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N GLN A1061 " --> pdb=" O LEU A1057 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS A1071 " --> pdb=" O LEU A1067 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 457 removed outlier: 3.975A pdb=" N PHE B 452 " --> pdb=" O SER B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 467 Processing helix chain 'B' and resid 484 through 492 removed outlier: 3.533A pdb=" N ALA B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN B 492 " --> pdb=" O LEU B 488 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 516 through 522 removed outlier: 4.208A pdb=" N HIS B 520 " --> pdb=" O THR B 516 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 537 removed outlier: 3.741A pdb=" N LEU B 534 " --> pdb=" O MET B 530 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN B 537 " --> pdb=" O ILE B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 550 through 556 Processing helix chain 'B' and resid 560 through 569 removed outlier: 4.355A pdb=" N VAL B 564 " --> pdb=" O HIS B 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 589 Processing helix chain 'B' and resid 592 through 602 removed outlier: 4.151A pdb=" N VAL B 596 " --> pdb=" O ARG B 592 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ILE B 600 " --> pdb=" O VAL B 596 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG B 601 " --> pdb=" O LEU B 597 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N SER B 602 " --> pdb=" O THR B 598 " (cutoff:3.500A) Processing helix chain 'B' and resid 620 through 627 Processing helix chain 'B' and resid 629 through 637 removed outlier: 3.575A pdb=" N CYS B 633 " --> pdb=" O TYR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 691 Processing helix chain 'B' and resid 703 through 740 removed outlier: 3.763A pdb=" N TYR B 714 " --> pdb=" O LYS B 710 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET B 721 " --> pdb=" O ARG B 717 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY B 729 " --> pdb=" O SER B 725 " (cutoff:3.500A) Proline residue: B 732 - end of helix Processing helix chain 'B' and resid 766 through 783 removed outlier: 3.546A pdb=" N ILE B 770 " --> pdb=" O ASN B 766 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE B 782 " --> pdb=" O PHE B 778 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N PHE B 783 " --> pdb=" O LEU B 779 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 820 removed outlier: 3.753A pdb=" N TYR B 812 " --> pdb=" O GLU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 821 through 823 No H-bonds generated for 'chain 'B' and resid 821 through 823' Processing helix chain 'B' and resid 828 through 850 removed outlier: 3.696A pdb=" N ALA B 836 " --> pdb=" O TRP B 832 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE B 837 " --> pdb=" O GLN B 833 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU B 848 " --> pdb=" O MET B 844 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR B 849 " --> pdb=" O ASN B 845 " (cutoff:3.500A) Processing helix chain 'B' and resid 858 through 892 removed outlier: 3.904A pdb=" N ARG B 872 " --> pdb=" O LYS B 868 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SER B 873 " --> pdb=" O THR B 869 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU B 882 " --> pdb=" O ILE B 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 900 through 913 removed outlier: 4.277A pdb=" N LEU B 913 " --> pdb=" O PHE B 909 " (cutoff:3.500A) Processing helix chain 'B' and resid 922 through 929 Processing helix chain 'B' and resid 933 through 948 removed outlier: 4.002A pdb=" N ALA B 939 " --> pdb=" O VAL B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 950 through 970 removed outlier: 3.964A pdb=" N HIS B 970 " --> pdb=" O ASP B 966 " (cutoff:3.500A) Processing helix chain 'B' and resid 970 through 988 removed outlier: 4.265A pdb=" N LYS B 974 " --> pdb=" O HIS B 970 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1071 removed outlier: 4.217A pdb=" N ILE B1044 " --> pdb=" O LEU B1040 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR B1049 " --> pdb=" O LEU B1045 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG B1050 " --> pdb=" O LYS B1046 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS B1060 " --> pdb=" O PHE B1056 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N GLN B1061 " --> pdb=" O LEU B1057 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LYS B1071 " --> pdb=" O LEU B1067 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 457 removed outlier: 3.976A pdb=" N PHE C 452 " --> pdb=" O SER C 448 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 467 Processing helix chain 'C' and resid 484 through 492 removed outlier: 3.533A pdb=" N ALA C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ASN C 492 " --> pdb=" O LEU C 488 " (cutoff:3.500A) Processing helix chain 'C' and resid 494 through 505 Processing helix chain 'C' and resid 516 through 522 removed outlier: 4.207A pdb=" N HIS C 520 " --> pdb=" O THR C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 527 through 537 removed outlier: 3.740A pdb=" N LEU C 534 " --> pdb=" O MET C 530 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASN C 537 " --> pdb=" O ILE C 533 " (cutoff:3.500A) Processing helix chain 'C' and resid 550 through 556 Processing helix chain 'C' and resid 560 through 569 removed outlier: 4.356A pdb=" N VAL C 564 " --> pdb=" O HIS C 560 " (cutoff:3.500A) Processing helix chain 'C' and resid 582 through 589 Processing helix chain 'C' and resid 592 through 602 removed outlier: 4.151A pdb=" N VAL C 596 " --> pdb=" O ARG C 592 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE C 600 " --> pdb=" O VAL C 596 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N ARG C 601 " --> pdb=" O LEU C 597 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N SER C 602 " --> pdb=" O THR C 598 " (cutoff:3.500A) Processing helix chain 'C' and resid 620 through 627 Processing helix chain 'C' and resid 629 through 637 removed outlier: 3.574A pdb=" N CYS C 633 " --> pdb=" O TYR C 629 " (cutoff:3.500A) Processing helix chain 'C' and resid 684 through 691 Processing helix chain 'C' and resid 703 through 740 removed outlier: 3.764A pdb=" N TYR C 714 " --> pdb=" O LYS C 710 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N MET C 721 " --> pdb=" O ARG C 717 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLY C 729 " --> pdb=" O SER C 725 " (cutoff:3.500A) Proline residue: C 732 - end of helix Processing helix chain 'C' and resid 766 through 783 removed outlier: 3.548A pdb=" N ILE C 770 " --> pdb=" O ASN C 766 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ILE C 782 " --> pdb=" O PHE C 778 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N PHE C 783 " --> pdb=" O LEU C 779 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 820 removed outlier: 3.752A pdb=" N TYR C 812 " --> pdb=" O GLU C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 821 through 823 No H-bonds generated for 'chain 'C' and resid 821 through 823' Processing helix chain 'C' and resid 828 through 850 removed outlier: 3.694A pdb=" N ALA C 836 " --> pdb=" O TRP C 832 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N ILE C 837 " --> pdb=" O GLN C 833 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU C 848 " --> pdb=" O MET C 844 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR C 849 " --> pdb=" O ASN C 845 " (cutoff:3.500A) Processing helix chain 'C' and resid 858 through 892 removed outlier: 3.904A pdb=" N ARG C 872 " --> pdb=" O LYS C 868 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N SER C 873 " --> pdb=" O THR C 869 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU C 882 " --> pdb=" O ILE C 878 " (cutoff:3.500A) Processing helix chain 'C' and resid 900 through 913 removed outlier: 4.278A pdb=" N LEU C 913 " --> pdb=" O PHE C 909 " (cutoff:3.500A) Processing helix chain 'C' and resid 922 through 929 Processing helix chain 'C' and resid 933 through 948 removed outlier: 4.001A pdb=" N ALA C 939 " --> pdb=" O VAL C 935 " (cutoff:3.500A) Processing helix chain 'C' and resid 950 through 970 removed outlier: 3.963A pdb=" N HIS C 970 " --> pdb=" O ASP C 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 970 through 988 removed outlier: 4.265A pdb=" N LYS C 974 " --> pdb=" O HIS C 970 " (cutoff:3.500A) Processing helix chain 'C' and resid 1040 through 1071 removed outlier: 4.217A pdb=" N ILE C1044 " --> pdb=" O LEU C1040 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR C1049 " --> pdb=" O LEU C1045 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ARG C1050 " --> pdb=" O LYS C1046 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS C1060 " --> pdb=" O PHE C1056 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N GLN C1061 " --> pdb=" O LEU C1057 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS C1071 " --> pdb=" O LEU C1067 " (cutoff:3.500A) 904 hydrogen bonds defined for protein. 2712 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: 4.60 Time building geometry restraints manager: 5.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2661 1.32 - 1.44: 4574 1.44 - 1.57: 9837 1.57 - 1.69: 36 1.69 - 1.82: 196 Bond restraints: 17304 Sorted by residual: bond pdb=" CA VAL C 824 " pdb=" CB VAL C 824 " ideal model delta sigma weight residual 1.540 1.612 -0.072 1.36e-02 5.41e+03 2.82e+01 bond pdb=" CA VAL B 824 " pdb=" CB VAL B 824 " ideal model delta sigma weight residual 1.540 1.612 -0.072 1.36e-02 5.41e+03 2.81e+01 bond pdb=" CA VAL D 824 " pdb=" CB VAL D 824 " ideal model delta sigma weight residual 1.540 1.612 -0.072 1.36e-02 5.41e+03 2.80e+01 bond pdb=" CA VAL A 824 " pdb=" CB VAL A 824 " ideal model delta sigma weight residual 1.540 1.612 -0.071 1.36e-02 5.41e+03 2.76e+01 bond pdb=" CA LEU D 480 " pdb=" C LEU D 480 " ideal model delta sigma weight residual 1.524 1.578 -0.055 1.26e-02 6.30e+03 1.89e+01 ... (remaining 17299 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 21057 2.90 - 5.79: 2065 5.79 - 8.69: 298 8.69 - 11.58: 60 11.58 - 14.48: 8 Bond angle restraints: 23488 Sorted by residual: angle pdb=" C GLU C 681 " pdb=" N PRO C 682 " pdb=" CA PRO C 682 " ideal model delta sigma weight residual 119.78 129.49 -9.71 1.03e+00 9.43e-01 8.89e+01 angle pdb=" C GLU D 681 " pdb=" N PRO D 682 " pdb=" CA PRO D 682 " ideal model delta sigma weight residual 119.78 129.47 -9.69 1.03e+00 9.43e-01 8.84e+01 angle pdb=" C GLU A 681 " pdb=" N PRO A 682 " pdb=" CA PRO A 682 " ideal model delta sigma weight residual 119.78 129.46 -9.68 1.03e+00 9.43e-01 8.83e+01 angle pdb=" C GLU B 681 " pdb=" N PRO B 682 " pdb=" CA PRO B 682 " ideal model delta sigma weight residual 119.78 129.45 -9.67 1.03e+00 9.43e-01 8.81e+01 angle pdb=" N ASN A 766 " pdb=" CA ASN A 766 " pdb=" CB ASN A 766 " ideal model delta sigma weight residual 112.41 126.89 -14.48 1.55e+00 4.16e-01 8.73e+01 ... (remaining 23483 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.99: 9343 22.99 - 45.98: 729 45.98 - 68.97: 152 68.97 - 91.97: 20 91.97 - 114.96: 4 Dihedral angle restraints: 10248 sinusoidal: 3652 harmonic: 6596 Sorted by residual: dihedral pdb=" CA PHE A 612 " pdb=" C PHE A 612 " pdb=" N SER A 613 " pdb=" CA SER A 613 " ideal model delta harmonic sigma weight residual -180.00 -65.04 -114.96 0 5.00e+00 4.00e-02 5.29e+02 dihedral pdb=" CA PHE B 612 " pdb=" C PHE B 612 " pdb=" N SER B 613 " pdb=" CA SER B 613 " ideal model delta harmonic sigma weight residual -180.00 -65.09 -114.91 0 5.00e+00 4.00e-02 5.28e+02 dihedral pdb=" CA PHE C 612 " pdb=" C PHE C 612 " pdb=" N SER C 613 " pdb=" CA SER C 613 " ideal model delta harmonic sigma weight residual -180.00 -65.12 -114.88 0 5.00e+00 4.00e-02 5.28e+02 ... (remaining 10245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 2146 0.077 - 0.155: 580 0.155 - 0.232: 58 0.232 - 0.309: 16 0.309 - 0.386: 8 Chirality restraints: 2808 Sorted by residual: chirality pdb=" CA VAL A 824 " pdb=" N VAL A 824 " pdb=" C VAL A 824 " pdb=" CB VAL A 824 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.39 2.00e-01 2.50e+01 3.73e+00 chirality pdb=" CA VAL C 824 " pdb=" N VAL C 824 " pdb=" C VAL C 824 " pdb=" CB VAL C 824 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.38 2.00e-01 2.50e+01 3.70e+00 chirality pdb=" CA VAL D 824 " pdb=" N VAL D 824 " pdb=" C VAL D 824 " pdb=" CB VAL D 824 " both_signs ideal model delta sigma weight residual False 2.44 2.83 -0.38 2.00e-01 2.50e+01 3.69e+00 ... (remaining 2805 not shown) Planarity restraints: 2888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D1047 " -0.038 2.00e-02 2.50e+03 7.60e-02 5.77e+01 pdb=" CD GLN D1047 " 0.131 2.00e-02 2.50e+03 pdb=" OE1 GLN D1047 " -0.049 2.00e-02 2.50e+03 pdb=" NE2 GLN D1047 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C1047 " -0.038 2.00e-02 2.50e+03 7.58e-02 5.75e+01 pdb=" CD GLN C1047 " 0.131 2.00e-02 2.50e+03 pdb=" OE1 GLN C1047 " -0.049 2.00e-02 2.50e+03 pdb=" NE2 GLN C1047 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN B1047 " 0.038 2.00e-02 2.50e+03 7.55e-02 5.71e+01 pdb=" CD GLN B1047 " -0.131 2.00e-02 2.50e+03 pdb=" OE1 GLN B1047 " 0.049 2.00e-02 2.50e+03 pdb=" NE2 GLN B1047 " 0.044 2.00e-02 2.50e+03 ... (remaining 2885 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 628 2.67 - 3.23: 18247 3.23 - 3.79: 25629 3.79 - 4.34: 31485 4.34 - 4.90: 48026 Nonbonded interactions: 124015 Sorted by model distance: nonbonded pdb=" O MET A1072 " pdb=" NH2 ARG B 458 " model vdw 2.113 3.120 nonbonded pdb=" O HIS C 970 " pdb=" ND1 HIS C 970 " model vdw 2.123 3.120 nonbonded pdb=" O HIS D 970 " pdb=" ND1 HIS D 970 " model vdw 2.123 3.120 nonbonded pdb=" O HIS B 970 " pdb=" ND1 HIS B 970 " model vdw 2.123 3.120 nonbonded pdb=" O HIS A 970 " pdb=" ND1 HIS A 970 " model vdw 2.123 3.120 ... (remaining 124010 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' selection = chain 'C' selection = chain 'D' } 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.150 Process input model: 37.730 Find NCS groups from input model: 0.620 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.009 0.072 17304 Z= 0.573 Angle : 1.852 14.481 23488 Z= 1.228 Chirality : 0.070 0.386 2808 Planarity : 0.006 0.076 2888 Dihedral : 17.684 114.956 5952 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 26.35 Ramachandran Plot: Outliers : 1.64 % Allowed : 10.18 % Favored : 88.18 % Rotamer: Outliers : 4.64 % Allowed : 24.04 % Favored : 71.33 % Cbeta Deviations : 0.19 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.68 % Twisted Proline : 5.56 % Twisted General : 3.96 % 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: -3.58 (0.15), residues: 2200 helix: -1.89 (0.11), residues: 1412 sheet: None (None), residues: 0 loop : -3.09 (0.20), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP C 605 HIS 0.055 0.005 HIS A 481 PHE 0.041 0.004 PHE B 877 TYR 0.041 0.004 TYR B 842 ARG 0.011 0.001 ARG C 604 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 443 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 819 VAL cc_start: 0.9191 (OUTLIER) cc_final: 0.8948 (m) REVERT: D 844 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.8205 (tmm) REVERT: D 955 LEU cc_start: 0.9112 (tt) cc_final: 0.8700 (tt) REVERT: D 959 LEU cc_start: 0.9194 (mp) cc_final: 0.8600 (mp) REVERT: A 819 VAL cc_start: 0.9210 (OUTLIER) cc_final: 0.8968 (m) REVERT: A 844 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8222 (tmm) REVERT: A 955 LEU cc_start: 0.9055 (tt) cc_final: 0.8643 (tt) REVERT: A 959 LEU cc_start: 0.9172 (mp) cc_final: 0.8574 (mp) REVERT: A 1050 ARG cc_start: 0.8118 (OUTLIER) cc_final: 0.7698 (mtt-85) REVERT: B 819 VAL cc_start: 0.9194 (OUTLIER) cc_final: 0.8972 (m) REVERT: B 955 LEU cc_start: 0.9072 (tt) cc_final: 0.8641 (tt) REVERT: B 959 LEU cc_start: 0.9196 (mp) cc_final: 0.8615 (mp) REVERT: B 1050 ARG cc_start: 0.8120 (OUTLIER) cc_final: 0.7697 (mtt-85) REVERT: C 819 VAL cc_start: 0.9209 (OUTLIER) cc_final: 0.8960 (m) REVERT: C 844 MET cc_start: 0.8416 (OUTLIER) cc_final: 0.8181 (tmm) REVERT: C 959 LEU cc_start: 0.9197 (mp) cc_final: 0.8682 (mp) REVERT: C 1050 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7700 (mtt-85) outliers start: 77 outliers final: 20 residues processed: 492 average time/residue: 0.2979 time to fit residues: 214.8337 Evaluate side-chains 297 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 267 time to evaluate : 1.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 189 optimal weight: 0.0570 chunk 169 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 8.9990 chunk 114 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 chunk 67 optimal weight: 0.0170 chunk 106 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 203 optimal weight: 6.9990 overall best weight: 1.1940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 570 HIS D 766 ASN ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D1047 GLN A 570 HIS A 766 ASN ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 570 HIS B 766 ASN ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 570 HIS C 766 ASN ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.5004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17304 Z= 0.261 Angle : 1.011 13.010 23488 Z= 0.524 Chirality : 0.049 0.197 2808 Planarity : 0.005 0.033 2888 Dihedral : 7.944 46.593 2356 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 17.13 Ramachandran Plot: Outliers : 1.09 % Allowed : 7.05 % Favored : 91.86 % Rotamer: Outliers : 0.24 % Allowed : 5.12 % Favored : 94.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 4.10 % Twisted Proline : 0.00 % Twisted General : 0.56 % 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: -2.28 (0.17), residues: 2200 helix: -0.71 (0.13), residues: 1400 sheet: None (None), residues: 0 loop : -2.92 (0.20), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 605 HIS 0.007 0.002 HIS A 494 PHE 0.043 0.002 PHE C 877 TYR 0.026 0.002 TYR B 842 ARG 0.010 0.001 ARG B 604 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 381 time to evaluate : 2.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 486 LEU cc_start: 0.9398 (mp) cc_final: 0.9118 (tp) REVERT: D 634 MET cc_start: 0.8957 (tmm) cc_final: 0.8755 (tmm) REVERT: D 697 LEU cc_start: 0.8411 (mt) cc_final: 0.8143 (mt) REVERT: D 711 TRP cc_start: 0.8387 (m100) cc_final: 0.8164 (m100) REVERT: D 721 MET cc_start: 0.8440 (tmm) cc_final: 0.8225 (tmm) REVERT: D 727 CYS cc_start: 0.8644 (t) cc_final: 0.8443 (t) REVERT: D 834 CYS cc_start: 0.9078 (m) cc_final: 0.8237 (p) REVERT: D 844 MET cc_start: 0.8485 (ttm) cc_final: 0.8191 (tpt) REVERT: D 959 LEU cc_start: 0.9054 (mp) cc_final: 0.8762 (mt) REVERT: A 486 LEU cc_start: 0.9399 (mp) cc_final: 0.9117 (tp) REVERT: A 634 MET cc_start: 0.8948 (tmm) cc_final: 0.8729 (tmm) REVERT: A 697 LEU cc_start: 0.8404 (mt) cc_final: 0.8137 (mt) REVERT: A 711 TRP cc_start: 0.8360 (m100) cc_final: 0.8135 (m100) REVERT: A 721 MET cc_start: 0.8443 (tmm) cc_final: 0.8223 (tmm) REVERT: A 844 MET cc_start: 0.8503 (ttm) cc_final: 0.8187 (tpt) REVERT: A 955 LEU cc_start: 0.8765 (tt) cc_final: 0.8545 (tt) REVERT: B 486 LEU cc_start: 0.9393 (mp) cc_final: 0.9117 (tp) REVERT: B 634 MET cc_start: 0.8953 (tmm) cc_final: 0.8733 (tmm) REVERT: B 697 LEU cc_start: 0.8405 (mt) cc_final: 0.8128 (mt) REVERT: B 721 MET cc_start: 0.8444 (tmm) cc_final: 0.8208 (tmm) REVERT: B 727 CYS cc_start: 0.8598 (t) cc_final: 0.8372 (t) REVERT: B 834 CYS cc_start: 0.9074 (m) cc_final: 0.8228 (p) REVERT: B 844 MET cc_start: 0.8081 (tmm) cc_final: 0.7532 (tpt) REVERT: B 955 LEU cc_start: 0.8778 (tt) cc_final: 0.8552 (tt) REVERT: B 1042 MET cc_start: 0.8421 (ppp) cc_final: 0.8208 (ppp) REVERT: C 486 LEU cc_start: 0.9391 (mp) cc_final: 0.9113 (tp) REVERT: C 697 LEU cc_start: 0.8408 (mt) cc_final: 0.8134 (mt) REVERT: C 721 MET cc_start: 0.8440 (tmm) cc_final: 0.8197 (tmm) REVERT: C 727 CYS cc_start: 0.8655 (t) cc_final: 0.8450 (t) REVERT: C 834 CYS cc_start: 0.9086 (m) cc_final: 0.8229 (p) REVERT: C 844 MET cc_start: 0.8472 (ttm) cc_final: 0.8161 (tpt) outliers start: 4 outliers final: 0 residues processed: 381 average time/residue: 0.2821 time to fit residues: 166.4843 Evaluate side-chains 240 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 113 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 169 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 203 optimal weight: 2.9990 chunk 220 optimal weight: 0.5980 chunk 181 optimal weight: 10.0000 chunk 202 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 163 optimal weight: 50.0000 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 549 ASN D 829 HIS ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 549 ASN A 829 HIS ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 549 ASN B 829 HIS ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 829 HIS ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17304 Z= 0.227 Angle : 0.915 12.027 23488 Z= 0.474 Chirality : 0.046 0.199 2808 Planarity : 0.004 0.037 2888 Dihedral : 6.655 28.909 2356 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 1.09 % Allowed : 8.00 % Favored : 90.91 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 4.10 % 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: -2.03 (0.17), residues: 2200 helix: -0.42 (0.13), residues: 1400 sheet: -3.64 (0.72), residues: 36 loop : -2.94 (0.21), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 605 HIS 0.007 0.001 HIS C 512 PHE 0.043 0.002 PHE B 716 TYR 0.017 0.002 TYR A 842 ARG 0.005 0.001 ARG C 604 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 315 time to evaluate : 2.000 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 502 LEU cc_start: 0.8935 (mm) cc_final: 0.8685 (pp) REVERT: D 697 LEU cc_start: 0.8367 (mt) cc_final: 0.7808 (mp) REVERT: D 706 TYR cc_start: 0.8774 (m-80) cc_final: 0.8564 (m-80) REVERT: D 844 MET cc_start: 0.8614 (ttm) cc_final: 0.8105 (tpt) REVERT: D 1056 PHE cc_start: 0.9110 (t80) cc_final: 0.8763 (t80) REVERT: D 1068 ILE cc_start: 0.9164 (mm) cc_final: 0.8907 (mm) REVERT: A 486 LEU cc_start: 0.9277 (mp) cc_final: 0.9073 (tp) REVERT: A 697 LEU cc_start: 0.8382 (mt) cc_final: 0.7428 (mt) REVERT: A 704 LYS cc_start: 0.8671 (mppt) cc_final: 0.8322 (mttt) REVERT: A 706 TYR cc_start: 0.8788 (m-80) cc_final: 0.8563 (m-80) REVERT: A 720 MET cc_start: 0.8319 (mpp) cc_final: 0.8105 (mpp) REVERT: A 844 MET cc_start: 0.8568 (ttm) cc_final: 0.8077 (tpt) REVERT: A 877 PHE cc_start: 0.8358 (p90) cc_final: 0.8148 (p90) REVERT: A 1068 ILE cc_start: 0.9207 (mm) cc_final: 0.8931 (mm) REVERT: B 697 LEU cc_start: 0.8370 (mt) cc_final: 0.7793 (mp) REVERT: B 706 TYR cc_start: 0.8791 (m-80) cc_final: 0.8567 (m-80) REVERT: B 844 MET cc_start: 0.8615 (ttp) cc_final: 0.8082 (tpt) REVERT: B 877 PHE cc_start: 0.8350 (p90) cc_final: 0.8118 (p90) REVERT: B 1068 ILE cc_start: 0.9188 (mm) cc_final: 0.8913 (mm) REVERT: C 479 ASP cc_start: 0.7991 (p0) cc_final: 0.7532 (p0) REVERT: C 502 LEU cc_start: 0.8962 (mm) cc_final: 0.8725 (pp) REVERT: C 697 LEU cc_start: 0.8373 (mt) cc_final: 0.7605 (mp) REVERT: C 706 TYR cc_start: 0.8793 (m-80) cc_final: 0.8569 (m-80) REVERT: C 720 MET cc_start: 0.8315 (mpp) cc_final: 0.8109 (mpp) REVERT: C 844 MET cc_start: 0.8613 (ttm) cc_final: 0.8037 (tpt) REVERT: C 915 ASP cc_start: 0.7299 (p0) cc_final: 0.6767 (p0) REVERT: C 1056 PHE cc_start: 0.9126 (t80) cc_final: 0.8784 (t80) REVERT: C 1068 ILE cc_start: 0.9184 (mm) cc_final: 0.8909 (mm) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.2544 time to fit residues: 125.1170 Evaluate side-chains 238 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 238 time to evaluate : 1.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 201 optimal weight: 6.9990 chunk 153 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 97 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 216 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 193 optimal weight: 0.8980 chunk 58 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 549 ASN ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.6570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17304 Z= 0.215 Angle : 0.873 11.573 23488 Z= 0.454 Chirality : 0.044 0.177 2808 Planarity : 0.004 0.043 2888 Dihedral : 6.316 31.153 2356 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.00 % Favored : 90.45 % Rotamer: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.92 (0.17), residues: 2200 helix: -0.37 (0.13), residues: 1412 sheet: None (None), residues: 0 loop : -2.94 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP C 711 HIS 0.006 0.001 HIS A 512 PHE 0.037 0.002 PHE C 877 TYR 0.016 0.002 TYR C 714 ARG 0.004 0.000 ARG A 604 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 325 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 720 MET cc_start: 0.8272 (mpp) cc_final: 0.8031 (mpp) REVERT: D 844 MET cc_start: 0.8691 (ttm) cc_final: 0.8236 (tpt) REVERT: D 862 MET cc_start: 0.8740 (ptp) cc_final: 0.8435 (ptm) REVERT: D 877 PHE cc_start: 0.8310 (p90) cc_final: 0.7956 (p90) REVERT: D 1056 PHE cc_start: 0.9112 (t80) cc_final: 0.8750 (t80) REVERT: D 1068 ILE cc_start: 0.9023 (mm) cc_final: 0.8820 (mm) REVERT: A 486 LEU cc_start: 0.9308 (mp) cc_final: 0.9038 (tp) REVERT: A 697 LEU cc_start: 0.8377 (mt) cc_final: 0.8138 (mp) REVERT: A 844 MET cc_start: 0.8729 (ttm) cc_final: 0.8234 (tpt) REVERT: A 880 LEU cc_start: 0.9624 (tt) cc_final: 0.9363 (pp) REVERT: A 913 LEU cc_start: 0.8720 (tp) cc_final: 0.8425 (tp) REVERT: B 706 TYR cc_start: 0.8853 (m-80) cc_final: 0.8572 (m-80) REVERT: B 720 MET cc_start: 0.8281 (mpp) cc_final: 0.8049 (mpp) REVERT: B 840 TYR cc_start: 0.8985 (t80) cc_final: 0.8662 (t80) REVERT: B 844 MET cc_start: 0.8759 (ttp) cc_final: 0.8300 (tpt) REVERT: B 877 PHE cc_start: 0.8345 (p90) cc_final: 0.7993 (p90) REVERT: C 706 TYR cc_start: 0.8851 (m-80) cc_final: 0.8572 (m-80) REVERT: C 844 MET cc_start: 0.8705 (ttm) cc_final: 0.8231 (tpt) REVERT: C 877 PHE cc_start: 0.8311 (p90) cc_final: 0.8015 (p90) REVERT: C 1056 PHE cc_start: 0.9125 (t80) cc_final: 0.8796 (t80) REVERT: C 1068 ILE cc_start: 0.9043 (mm) cc_final: 0.8841 (mm) outliers start: 0 outliers final: 0 residues processed: 325 average time/residue: 0.2726 time to fit residues: 138.5928 Evaluate side-chains 249 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 249 time to evaluate : 2.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 180 optimal weight: 0.2980 chunk 122 optimal weight: 5.9990 chunk 3 optimal weight: 0.0070 chunk 161 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 184 optimal weight: 8.9990 chunk 149 optimal weight: 0.9990 chunk 0 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 194 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 HIS ** A 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.7058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17304 Z= 0.232 Angle : 0.884 11.137 23488 Z= 0.458 Chirality : 0.045 0.197 2808 Planarity : 0.005 0.045 2888 Dihedral : 6.133 32.359 2356 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.09 % Favored : 90.36 % Rotamer: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.98 (0.17), residues: 2200 helix: -0.40 (0.13), residues: 1412 sheet: None (None), residues: 0 loop : -3.01 (0.21), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 711 HIS 0.007 0.001 HIS A 512 PHE 0.028 0.001 PHE B 716 TYR 0.016 0.002 TYR A 840 ARG 0.004 0.000 ARG D 604 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 303 time to evaluate : 1.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 626 MET cc_start: 0.8742 (mmm) cc_final: 0.8502 (mmp) REVERT: D 844 MET cc_start: 0.8747 (ttm) cc_final: 0.8381 (tpt) REVERT: D 862 MET cc_start: 0.8660 (ptp) cc_final: 0.8326 (ptp) REVERT: A 626 MET cc_start: 0.8736 (mmm) cc_final: 0.8496 (mmp) REVERT: A 697 LEU cc_start: 0.8348 (mt) cc_final: 0.7951 (mp) REVERT: A 720 MET cc_start: 0.8238 (mpp) cc_final: 0.7958 (mpp) REVERT: A 844 MET cc_start: 0.8733 (ttm) cc_final: 0.8307 (tpt) REVERT: A 862 MET cc_start: 0.8830 (ptp) cc_final: 0.8604 (ptm) REVERT: B 626 MET cc_start: 0.8748 (mmm) cc_final: 0.8513 (mmp) REVERT: B 706 TYR cc_start: 0.8874 (m-80) cc_final: 0.8613 (m-80) REVERT: B 844 MET cc_start: 0.8697 (ttp) cc_final: 0.8314 (tpt) REVERT: B 862 MET cc_start: 0.8847 (ptp) cc_final: 0.8549 (ptm) REVERT: C 626 MET cc_start: 0.8753 (mmm) cc_final: 0.8519 (mmp) REVERT: C 706 TYR cc_start: 0.8788 (m-80) cc_final: 0.8545 (m-80) REVERT: C 720 MET cc_start: 0.8246 (mpp) cc_final: 0.7961 (mpp) REVERT: C 844 MET cc_start: 0.8735 (ttm) cc_final: 0.8376 (tpt) REVERT: C 877 PHE cc_start: 0.8545 (p90) cc_final: 0.8111 (p90) REVERT: C 913 LEU cc_start: 0.8747 (tp) cc_final: 0.8457 (tp) outliers start: 0 outliers final: 0 residues processed: 303 average time/residue: 0.2433 time to fit residues: 114.9865 Evaluate side-chains 227 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 72 optimal weight: 10.0000 chunk 194 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 216 optimal weight: 3.9990 chunk 179 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 113 optimal weight: 0.7980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 970 HIS A 691 GLN A 970 HIS B 691 GLN B 970 HIS C 970 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.7356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17304 Z= 0.236 Angle : 0.876 10.906 23488 Z= 0.455 Chirality : 0.044 0.188 2808 Planarity : 0.005 0.044 2888 Dihedral : 6.002 33.031 2356 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.55 % Allowed : 9.36 % Favored : 90.09 % Rotamer: Outliers : 0.12 % Allowed : 3.43 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.96 (0.17), residues: 2200 helix: -0.40 (0.13), residues: 1400 sheet: None (None), residues: 0 loop : -2.92 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP D 711 HIS 0.011 0.001 HIS D 933 PHE 0.027 0.001 PHE A 716 TYR 0.039 0.002 TYR B 842 ARG 0.004 0.000 ARG B 919 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 295 time to evaluate : 1.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 626 MET cc_start: 0.8725 (mmm) cc_final: 0.8507 (mmp) REVERT: D 844 MET cc_start: 0.8629 (ttm) cc_final: 0.8239 (tpt) REVERT: D 877 PHE cc_start: 0.8501 (p90) cc_final: 0.8161 (p90) REVERT: D 913 LEU cc_start: 0.8757 (tp) cc_final: 0.8536 (tp) REVERT: D 1056 PHE cc_start: 0.9255 (t80) cc_final: 0.8912 (t80) REVERT: A 691 GLN cc_start: 0.8373 (OUTLIER) cc_final: 0.8135 (pp30) REVERT: A 697 LEU cc_start: 0.8554 (mt) cc_final: 0.8167 (mp) REVERT: A 706 TYR cc_start: 0.8871 (m-80) cc_final: 0.8522 (m-10) REVERT: A 720 MET cc_start: 0.8235 (mpp) cc_final: 0.7941 (mpp) REVERT: A 844 MET cc_start: 0.8697 (ttm) cc_final: 0.8236 (tpt) REVERT: B 626 MET cc_start: 0.8744 (mmm) cc_final: 0.8534 (mmp) REVERT: B 691 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.8247 (pp30) REVERT: B 706 TYR cc_start: 0.8871 (m-80) cc_final: 0.8612 (m-10) REVERT: B 844 MET cc_start: 0.8706 (ttp) cc_final: 0.8505 (tpt) REVERT: B 877 PHE cc_start: 0.8542 (p90) cc_final: 0.8174 (p90) REVERT: C 503 LYS cc_start: 0.9419 (ttpt) cc_final: 0.9194 (ptmt) REVERT: C 626 MET cc_start: 0.8751 (mmm) cc_final: 0.8540 (mmp) REVERT: C 706 TYR cc_start: 0.8826 (m-80) cc_final: 0.8550 (m-80) REVERT: C 720 MET cc_start: 0.8249 (mpp) cc_final: 0.7929 (mpp) REVERT: C 774 MET cc_start: 0.8637 (ptp) cc_final: 0.8410 (ppp) REVERT: C 844 MET cc_start: 0.8676 (ttm) cc_final: 0.8444 (mtp) REVERT: C 862 MET cc_start: 0.8716 (ptp) cc_final: 0.8444 (ptm) REVERT: C 1056 PHE cc_start: 0.9271 (t80) cc_final: 0.8932 (t80) outliers start: 2 outliers final: 0 residues processed: 297 average time/residue: 0.2442 time to fit residues: 114.0974 Evaluate side-chains 230 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 228 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 208 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 158 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 182 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 215 optimal weight: 0.0870 chunk 135 optimal weight: 7.9990 chunk 131 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 691 GLN A 954 ASN C 691 GLN ** C 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.7677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17304 Z= 0.258 Angle : 0.883 10.510 23488 Z= 0.461 Chirality : 0.045 0.184 2808 Planarity : 0.005 0.044 2888 Dihedral : 6.041 34.444 2356 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.14 % Favored : 89.27 % Rotamer: Outliers : 0.18 % Allowed : 2.47 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.99 (0.17), residues: 2200 helix: -0.40 (0.13), residues: 1396 sheet: None (None), residues: 0 loop : -2.95 (0.22), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.002 TRP D 711 HIS 0.009 0.001 HIS D 933 PHE 0.031 0.002 PHE B 877 TYR 0.037 0.002 TYR B 842 ARG 0.004 0.001 ARG B 919 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 283 time to evaluate : 1.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 642 MET cc_start: 0.6410 (pmm) cc_final: 0.6101 (pmm) REVERT: D 877 PHE cc_start: 0.8627 (p90) cc_final: 0.8250 (p90) REVERT: A 642 MET cc_start: 0.6402 (pmm) cc_final: 0.6077 (pmm) REVERT: A 697 LEU cc_start: 0.8522 (mt) cc_final: 0.8076 (mp) REVERT: A 706 TYR cc_start: 0.8879 (m-80) cc_final: 0.8471 (m-10) REVERT: A 840 TYR cc_start: 0.8885 (t80) cc_final: 0.8487 (t80) REVERT: A 911 MET cc_start: 0.8131 (tpp) cc_final: 0.7538 (tpp) REVERT: B 642 MET cc_start: 0.6367 (pmm) cc_final: 0.6041 (pmm) REVERT: B 706 TYR cc_start: 0.8802 (m-80) cc_final: 0.8537 (m-10) REVERT: B 877 PHE cc_start: 0.8605 (p90) cc_final: 0.8159 (p90) REVERT: C 642 MET cc_start: 0.6558 (pmm) cc_final: 0.6267 (pmm) REVERT: C 706 TYR cc_start: 0.8890 (m-80) cc_final: 0.8536 (m-10) REVERT: C 877 PHE cc_start: 0.8527 (p90) cc_final: 0.8159 (p90) REVERT: C 950 ILE cc_start: 0.8930 (pt) cc_final: 0.8699 (tp) outliers start: 3 outliers final: 2 residues processed: 286 average time/residue: 0.2416 time to fit residues: 108.8006 Evaluate side-chains 219 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 217 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 133 optimal weight: 10.0000 chunk 86 optimal weight: 5.9990 chunk 128 optimal weight: 10.0000 chunk 65 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 137 optimal weight: 6.9990 chunk 147 optimal weight: 8.9990 chunk 106 optimal weight: 0.0030 chunk 20 optimal weight: 20.0000 chunk 169 optimal weight: 8.9990 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 494 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 700 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.8030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 17304 Z= 0.312 Angle : 0.938 10.236 23488 Z= 0.492 Chirality : 0.047 0.183 2808 Planarity : 0.005 0.047 2888 Dihedral : 6.374 34.970 2356 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.77 % Favored : 89.50 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.19 (0.17), residues: 2200 helix: -0.64 (0.13), residues: 1404 sheet: None (None), residues: 0 loop : -2.89 (0.21), residues: 796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP D 711 HIS 0.010 0.002 HIS B 933 PHE 0.040 0.002 PHE A 877 TYR 0.043 0.002 TYR C 842 ARG 0.003 0.001 ARG B 919 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 264 time to evaluate : 2.002 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 545 ASP cc_start: 0.7023 (p0) cc_final: 0.6821 (p0) REVERT: D 642 MET cc_start: 0.6407 (pmm) cc_final: 0.6035 (pmm) REVERT: D 720 MET cc_start: 0.8274 (mpp) cc_final: 0.7906 (mpp) REVERT: D 910 SER cc_start: 0.9446 (t) cc_final: 0.9203 (p) REVERT: A 545 ASP cc_start: 0.7047 (p0) cc_final: 0.6845 (p0) REVERT: A 642 MET cc_start: 0.6774 (pmm) cc_final: 0.6412 (pmm) REVERT: A 706 TYR cc_start: 0.8887 (m-80) cc_final: 0.8466 (m-10) REVERT: A 720 MET cc_start: 0.8260 (mpp) cc_final: 0.7959 (mpp) REVERT: A 840 TYR cc_start: 0.8829 (t80) cc_final: 0.8311 (t80) REVERT: A 877 PHE cc_start: 0.8494 (p90) cc_final: 0.8109 (p90) REVERT: A 911 MET cc_start: 0.8115 (tpp) cc_final: 0.7598 (tpp) REVERT: A 950 ILE cc_start: 0.9126 (pt) cc_final: 0.8875 (mm) REVERT: B 642 MET cc_start: 0.6553 (pmm) cc_final: 0.6214 (pmm) REVERT: B 706 TYR cc_start: 0.8819 (m-80) cc_final: 0.8488 (m-10) REVERT: B 720 MET cc_start: 0.8243 (mpp) cc_final: 0.7882 (mpp) REVERT: B 774 MET cc_start: 0.8849 (ptp) cc_final: 0.8646 (ppp) REVERT: B 840 TYR cc_start: 0.9009 (t80) cc_final: 0.8359 (t80) REVERT: C 503 LYS cc_start: 0.9484 (ttpt) cc_final: 0.9283 (ptmt) REVERT: C 545 ASP cc_start: 0.7955 (m-30) cc_final: 0.7720 (p0) REVERT: C 642 MET cc_start: 0.6616 (pmm) cc_final: 0.6307 (pmm) REVERT: C 706 TYR cc_start: 0.8908 (m-80) cc_final: 0.8530 (m-10) REVERT: C 720 MET cc_start: 0.8257 (mpp) cc_final: 0.7943 (mpp) REVERT: C 774 MET cc_start: 0.8854 (ptp) cc_final: 0.8630 (ppp) outliers start: 0 outliers final: 0 residues processed: 264 average time/residue: 0.2746 time to fit residues: 114.8355 Evaluate side-chains 202 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 196 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 chunk 201 optimal weight: 7.9990 chunk 121 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 181 optimal weight: 3.9990 chunk 190 optimal weight: 0.9980 chunk 200 optimal weight: 2.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 940 GLN ** A 691 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 494 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.8182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17304 Z= 0.255 Angle : 0.898 10.504 23488 Z= 0.466 Chirality : 0.046 0.204 2808 Planarity : 0.005 0.046 2888 Dihedral : 6.039 34.190 2356 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 18.75 Ramachandran Plot: Outliers : 0.73 % Allowed : 9.50 % Favored : 89.77 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.04 (0.17), residues: 2200 helix: -0.53 (0.13), residues: 1408 sheet: None (None), residues: 0 loop : -2.83 (0.22), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP D 711 HIS 0.007 0.001 HIS B 933 PHE 0.054 0.002 PHE A 877 TYR 0.053 0.002 TYR A 840 ARG 0.004 0.000 ARG B 919 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 503 LYS cc_start: 0.9498 (ptmm) cc_final: 0.9119 (ptmm) REVERT: D 642 MET cc_start: 0.6526 (pmm) cc_final: 0.6206 (pmm) REVERT: D 720 MET cc_start: 0.8252 (mpp) cc_final: 0.7889 (mpp) REVERT: A 642 MET cc_start: 0.6712 (pmm) cc_final: 0.6370 (pmm) REVERT: A 706 TYR cc_start: 0.8865 (m-80) cc_final: 0.8438 (m-10) REVERT: A 844 MET cc_start: 0.8759 (mpp) cc_final: 0.8430 (mpp) REVERT: A 845 ASN cc_start: 0.8977 (t0) cc_final: 0.8619 (t0) REVERT: A 847 LEU cc_start: 0.9649 (tt) cc_final: 0.9405 (mt) REVERT: A 877 PHE cc_start: 0.8423 (p90) cc_final: 0.8113 (p90) REVERT: A 911 MET cc_start: 0.8106 (tpp) cc_final: 0.7506 (tpp) REVERT: A 1068 ILE cc_start: 0.9285 (mm) cc_final: 0.9068 (mm) REVERT: B 642 MET cc_start: 0.6704 (pmm) cc_final: 0.6381 (pmm) REVERT: B 706 TYR cc_start: 0.8745 (m-80) cc_final: 0.8439 (m-10) REVERT: B 733 MET cc_start: 0.8974 (mmp) cc_final: 0.8710 (mmp) REVERT: B 840 TYR cc_start: 0.8702 (t80) cc_final: 0.8357 (t80) REVERT: B 844 MET cc_start: 0.8479 (mmm) cc_final: 0.8239 (mmm) REVERT: B 1068 ILE cc_start: 0.9470 (mm) cc_final: 0.9222 (mm) REVERT: B 1069 ILE cc_start: 0.9363 (mp) cc_final: 0.9007 (tp) REVERT: C 642 MET cc_start: 0.6554 (pmm) cc_final: 0.6244 (pmm) REVERT: C 706 TYR cc_start: 0.8900 (m-80) cc_final: 0.8523 (m-10) REVERT: C 774 MET cc_start: 0.8957 (ptp) cc_final: 0.8731 (ppp) REVERT: C 950 ILE cc_start: 0.8842 (pt) cc_final: 0.8586 (tt) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2289 time to fit residues: 96.9767 Evaluate side-chains 209 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 209 time to evaluate : 2.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 132 optimal weight: 5.9990 chunk 212 optimal weight: 0.9980 chunk 129 optimal weight: 0.0040 chunk 100 optimal weight: 3.9990 chunk 147 optimal weight: 1.9990 chunk 223 optimal weight: 3.9990 chunk 205 optimal weight: 6.9990 chunk 177 optimal weight: 0.2980 chunk 18 optimal weight: 0.3980 chunk 137 optimal weight: 7.9990 chunk 108 optimal weight: 0.0670 overall best weight: 0.3530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 494 HIS D 851 GLN A 691 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.8346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17304 Z= 0.219 Angle : 0.915 11.009 23488 Z= 0.467 Chirality : 0.045 0.207 2808 Planarity : 0.005 0.047 2888 Dihedral : 5.675 32.058 2356 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 16.53 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.27 % Favored : 91.00 % Rotamer: Outliers : 0.06 % Allowed : 0.60 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.90 (0.17), residues: 2200 helix: -0.35 (0.13), residues: 1384 sheet: None (None), residues: 0 loop : -2.87 (0.22), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.002 TRP D 711 HIS 0.006 0.001 HIS D 512 PHE 0.053 0.001 PHE A 877 TYR 0.027 0.002 TYR A 840 ARG 0.004 0.000 ARG C 601 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4400 Ramachandran restraints generated. 2200 Oldfield, 0 Emsley, 2200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 292 time to evaluate : 1.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 642 MET cc_start: 0.6471 (pmm) cc_final: 0.6221 (pmm) REVERT: D 706 TYR cc_start: 0.8692 (m-80) cc_final: 0.8439 (m-10) REVERT: D 845 ASN cc_start: 0.9021 (t0) cc_final: 0.8684 (t0) REVERT: A 642 MET cc_start: 0.6471 (pmm) cc_final: 0.6207 (pmm) REVERT: A 691 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.8102 (pp30) REVERT: A 706 TYR cc_start: 0.8917 (m-80) cc_final: 0.8477 (m-10) REVERT: A 720 MET cc_start: 0.8257 (mpp) cc_final: 0.7877 (mpp) REVERT: A 733 MET cc_start: 0.8929 (mmp) cc_final: 0.8665 (mmp) REVERT: A 847 LEU cc_start: 0.9632 (tt) cc_final: 0.9400 (mt) REVERT: A 911 MET cc_start: 0.8059 (tpp) cc_final: 0.7390 (tpp) REVERT: B 545 ASP cc_start: 0.8054 (m-30) cc_final: 0.7675 (p0) REVERT: B 642 MET cc_start: 0.6485 (pmm) cc_final: 0.6212 (pmm) REVERT: B 706 TYR cc_start: 0.8760 (m-80) cc_final: 0.8487 (m-10) REVERT: B 720 MET cc_start: 0.8264 (mpp) cc_final: 0.7881 (mpp) REVERT: B 733 MET cc_start: 0.8967 (mmp) cc_final: 0.8718 (mmp) REVERT: B 840 TYR cc_start: 0.8697 (t80) cc_final: 0.8215 (t80) REVERT: B 1068 ILE cc_start: 0.9339 (mm) cc_final: 0.9032 (mm) REVERT: B 1069 ILE cc_start: 0.9498 (mp) cc_final: 0.9133 (tp) REVERT: C 642 MET cc_start: 0.6528 (pmm) cc_final: 0.6272 (pmm) REVERT: C 706 TYR cc_start: 0.8863 (m-80) cc_final: 0.8568 (m-10) REVERT: C 720 MET cc_start: 0.8240 (mpp) cc_final: 0.7879 (mpp) REVERT: C 840 TYR cc_start: 0.8770 (t80) cc_final: 0.8346 (t80) REVERT: C 844 MET cc_start: 0.8656 (mmp) cc_final: 0.8302 (mmp) REVERT: C 950 ILE cc_start: 0.8852 (pt) cc_final: 0.8634 (tt) outliers start: 1 outliers final: 0 residues processed: 293 average time/residue: 0.2305 time to fit residues: 109.7448 Evaluate side-chains 229 residues out of total 2020 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 2.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 224 random chunks: chunk 141 optimal weight: 0.9990 chunk 189 optimal weight: 0.0980 chunk 54 optimal weight: 0.9990 chunk 163 optimal weight: 40.0000 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 177 optimal weight: 0.7980 chunk 74 optimal weight: 9.9990 chunk 182 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 940 GLN ** C 700 HIS ** 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 = 0.2932 r_free = 0.2932 target = 0.043027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.033870 restraints weight = 119497.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.034895 restraints weight = 85527.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.035700 restraints weight = 64983.024| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.8480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17304 Z= 0.222 Angle : 0.920 11.024 23488 Z= 0.470 Chirality : 0.045 0.259 2808 Planarity : 0.005 0.047 2888 Dihedral : 5.616 31.513 2356 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.73 % Allowed : 8.73 % Favored : 90.55 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 3.91 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.91 (0.17), residues: 2200 helix: -0.37 (0.13), residues: 1392 sheet: None (None), residues: 0 loop : -2.87 (0.22), residues: 808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.002 TRP D 711 HIS 0.006 0.001 HIS D 512 PHE 0.030 0.002 PHE B 716 TYR 0.060 0.002 TYR B 840 ARG 0.004 0.000 ARG C 601 =============================================================================== Job complete usr+sys time: 3237.80 seconds wall clock time: 59 minutes 38.70 seconds (3578.70 seconds total)