Starting phenix.real_space_refine on Thu Aug 6 03:51:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yq8_34022/08_2026/7yq8_34022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yq8_34022/08_2026/7yq8_34022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7yq8_34022/08_2026/7yq8_34022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yq8_34022/08_2026/7yq8_34022.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yq8_34022/08_2026/7yq8_34022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yq8_34022/08_2026/7yq8_34022.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yq8_34022/08_2026/7yq8_34022.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yq8_34022/08_2026/7yq8_34022.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 56 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 8123 2.51 5 N 2247 2.21 5 O 2560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13036 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5901 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 25, 'TRANS': 704} Chain breaks: 1 Chain: "B" Number of atoms: 5901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5901 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 25, 'TRANS': 704} Chain breaks: 1 Chain: "C" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 245 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 243 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "F" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.51, per 1000 atoms: 0.19 Number of scatterers: 13036 At special positions: 0 Unit cell: (103.335, 123.255, 117.03, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 48 16.00 P 56 15.00 Mg 2 11.99 O 2560 8.00 N 2247 7.00 C 8123 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: 0.87 Conformation dependent library (CDL) restraints added in 411.1 milliseconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 16 sheets defined 54.6% alpha, 11.2% beta 28 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 483 through 498 removed outlier: 3.844A pdb=" N GLY A 495 " --> pdb=" O VAL A 491 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 513 through 517 Processing helix chain 'A' and resid 518 through 525 Processing helix chain 'A' and resid 525 through 536 Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'A' and resid 564 through 582 removed outlier: 3.673A pdb=" N SER A 568 " --> pdb=" O ASP A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 589 Processing helix chain 'A' and resid 612 through 621 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 641 through 650 removed outlier: 3.631A pdb=" N LYS A 646 " --> pdb=" O ALA A 642 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 647 " --> pdb=" O LYS A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 675 removed outlier: 3.704A pdb=" N ASP A 667 " --> pdb=" O GLY A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 700 Processing helix chain 'A' and resid 715 through 723 Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 744 through 758 Processing helix chain 'A' and resid 765 through 776 Processing helix chain 'A' and resid 781 through 793 removed outlier: 3.611A pdb=" N LEU A 785 " --> pdb=" O GLY A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 839 removed outlier: 4.320A pdb=" N ARG A 836 " --> pdb=" O SER A 832 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N LEU A 837 " --> pdb=" O THR A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 840 through 846 Processing helix chain 'A' and resid 868 through 873 removed outlier: 3.678A pdb=" N ASN A 872 " --> pdb=" O MET A 868 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLY A 873 " --> pdb=" O VAL A 869 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 868 through 873' Processing helix chain 'A' and resid 889 through 902 Processing helix chain 'A' and resid 952 through 966 removed outlier: 4.846A pdb=" N GLU A 962 " --> pdb=" O GLU A 958 " (cutoff:3.500A) Proline residue: A 963 - end of helix removed outlier: 3.514A pdb=" N ASN A 966 " --> pdb=" O GLU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 994 through 1005 Processing helix chain 'A' and resid 1005 through 1011 Processing helix chain 'A' and resid 1035 through 1081 removed outlier: 3.987A pdb=" N ILE A1039 " --> pdb=" O THR A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1090 through 1102 Processing helix chain 'A' and resid 1106 through 1118 removed outlier: 3.548A pdb=" N ALA A1114 " --> pdb=" O ALA A1110 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLN A1115 " --> pdb=" O TRP A1111 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA A1118 " --> pdb=" O ALA A1114 " (cutoff:3.500A) Processing helix chain 'A' and resid 1143 through 1148 Processing helix chain 'A' and resid 1150 through 1154 Processing helix chain 'A' and resid 1155 through 1178 removed outlier: 3.830A pdb=" N ASN A1174 " --> pdb=" O GLY A1170 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1195 removed outlier: 3.696A pdb=" N LYS A1186 " --> pdb=" O SER A1182 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU A1187 " --> pdb=" O ASP A1183 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU A1195 " --> pdb=" O ALA A1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1206 removed outlier: 3.526A pdb=" N ASP A1206 " --> pdb=" O GLN A1202 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 476 Processing helix chain 'B' and resid 483 through 498 removed outlier: 3.747A pdb=" N GLY B 495 " --> pdb=" O VAL B 491 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL B 496 " --> pdb=" O SER B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 525 Processing helix chain 'B' and resid 525 through 536 Processing helix chain 'B' and resid 545 through 550 Processing helix chain 'B' and resid 564 through 582 removed outlier: 3.642A pdb=" N SER B 568 " --> pdb=" O ASP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 589 Processing helix chain 'B' and resid 612 through 621 Processing helix chain 'B' and resid 625 through 629 Processing helix chain 'B' and resid 641 through 649 removed outlier: 3.555A pdb=" N LYS B 646 " --> pdb=" O ALA B 642 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLU B 647 " --> pdb=" O LYS B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 675 removed outlier: 3.680A pdb=" N ASP B 667 " --> pdb=" O GLY B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 700 Processing helix chain 'B' and resid 715 through 723 removed outlier: 3.699A pdb=" N GLU B 723 " --> pdb=" O PHE B 719 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 736 Processing helix chain 'B' and resid 744 through 758 Processing helix chain 'B' and resid 765 through 776 Processing helix chain 'B' and resid 781 through 793 removed outlier: 3.595A pdb=" N LEU B 785 " --> pdb=" O GLY B 781 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 839 removed outlier: 4.287A pdb=" N ARG B 836 " --> pdb=" O SER B 832 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LEU B 837 " --> pdb=" O THR B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 840 through 846 Processing helix chain 'B' and resid 868 through 873 removed outlier: 3.655A pdb=" N ASN B 872 " --> pdb=" O MET B 868 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY B 873 " --> pdb=" O VAL B 869 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 868 through 873' Processing helix chain 'B' and resid 889 through 902 Processing helix chain 'B' and resid 952 through 966 removed outlier: 4.681A pdb=" N GLU B 962 " --> pdb=" O GLU B 958 " (cutoff:3.500A) Proline residue: B 963 - end of helix removed outlier: 3.519A pdb=" N ASN B 966 " --> pdb=" O GLU B 962 " (cutoff:3.500A) Processing helix chain 'B' and resid 994 through 1005 Processing helix chain 'B' and resid 1005 through 1011 Processing helix chain 'B' and resid 1035 through 1081 removed outlier: 3.940A pdb=" N ILE B1039 " --> pdb=" O THR B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1090 through 1102 Processing helix chain 'B' and resid 1106 through 1118 removed outlier: 3.527A pdb=" N ALA B1118 " --> pdb=" O ALA B1114 " (cutoff:3.500A) Processing helix chain 'B' and resid 1150 through 1154 Processing helix chain 'B' and resid 1155 through 1178 removed outlier: 3.810A pdb=" N ASN B1174 " --> pdb=" O GLY B1170 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1195 removed outlier: 3.537A pdb=" N TRP B1185 " --> pdb=" O PRO B1181 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS B1186 " --> pdb=" O SER B1182 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B1187 " --> pdb=" O ASP B1183 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP B1188 " --> pdb=" O LEU B1184 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU B1195 " --> pdb=" O ALA B1191 " (cutoff:3.500A) Processing helix chain 'B' and resid 1195 through 1206 removed outlier: 3.514A pdb=" N VAL B1199 " --> pdb=" O GLU B1195 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ASP B1206 " --> pdb=" O GLN B1202 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 502 through 507 removed outlier: 3.805A pdb=" N GLY A 503 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N GLU A 482 " --> pdb=" O MET A 560 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N ILE A 557 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU A 591 " --> pdb=" O PHE A 659 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LEU A 658 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 606 through 610 Processing sheet with id=AA3, first strand: chain 'A' and resid 763 through 764 Processing sheet with id=AA4, first strand: chain 'A' and resid 849 through 851 removed outlier: 3.720A pdb=" N LEU A 850 " --> pdb=" O VAL A 857 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 874 through 877 Processing sheet with id=AA6, first strand: chain 'A' and resid 919 through 924 removed outlier: 5.602A pdb=" N ILE A 920 " --> pdb=" O SER A 931 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N SER A 931 " --> pdb=" O ILE A 920 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N GLU A 922 " --> pdb=" O ALA A 929 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ALA A 929 " --> pdb=" O GLU A 922 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 933 through 938 removed outlier: 5.700A pdb=" N GLU A 933 " --> pdb=" O THR A 945 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N THR A 941 " --> pdb=" O VAL A 937 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1021 through 1024 removed outlier: 4.111A pdb=" N MET A1021 " --> pdb=" O TYR A1033 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 502 through 507 removed outlier: 3.775A pdb=" N GLY B 503 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N GLU B 482 " --> pdb=" O MET B 560 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE B 557 " --> pdb=" O GLU B 592 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU B 591 " --> pdb=" O PHE B 659 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N LEU B 658 " --> pdb=" O LEU B 714 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 606 through 610 Processing sheet with id=AB2, first strand: chain 'B' and resid 763 through 764 removed outlier: 3.996A pdb=" N MET B 830 " --> pdb=" O GLN B 806 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 849 through 851 removed outlier: 3.781A pdb=" N LEU B 850 " --> pdb=" O VAL B 857 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 874 through 876 Processing sheet with id=AB5, first strand: chain 'B' and resid 919 through 924 removed outlier: 5.567A pdb=" N ILE B 920 " --> pdb=" O SER B 931 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N SER B 931 " --> pdb=" O ILE B 920 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLU B 922 " --> pdb=" O ALA B 929 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ALA B 929 " --> pdb=" O GLU B 922 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 933 through 938 removed outlier: 5.780A pdb=" N GLU B 933 " --> pdb=" O THR B 945 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N THR B 941 " --> pdb=" O VAL B 937 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 1021 through 1024 removed outlier: 4.094A pdb=" N MET B1021 " --> pdb=" O TYR B1033 " (cutoff:3.500A) 602 hydrogen bonds defined for protein. 1668 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 75 hydrogen bonds 150 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 1.69 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3928 1.34 - 1.46: 2544 1.46 - 1.58: 6754 1.58 - 1.70: 108 1.70 - 1.82: 86 Bond restraints: 13420 Sorted by residual: bond pdb=" C7 EVP D 101 " pdb=" O4 EVP D 101 " ideal model delta sigma weight residual 1.200 1.296 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C7 EVP F 101 " pdb=" O4 EVP F 101 " ideal model delta sigma weight residual 1.200 1.295 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C3' DT F 38 " pdb=" C2' DT F 38 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DC E 14 " pdb=" C2' DC E 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.53e+00 bond pdb=" C3' DT D 30 " pdb=" C2' DT D 30 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.73e+00 ... (remaining 13415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 17893 1.82 - 3.64: 357 3.64 - 5.45: 53 5.45 - 7.27: 26 7.27 - 9.09: 13 Bond angle restraints: 18342 Sorted by residual: angle pdb=" N3 DT D 30 " pdb=" C4 DT D 30 " pdb=" O4 DT D 30 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT F 33 " pdb=" C4 DT F 33 " pdb=" O4 DT F 33 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT E 23 " pdb=" C4 DT E 23 " pdb=" O4 DT E 23 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT C 14 " pdb=" C4 DT C 14 " pdb=" O4 DT C 14 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT F 38 " pdb=" C4 DT F 38 " pdb=" O4 DT F 38 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 18337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 6893 17.65 - 35.29: 819 35.29 - 52.94: 262 52.94 - 70.59: 53 70.59 - 88.23: 19 Dihedral angle restraints: 8046 sinusoidal: 3802 harmonic: 4244 Sorted by residual: dihedral pdb=" CA ALA A 673 " pdb=" C ALA A 673 " pdb=" N PHE A 674 " pdb=" CA PHE A 674 " ideal model delta harmonic sigma weight residual -180.00 -164.37 -15.63 0 5.00e+00 4.00e-02 9.77e+00 dihedral pdb=" CA ALA B 673 " pdb=" C ALA B 673 " pdb=" N PHE B 674 " pdb=" CA PHE B 674 " ideal model delta harmonic sigma weight residual 180.00 -164.40 -15.60 0 5.00e+00 4.00e-02 9.74e+00 dihedral pdb=" N LYS B 540 " pdb=" CA LYS B 540 " pdb=" CB LYS B 540 " pdb=" CG LYS B 540 " ideal model delta sinusoidal sigma weight residual -60.00 -118.10 58.10 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 8043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1959 0.110 - 0.220: 45 0.220 - 0.330: 2 0.330 - 0.441: 0 0.441 - 0.551: 2 Chirality restraints: 2008 Sorted by residual: chirality pdb=" C6 EVP D 101 " pdb=" C5 EVP D 101 " pdb=" C7 EVP D 101 " pdb=" C9 EVP D 101 " both_signs ideal model delta sigma weight residual False -2.41 -1.86 -0.55 2.00e-01 2.50e+01 7.58e+00 chirality pdb=" C6 EVP F 101 " pdb=" C5 EVP F 101 " pdb=" C7 EVP F 101 " pdb=" C9 EVP F 101 " both_signs ideal model delta sigma weight residual False -2.41 -1.87 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" CA GLU B 723 " pdb=" N GLU B 723 " pdb=" C GLU B 723 " pdb=" CB GLU B 723 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 2005 not shown) Planarity restraints: 2148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 723 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.73e+00 pdb=" CD GLU B 723 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU B 723 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU B 723 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1051 " 0.019 2.00e-02 2.50e+03 1.15e-02 2.62e+00 pdb=" CG TYR B1051 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B1051 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B1051 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B1051 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B1051 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B1051 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B1051 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 482 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C GLU A 482 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU A 482 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY A 483 " -0.009 2.00e-02 2.50e+03 ... (remaining 2145 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 188 2.61 - 3.18: 11391 3.18 - 3.76: 21704 3.76 - 4.33: 29009 4.33 - 4.90: 45737 Nonbonded interactions: 108029 Sorted by model distance: nonbonded pdb=" OD2 ASP A 564 " pdb="MG MG A1701 " model vdw 2.038 2.170 nonbonded pdb=" OD2 ASP B 564 " pdb="MG MG B1701 " model vdw 2.045 2.170 nonbonded pdb=" OD2 ASP A 562 " pdb="MG MG A1701 " model vdw 2.053 2.170 nonbonded pdb=" OD2 ASP B 562 " pdb="MG MG B1701 " model vdw 2.056 2.170 nonbonded pdb=" O VAL B 772 " pdb=" OG SER B 776 " model vdw 2.205 3.040 ... (remaining 108024 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: 0.440 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.730 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 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 : 0.004 0.096 13420 Z= 0.285 Angle : 0.679 9.090 18342 Z= 0.399 Chirality : 0.047 0.551 2008 Planarity : 0.003 0.032 2148 Dihedral : 17.079 88.235 5310 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.24), residues: 1452 helix: 1.92 (0.20), residues: 678 sheet: -1.08 (0.43), residues: 166 loop : -0.63 (0.28), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1047 TYR 0.025 0.001 TYR B1051 PHE 0.026 0.002 PHE A 674 TRP 0.017 0.002 TRP B 582 HIS 0.002 0.000 HIS B 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.29 (13420) covalent geometry : angle 0.67907 / 0.40 (18342) hydrogen bonds : bond 0.15371 / 9.75 ( 677) hydrogen bonds : angle 5.29969 / 3.67 ( 1818) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.375 Fit side-chains REVERT: A 900 MET cc_start: 0.8665 (mtp) cc_final: 0.8413 (mtp) REVERT: B 463 ASP cc_start: 0.8325 (m-30) cc_final: 0.8078 (m-30) REVERT: B 830 MET cc_start: 0.7527 (ppp) cc_final: 0.7260 (ppp) REVERT: B 900 MET cc_start: 0.8725 (mtp) cc_final: 0.8480 (mtp) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.0723 time to fit residues: 11.5098 Evaluate side-chains 81 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 519 HIS ** B 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.061065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.049115 restraints weight = 57665.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.050877 restraints weight = 29472.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.052078 restraints weight = 18548.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.052965 restraints weight = 13413.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.053505 restraints weight = 10576.725| |-----------------------------------------------------------------------------| r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 13420 Z= 0.304 Angle : 0.720 8.471 18342 Z= 0.385 Chirality : 0.045 0.201 2008 Planarity : 0.005 0.081 2148 Dihedral : 16.764 63.442 2306 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.55 % Allowed : 7.81 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.23), residues: 1452 helix: 1.42 (0.19), residues: 680 sheet: -1.58 (0.40), residues: 170 loop : -0.80 (0.27), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 501 TYR 0.016 0.002 TYR B1051 PHE 0.027 0.003 PHE A 674 TRP 0.012 0.002 TRP B 582 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00645 / 0.30 (13420) covalent geometry : angle 0.71955 / 0.38 (18342) hydrogen bonds : bond 0.05594 / 3.65 ( 677) hydrogen bonds : angle 4.79139 / 3.36 ( 1818) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.471 Fit side-chains REVERT: A 481 THR cc_start: 0.7267 (p) cc_final: 0.7034 (p) REVERT: A 560 MET cc_start: 0.6293 (ppp) cc_final: 0.5963 (ppp) REVERT: A 830 MET cc_start: 0.7760 (ppp) cc_final: 0.7390 (ppp) REVERT: A 1154 LEU cc_start: 0.8875 (mm) cc_final: 0.8345 (tp) REVERT: B 561 THR cc_start: 0.8049 (p) cc_final: 0.7843 (t) REVERT: B 1149 MET cc_start: 0.8772 (mpp) cc_final: 0.8554 (mpp) outliers start: 7 outliers final: 5 residues processed: 93 average time/residue: 0.0935 time to fit residues: 13.6754 Evaluate side-chains 86 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 81 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 149 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 chunk 117 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 136 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1072 GLN B 806 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.062619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.050326 restraints weight = 56356.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.052237 restraints weight = 27976.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.053510 restraints weight = 17276.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.054469 restraints weight = 12351.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.055117 restraints weight = 9618.424| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.1211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 13420 Z= 0.145 Angle : 0.562 7.946 18342 Z= 0.308 Chirality : 0.039 0.167 2008 Planarity : 0.004 0.048 2148 Dihedral : 16.723 64.761 2306 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.47 % Allowed : 9.45 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.23), residues: 1452 helix: 1.74 (0.20), residues: 670 sheet: -1.60 (0.40), residues: 168 loop : -0.81 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 939 TYR 0.017 0.001 TYR A 978 PHE 0.027 0.002 PHE B 674 TRP 0.013 0.002 TRP B 582 HIS 0.002 0.000 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (13420) covalent geometry : angle 0.56164 / 0.31 (18342) hydrogen bonds : bond 0.04437 / 2.91 ( 677) hydrogen bonds : angle 4.43259 / 3.11 ( 1818) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.506 Fit side-chains REVERT: A 481 THR cc_start: 0.7518 (p) cc_final: 0.7154 (p) REVERT: A 560 MET cc_start: 0.6254 (ppp) cc_final: 0.6011 (ppp) REVERT: A 900 MET cc_start: 0.8960 (ttm) cc_final: 0.8398 (mtp) REVERT: A 1154 LEU cc_start: 0.8856 (mm) cc_final: 0.8322 (tp) REVERT: B 561 THR cc_start: 0.8142 (p) cc_final: 0.7923 (t) REVERT: B 830 MET cc_start: 0.6936 (ppp) cc_final: 0.6711 (ppp) REVERT: B 900 MET cc_start: 0.8954 (ttm) cc_final: 0.8399 (mtp) REVERT: B 993 MET cc_start: 0.7216 (pmm) cc_final: 0.6917 (pmm) outliers start: 6 outliers final: 3 residues processed: 92 average time/residue: 0.0848 time to fit residues: 12.7401 Evaluate side-chains 90 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 87 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain B residue 591 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 145 optimal weight: 0.0070 chunk 32 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 120 optimal weight: 5.9990 chunk 7 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1072 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.063538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.051455 restraints weight = 55213.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.053354 restraints weight = 27432.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.054691 restraints weight = 16929.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.055487 restraints weight = 11921.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.056206 restraints weight = 9481.940| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13420 Z= 0.123 Angle : 0.532 7.318 18342 Z= 0.290 Chirality : 0.039 0.165 2008 Planarity : 0.003 0.034 2148 Dihedral : 16.685 64.776 2306 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 0.86 % Allowed : 10.94 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.23), residues: 1452 helix: 1.95 (0.20), residues: 672 sheet: -1.56 (0.40), residues: 168 loop : -0.79 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 939 TYR 0.022 0.001 TYR A 978 PHE 0.027 0.001 PHE A 674 TRP 0.011 0.001 TRP B 582 HIS 0.002 0.000 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (13420) covalent geometry : angle 0.53162 / 0.29 (18342) hydrogen bonds : bond 0.03958 / 2.61 ( 677) hydrogen bonds : angle 4.21888 / 2.96 ( 1818) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.394 Fit side-chains REVERT: A 561 THR cc_start: 0.8042 (p) cc_final: 0.7768 (t) REVERT: A 830 MET cc_start: 0.7665 (ppp) cc_final: 0.7337 (ppp) REVERT: A 900 MET cc_start: 0.8942 (ttm) cc_final: 0.8370 (mtp) REVERT: A 1154 LEU cc_start: 0.8854 (mm) cc_final: 0.8303 (tp) REVERT: A 1186 LYS cc_start: 0.9704 (mttt) cc_final: 0.9274 (mmmt) REVERT: B 900 MET cc_start: 0.8966 (ttm) cc_final: 0.8367 (mtp) REVERT: B 993 MET cc_start: 0.7179 (pmm) cc_final: 0.6902 (pmm) REVERT: B 1051 TYR cc_start: 0.6661 (OUTLIER) cc_final: 0.5812 (m-10) REVERT: B 1149 MET cc_start: 0.8984 (mpp) cc_final: 0.8737 (mpp) REVERT: B 1154 LEU cc_start: 0.9015 (mm) cc_final: 0.8316 (tp) REVERT: B 1188 ASP cc_start: 0.8859 (m-30) cc_final: 0.8474 (m-30) outliers start: 11 outliers final: 5 residues processed: 106 average time/residue: 0.0691 time to fit residues: 11.7446 Evaluate side-chains 96 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 90 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 1051 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 118 optimal weight: 0.5980 chunk 146 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 84 optimal weight: 10.0000 chunk 97 optimal weight: 0.5980 chunk 25 optimal weight: 10.0000 chunk 120 optimal weight: 2.9990 chunk 132 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1072 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.064586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.052441 restraints weight = 55046.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.054339 restraints weight = 26977.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.055676 restraints weight = 16510.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.056633 restraints weight = 11632.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.057267 restraints weight = 9047.347| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13420 Z= 0.111 Angle : 0.534 7.670 18342 Z= 0.286 Chirality : 0.038 0.191 2008 Planarity : 0.003 0.034 2148 Dihedral : 16.628 64.886 2306 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.94 % Allowed : 11.33 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.23), residues: 1452 helix: 2.03 (0.20), residues: 670 sheet: -1.50 (0.41), residues: 168 loop : -0.76 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 939 TYR 0.021 0.001 TYR A 978 PHE 0.020 0.001 PHE A 727 TRP 0.011 0.001 TRP A 685 HIS 0.003 0.000 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.11 (13420) covalent geometry : angle 0.53435 / 0.29 (18342) hydrogen bonds : bond 0.03745 / 2.49 ( 677) hydrogen bonds : angle 4.09665 / 2.88 ( 1818) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 99 time to evaluate : 0.437 Fit side-chains REVERT: A 900 MET cc_start: 0.8970 (ttm) cc_final: 0.8365 (mtp) REVERT: A 1051 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.6224 (m-10) REVERT: A 1154 LEU cc_start: 0.8842 (mm) cc_final: 0.8316 (tp) REVERT: A 1186 LYS cc_start: 0.9681 (mttt) cc_final: 0.9184 (mmmt) REVERT: B 900 MET cc_start: 0.8959 (ttm) cc_final: 0.8343 (mtp) REVERT: B 993 MET cc_start: 0.7275 (pmm) cc_final: 0.6988 (pmm) REVERT: B 1051 TYR cc_start: 0.6394 (OUTLIER) cc_final: 0.5570 (m-10) REVERT: B 1154 LEU cc_start: 0.8917 (mm) cc_final: 0.8306 (tp) REVERT: B 1188 ASP cc_start: 0.8749 (m-30) cc_final: 0.8427 (m-30) outliers start: 12 outliers final: 7 residues processed: 109 average time/residue: 0.0890 time to fit residues: 15.7936 Evaluate side-chains 100 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 121 optimal weight: 0.9990 chunk 145 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1072 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.061479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.049487 restraints weight = 57160.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.051261 restraints weight = 28984.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.052482 restraints weight = 18238.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.053347 restraints weight = 13143.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.053896 restraints weight = 10413.394| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 13420 Z= 0.255 Angle : 0.646 8.383 18342 Z= 0.343 Chirality : 0.042 0.189 2008 Planarity : 0.004 0.033 2148 Dihedral : 16.887 65.941 2306 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.88 % Allowed : 13.05 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.23), residues: 1452 helix: 1.80 (0.20), residues: 684 sheet: -1.63 (0.39), residues: 172 loop : -0.94 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 757 TYR 0.021 0.002 TYR A 978 PHE 0.023 0.002 PHE A 674 TRP 0.011 0.002 TRP B1185 HIS 0.003 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.26 (13420) covalent geometry : angle 0.64609 / 0.34 (18342) hydrogen bonds : bond 0.04867 / 3.19 ( 677) hydrogen bonds : angle 4.35277 / 3.07 ( 1818) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.454 Fit side-chains REVERT: A 1051 TYR cc_start: 0.7646 (OUTLIER) cc_final: 0.6352 (m-10) REVERT: A 1154 LEU cc_start: 0.8909 (mm) cc_final: 0.8319 (tp) REVERT: B 576 ASN cc_start: 0.6823 (OUTLIER) cc_final: 0.6410 (t0) REVERT: B 993 MET cc_start: 0.7434 (pmm) cc_final: 0.7152 (pmm) REVERT: B 1051 TYR cc_start: 0.7066 (OUTLIER) cc_final: 0.6195 (m-10) REVERT: B 1149 MET cc_start: 0.8869 (mpp) cc_final: 0.8652 (mpp) REVERT: B 1154 LEU cc_start: 0.8985 (mm) cc_final: 0.8337 (tp) REVERT: B 1188 ASP cc_start: 0.8984 (m-30) cc_final: 0.8548 (m-30) outliers start: 24 outliers final: 19 residues processed: 101 average time/residue: 0.0818 time to fit residues: 13.4987 Evaluate side-chains 104 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 107 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 140 optimal weight: 0.4980 chunk 8 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 141 optimal weight: 6.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1072 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.063041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.050946 restraints weight = 56041.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.052795 restraints weight = 28027.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.054096 restraints weight = 17425.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.055023 restraints weight = 12401.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.055558 restraints weight = 9705.271| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 13420 Z= 0.133 Angle : 0.553 7.348 18342 Z= 0.299 Chirality : 0.039 0.169 2008 Planarity : 0.003 0.034 2148 Dihedral : 16.832 66.724 2306 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.72 % Allowed : 13.52 % Favored : 84.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.23), residues: 1452 helix: 1.99 (0.20), residues: 672 sheet: -1.55 (0.40), residues: 168 loop : -0.88 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 939 TYR 0.019 0.001 TYR A 978 PHE 0.026 0.002 PHE A 674 TRP 0.011 0.001 TRP B 582 HIS 0.003 0.000 HIS B 579 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (13420) covalent geometry : angle 0.55342 / 0.30 (18342) hydrogen bonds : bond 0.03999 / 2.64 ( 677) hydrogen bonds : angle 4.19662 / 2.96 ( 1818) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.481 Fit side-chains revert: symmetry clash REVERT: A 739 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8477 (tt) REVERT: A 900 MET cc_start: 0.8646 (ttm) cc_final: 0.8442 (mtp) REVERT: A 1051 TYR cc_start: 0.7476 (OUTLIER) cc_final: 0.6289 (m-10) REVERT: A 1154 LEU cc_start: 0.8886 (mm) cc_final: 0.8310 (tp) REVERT: B 830 MET cc_start: 0.6879 (ppp) cc_final: 0.6616 (ppp) REVERT: B 900 MET cc_start: 0.8678 (ttm) cc_final: 0.8458 (mtp) REVERT: B 993 MET cc_start: 0.7385 (pmm) cc_final: 0.7088 (pmm) REVERT: B 1051 TYR cc_start: 0.6733 (OUTLIER) cc_final: 0.5937 (m-10) REVERT: B 1149 MET cc_start: 0.8787 (mpp) cc_final: 0.8530 (mpp) REVERT: B 1154 LEU cc_start: 0.8978 (mm) cc_final: 0.8351 (tp) REVERT: B 1188 ASP cc_start: 0.8889 (m-30) cc_final: 0.8496 (m-30) REVERT: B 1195 GLU cc_start: 0.8552 (pm20) cc_final: 0.8105 (mp0) outliers start: 22 outliers final: 14 residues processed: 108 average time/residue: 0.0839 time to fit residues: 14.9272 Evaluate side-chains 104 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 481 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 40 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 131 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 chunk 30 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1072 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.061003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.048874 restraints weight = 57016.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.050666 restraints weight = 29006.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.051848 restraints weight = 18255.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.052776 restraints weight = 13201.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.053331 restraints weight = 10380.516| |-----------------------------------------------------------------------------| r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13420 Z= 0.224 Angle : 0.637 12.088 18342 Z= 0.337 Chirality : 0.041 0.173 2008 Planarity : 0.004 0.031 2148 Dihedral : 16.993 68.641 2306 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.48 % Allowed : 14.69 % Favored : 83.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1452 helix: 1.74 (0.20), residues: 678 sheet: -1.80 (0.39), residues: 176 loop : -0.93 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 939 TYR 0.017 0.002 TYR A 978 PHE 0.033 0.002 PHE A 674 TRP 0.010 0.002 TRP B1185 HIS 0.003 0.001 HIS B 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (13420) covalent geometry : angle 0.63744 / 0.34 (18342) hydrogen bonds : bond 0.04799 / 3.16 ( 677) hydrogen bonds : angle 4.36543 / 3.08 ( 1818) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 89 time to evaluate : 0.471 Fit side-chains REVERT: A 571 LYS cc_start: 0.8539 (mptt) cc_final: 0.8305 (mmtt) REVERT: A 900 MET cc_start: 0.8726 (ttm) cc_final: 0.8353 (mtp) REVERT: A 1051 TYR cc_start: 0.7722 (OUTLIER) cc_final: 0.6514 (m-10) REVERT: A 1154 LEU cc_start: 0.8918 (mm) cc_final: 0.8319 (tp) REVERT: B 830 MET cc_start: 0.6850 (ppp) cc_final: 0.6612 (ppp) REVERT: B 900 MET cc_start: 0.8736 (ttm) cc_final: 0.8343 (mtp) REVERT: B 993 MET cc_start: 0.7341 (pmm) cc_final: 0.7128 (pmm) REVERT: B 1051 TYR cc_start: 0.6925 (OUTLIER) cc_final: 0.6117 (m-10) REVERT: B 1154 LEU cc_start: 0.9032 (mm) cc_final: 0.8399 (tp) REVERT: B 1188 ASP cc_start: 0.8999 (m-30) cc_final: 0.8601 (m-30) outliers start: 19 outliers final: 17 residues processed: 103 average time/residue: 0.0673 time to fit residues: 11.5648 Evaluate side-chains 102 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 55 optimal weight: 0.0870 chunk 131 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 44 optimal weight: 8.9990 chunk 54 optimal weight: 8.9990 overall best weight: 3.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1072 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.061851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.049710 restraints weight = 56931.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.051540 restraints weight = 28716.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.052789 restraints weight = 17927.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.053659 restraints weight = 12891.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.054200 restraints weight = 10190.825| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13420 Z= 0.190 Angle : 0.608 8.457 18342 Z= 0.325 Chirality : 0.040 0.167 2008 Planarity : 0.003 0.032 2148 Dihedral : 16.997 68.069 2306 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.88 % Allowed : 14.53 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.23), residues: 1452 helix: 1.76 (0.20), residues: 676 sheet: -1.83 (0.39), residues: 176 loop : -0.94 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 939 TYR 0.017 0.001 TYR A 978 PHE 0.033 0.002 PHE A 674 TRP 0.009 0.002 TRP B1152 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.19 (13420) covalent geometry : angle 0.60805 / 0.33 (18342) hydrogen bonds : bond 0.04394 / 2.89 ( 677) hydrogen bonds : angle 4.35116 / 3.07 ( 1818) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 571 LYS cc_start: 0.8524 (mptt) cc_final: 0.8294 (mmtt) REVERT: A 900 MET cc_start: 0.8740 (ttm) cc_final: 0.8341 (mtp) REVERT: A 1051 TYR cc_start: 0.7716 (OUTLIER) cc_final: 0.6623 (m-10) REVERT: A 1154 LEU cc_start: 0.8919 (mm) cc_final: 0.8321 (tp) REVERT: B 571 LYS cc_start: 0.8423 (mptt) cc_final: 0.8143 (mmtt) REVERT: B 576 ASN cc_start: 0.6678 (OUTLIER) cc_final: 0.6332 (t0) REVERT: B 900 MET cc_start: 0.8787 (ttm) cc_final: 0.8345 (mtp) REVERT: B 993 MET cc_start: 0.7374 (pmm) cc_final: 0.7105 (pmm) REVERT: B 1051 TYR cc_start: 0.6737 (OUTLIER) cc_final: 0.6054 (m-10) REVERT: B 1149 MET cc_start: 0.8834 (mpp) cc_final: 0.8593 (mpp) REVERT: B 1154 LEU cc_start: 0.9036 (mm) cc_final: 0.8399 (tp) REVERT: B 1188 ASP cc_start: 0.8978 (m-30) cc_final: 0.8605 (m-30) outliers start: 24 outliers final: 19 residues processed: 103 average time/residue: 0.0778 time to fit residues: 13.2176 Evaluate side-chains 108 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 122 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 chunk 22 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 77 optimal weight: 9.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1072 GLN ** A1096 GLN ** 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 = 0.3434 r_free = 0.3434 target = 0.060595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.048590 restraints weight = 57399.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.050339 restraints weight = 28960.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.051521 restraints weight = 18146.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.052402 restraints weight = 13086.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.053002 restraints weight = 10318.327| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13420 Z= 0.259 Angle : 0.676 8.636 18342 Z= 0.357 Chirality : 0.042 0.174 2008 Planarity : 0.004 0.032 2148 Dihedral : 17.137 69.059 2306 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 1.72 % Allowed : 15.08 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.23), residues: 1452 helix: 1.50 (0.20), residues: 678 sheet: -1.84 (0.39), residues: 176 loop : -1.05 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 939 TYR 0.016 0.002 TYR A 978 PHE 0.035 0.002 PHE A 674 TRP 0.010 0.002 TRP B1152 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.26 (13420) covalent geometry : angle 0.67563 / 0.36 (18342) hydrogen bonds : bond 0.05034 / 3.30 ( 677) hydrogen bonds : angle 4.51256 / 3.18 ( 1818) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.514 Fit side-chains REVERT: A 571 LYS cc_start: 0.8542 (mptt) cc_final: 0.8303 (mmtt) REVERT: A 900 MET cc_start: 0.8788 (ttm) cc_final: 0.8365 (mtp) REVERT: A 1051 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.6895 (m-10) REVERT: A 1154 LEU cc_start: 0.8950 (mm) cc_final: 0.8331 (tp) REVERT: A 1186 LYS cc_start: 0.9721 (mttt) cc_final: 0.9320 (mmmt) REVERT: B 571 LYS cc_start: 0.8476 (mptt) cc_final: 0.8213 (mmtt) REVERT: B 576 ASN cc_start: 0.6871 (OUTLIER) cc_final: 0.6499 (t0) REVERT: B 900 MET cc_start: 0.8794 (ttm) cc_final: 0.8368 (mtp) REVERT: B 993 MET cc_start: 0.7407 (pmm) cc_final: 0.7140 (pmm) REVERT: B 1051 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.6151 (m-10) REVERT: B 1149 MET cc_start: 0.8832 (mpp) cc_final: 0.8599 (mpp) REVERT: B 1154 LEU cc_start: 0.9123 (mm) cc_final: 0.8412 (tp) outliers start: 22 outliers final: 19 residues processed: 101 average time/residue: 0.0810 time to fit residues: 13.2324 Evaluate side-chains 106 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 117 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 73 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 148 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 5 optimal weight: 0.0370 overall best weight: 2.7864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1072 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.061639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.049561 restraints weight = 56407.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.051388 restraints weight = 28208.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.052576 restraints weight = 17497.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.053492 restraints weight = 12580.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.054098 restraints weight = 9894.214| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13420 Z= 0.168 Angle : 0.607 8.796 18342 Z= 0.324 Chirality : 0.040 0.165 2008 Planarity : 0.003 0.033 2148 Dihedral : 17.059 69.916 2306 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.72 % Allowed : 15.00 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.23), residues: 1452 helix: 1.76 (0.20), residues: 676 sheet: -1.85 (0.39), residues: 172 loop : -0.99 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 939 TYR 0.016 0.001 TYR A 978 PHE 0.032 0.002 PHE A 674 TRP 0.010 0.002 TRP A 952 HIS 0.003 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 (13420) covalent geometry : angle 0.60728 / 0.32 (18342) hydrogen bonds : bond 0.04302 / 2.84 ( 677) hydrogen bonds : angle 4.35596 / 3.07 ( 1818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1603.00 seconds wall clock time: 28 minutes 41.63 seconds (1721.63 seconds total)