Starting phenix.real_space_refine on Sat Aug 23 16:34:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yq8_34022/08_2025/7yq8_34022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yq8_34022/08_2025/7yq8_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_2025/7yq8_34022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yq8_34022/08_2025/7yq8_34022.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yq8_34022/08_2025/7yq8_34022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yq8_34022/08_2025/7yq8_34022.map" } 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-2.0-5787/lib/python3.9/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: 2.43, 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: 0.85 Conformation dependent library (CDL) restraints added in 465.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 1.54 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: 2.03 Time building geometry restraints manager: 1.12 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=" C14 EVP F 101 " pdb=" C5 EVP F 101 " ideal model delta sigma weight residual 1.518 1.575 -0.057 2.00e-02 2.50e+03 8.03e+00 bond pdb=" C13 EVP D 101 " pdb=" C2 EVP D 101 " ideal model delta sigma weight residual 1.388 1.440 -0.052 2.00e-02 2.50e+03 6.85e+00 bond pdb=" C13 EVP F 101 " pdb=" C2 EVP F 101 " ideal model delta sigma weight residual 1.388 1.440 -0.052 2.00e-02 2.50e+03 6.71e+00 ... (remaining 13415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 17957 1.82 - 3.64: 293 3.64 - 5.45: 53 5.45 - 7.27: 26 7.27 - 9.09: 13 Bond angle restraints: 18342 Sorted by residual: angle pdb=" CB ARG B 939 " pdb=" CG ARG B 939 " pdb=" CD ARG B 939 " ideal model delta sigma weight residual 111.30 120.39 -9.09 2.30e+00 1.89e-01 1.56e+01 angle pdb=" CB ARG A 939 " pdb=" CG ARG A 939 " pdb=" CD ARG A 939 " ideal model delta sigma weight residual 111.30 120.24 -8.94 2.30e+00 1.89e-01 1.51e+01 angle pdb=" CA GLU B 723 " pdb=" CB GLU B 723 " pdb=" CG GLU B 723 " ideal model delta sigma weight residual 114.10 120.70 -6.60 2.00e+00 2.50e-01 1.09e+01 angle pdb=" C11 EVP F 101 " pdb=" C10 EVP F 101 " pdb=" O8 EVP F 101 " ideal model delta sigma weight residual 107.62 116.67 -9.05 3.00e+00 1.11e-01 9.10e+00 angle pdb=" C ASN B 721 " pdb=" N LYS B 722 " pdb=" CA LYS B 722 " ideal model delta sigma weight residual 121.52 116.44 5.08 1.74e+00 3.30e-01 8.53e+00 ... (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: 1963 0.110 - 0.220: 41 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: 0.520 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.120 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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= 0.190 Angle : 0.649 9.090 18342 Z= 0.314 Chirality : 0.045 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 aren 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 covalent geometry : bond 0.00402 (13420) covalent geometry : angle 0.64866 (18342) hydrogen bonds : bond 0.15371 ( 677) hydrogen bonds : angle 5.29969 ( 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 : 0.361 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: 0.0905 time to fit residues: 14.2312 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 : 0.401 ------------------------------------------------------------------------------- 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: 0.6980 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1096 GLN B 519 HIS B 806 GLN B1096 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.061081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.049139 restraints weight = 57510.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.050881 restraints weight = 29846.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.052053 restraints weight = 18936.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.052927 restraints weight = 13814.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.053524 restraints weight = 10986.320| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13420 Z= 0.265 Angle : 0.651 6.445 18342 Z= 0.347 Chirality : 0.042 0.192 2008 Planarity : 0.004 0.038 2148 Dihedral : 16.862 65.366 2306 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.55 % Allowed : 7.89 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.23), residues: 1452 helix: 1.47 (0.20), residues: 676 sheet: -1.49 (0.40), residues: 172 loop : -0.70 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 501 TYR 0.020 0.002 TYR A 978 PHE 0.027 0.002 PHE A 674 TRP 0.011 0.002 TRP B 582 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00579 (13420) covalent geometry : angle 0.65063 (18342) hydrogen bonds : bond 0.05214 ( 677) hydrogen bonds : angle 4.63487 ( 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 100 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 0.510 Fit side-chains REVERT: A 561 THR cc_start: 0.8154 (p) cc_final: 0.7944 (t) REVERT: A 1055 LYS cc_start: 0.8952 (tttt) cc_final: 0.8662 (tmtt) REVERT: A 1154 LEU cc_start: 0.8924 (mm) cc_final: 0.8402 (tp) REVERT: B 561 THR cc_start: 0.8009 (p) cc_final: 0.7757 (t) REVERT: B 1149 MET cc_start: 0.8885 (mpp) cc_final: 0.8667 (mpp) outliers start: 7 outliers final: 5 residues processed: 95 average time/residue: 0.0876 time to fit residues: 13.1842 Evaluate side-chains 88 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 667 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: 6.9990 chunk 148 optimal weight: 6.9990 chunk 117 optimal weight: 0.3980 chunk 81 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 136 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1072 GLN A1096 GLN B1096 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.062562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.050394 restraints weight = 56305.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.052273 restraints weight = 28172.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.053552 restraints weight = 17432.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.054453 restraints weight = 12490.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.055105 restraints weight = 9825.642| |-----------------------------------------------------------------------------| r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13420 Z= 0.144 Angle : 0.542 7.821 18342 Z= 0.289 Chirality : 0.038 0.171 2008 Planarity : 0.003 0.039 2148 Dihedral : 16.799 69.254 2306 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.94 % Allowed : 10.00 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.23), residues: 1452 helix: 1.84 (0.20), residues: 674 sheet: -1.47 (0.41), residues: 168 loop : -0.66 (0.27), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 939 TYR 0.019 0.001 TYR A 978 PHE 0.025 0.002 PHE A 674 TRP 0.011 0.002 TRP B 582 HIS 0.002 0.000 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00315 (13420) covalent geometry : angle 0.54220 (18342) hydrogen bonds : bond 0.04026 ( 677) hydrogen bonds : angle 4.27298 ( 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 107 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.8953 (ttm) cc_final: 0.8408 (mtp) REVERT: A 993 MET cc_start: 0.7318 (pmm) cc_final: 0.7088 (pmm) REVERT: A 1051 TYR cc_start: 0.7534 (OUTLIER) cc_final: 0.6255 (m-10) REVERT: A 1154 LEU cc_start: 0.8898 (mm) cc_final: 0.8336 (tp) REVERT: B 900 MET cc_start: 0.8805 (ttm) cc_final: 0.8354 (mtp) REVERT: B 993 MET cc_start: 0.7019 (pmm) cc_final: 0.6702 (pmm) REVERT: B 1051 TYR cc_start: 0.6629 (OUTLIER) cc_final: 0.5864 (m-10) REVERT: B 1154 LEU cc_start: 0.9008 (mm) cc_final: 0.8398 (tp) REVERT: B 1188 ASP cc_start: 0.8899 (m-30) cc_final: 0.8542 (m-30) outliers start: 12 outliers final: 7 residues processed: 102 average time/residue: 0.0831 time to fit residues: 13.8595 Evaluate side-chains 95 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 86 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 715 THR 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 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 145 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 143 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 84 optimal weight: 7.9990 chunk 120 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 38 optimal weight: 0.0010 chunk 105 optimal weight: 5.9990 overall best weight: 1.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.063973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.051913 restraints weight = 54680.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.053816 restraints weight = 26823.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.055135 restraints weight = 16410.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.056106 restraints weight = 11561.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.056627 restraints weight = 8937.012| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.1620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13420 Z= 0.115 Angle : 0.516 7.991 18342 Z= 0.273 Chirality : 0.037 0.168 2008 Planarity : 0.003 0.033 2148 Dihedral : 16.704 69.007 2306 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.09 % Allowed : 11.02 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.75 (0.23), residues: 1452 helix: 2.06 (0.20), residues: 672 sheet: -1.54 (0.41), residues: 172 loop : -0.64 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 508 TYR 0.019 0.001 TYR A 978 PHE 0.020 0.001 PHE A 727 TRP 0.012 0.001 TRP B 685 HIS 0.001 0.000 HIS B 579 Details of bonding type rmsd covalent geometry : bond 0.00251 (13420) covalent geometry : angle 0.51579 (18342) hydrogen bonds : bond 0.03649 ( 677) hydrogen bonds : angle 4.08578 ( 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 117 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.8969 (ttm) cc_final: 0.8382 (mtp) REVERT: A 993 MET cc_start: 0.7525 (pmm) cc_final: 0.7256 (pmm) REVERT: A 1051 TYR cc_start: 0.7368 (OUTLIER) cc_final: 0.6217 (m-10) REVERT: A 1154 LEU cc_start: 0.8947 (mm) cc_final: 0.8369 (tp) REVERT: A 1188 ASP cc_start: 0.8901 (m-30) cc_final: 0.8460 (m-30) REVERT: B 576 ASN cc_start: 0.6793 (OUTLIER) cc_final: 0.6450 (t0) REVERT: B 900 MET cc_start: 0.8800 (ttm) cc_final: 0.8341 (mtp) REVERT: B 935 PHE cc_start: 0.8820 (m-10) cc_final: 0.8524 (m-10) REVERT: B 993 MET cc_start: 0.7264 (pmm) cc_final: 0.7053 (pmm) REVERT: B 1051 TYR cc_start: 0.6608 (OUTLIER) cc_final: 0.6022 (m-10) REVERT: B 1154 LEU cc_start: 0.8967 (mm) cc_final: 0.8363 (tp) REVERT: B 1188 ASP cc_start: 0.8750 (m-30) cc_final: 0.8498 (m-30) outliers start: 14 outliers final: 5 residues processed: 112 average time/residue: 0.0902 time to fit residues: 16.2326 Evaluate side-chains 102 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 94 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 1048 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: 0.8980 chunk 4 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 146 optimal weight: 8.9990 chunk 133 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 97 optimal weight: 7.9990 chunk 25 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 132 optimal weight: 2.9990 overall best weight: 2.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS ** 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 = 0.3470 r_free = 0.3470 target = 0.062070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.049872 restraints weight = 57014.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.051753 restraints weight = 28199.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.053045 restraints weight = 17430.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.053883 restraints weight = 12383.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.054553 restraints weight = 9796.048| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 13420 Z= 0.178 Angle : 0.562 7.999 18342 Z= 0.296 Chirality : 0.039 0.191 2008 Planarity : 0.003 0.032 2148 Dihedral : 16.775 69.732 2306 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.56 % Allowed : 13.28 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.23), residues: 1452 helix: 1.94 (0.20), residues: 676 sheet: -1.70 (0.39), residues: 176 loop : -0.69 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 697 TYR 0.018 0.001 TYR A 978 PHE 0.029 0.002 PHE A 674 TRP 0.009 0.001 TRP B 582 HIS 0.002 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00394 (13420) covalent geometry : angle 0.56153 (18342) hydrogen bonds : bond 0.04178 ( 677) hydrogen bonds : angle 4.18871 ( 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 115 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.487 Fit side-chains revert: symmetry clash REVERT: A 739 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8486 (tt) REVERT: A 900 MET cc_start: 0.8983 (ttm) cc_final: 0.8382 (mtp) REVERT: A 993 MET cc_start: 0.7660 (pmm) cc_final: 0.7367 (pmm) REVERT: A 1051 TYR cc_start: 0.7596 (OUTLIER) cc_final: 0.6343 (m-10) REVERT: A 1055 LYS cc_start: 0.8920 (tttt) cc_final: 0.8647 (tmtt) REVERT: A 1154 LEU cc_start: 0.8903 (mm) cc_final: 0.8326 (tp) REVERT: B 576 ASN cc_start: 0.6820 (OUTLIER) cc_final: 0.6396 (t0) REVERT: B 900 MET cc_start: 0.8841 (ttm) cc_final: 0.8339 (mtp) REVERT: B 993 MET cc_start: 0.7265 (pmm) cc_final: 0.7059 (pmm) REVERT: B 1051 TYR cc_start: 0.6853 (OUTLIER) cc_final: 0.6241 (m-10) REVERT: B 1154 LEU cc_start: 0.9031 (mm) cc_final: 0.8420 (tp) REVERT: B 1188 ASP cc_start: 0.8920 (m-30) cc_final: 0.8577 (m-30) REVERT: B 1195 GLU cc_start: 0.8526 (pm20) cc_final: 0.8120 (mp0) outliers start: 20 outliers final: 14 residues processed: 107 average time/residue: 0.0791 time to fit residues: 13.8087 Evaluate side-chains 109 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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 715 THR Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 838 LEU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 121 optimal weight: 4.9990 chunk 145 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 128 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 125 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.061897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.049761 restraints weight = 55920.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.051581 restraints weight = 28120.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.052817 restraints weight = 17485.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.053733 restraints weight = 12534.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.054326 restraints weight = 9823.316| |-----------------------------------------------------------------------------| r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 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 0.042 13420 Z= 0.178 Angle : 0.564 7.189 18342 Z= 0.298 Chirality : 0.039 0.177 2008 Planarity : 0.003 0.034 2148 Dihedral : 16.829 70.985 2306 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.19 % Allowed : 13.83 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.23), residues: 1452 helix: 1.94 (0.20), residues: 676 sheet: -1.75 (0.39), residues: 176 loop : -0.71 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1047 TYR 0.014 0.001 TYR A 978 PHE 0.028 0.002 PHE A 674 TRP 0.009 0.001 TRP B 685 HIS 0.002 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00392 (13420) covalent geometry : angle 0.56445 (18342) hydrogen bonds : bond 0.04077 ( 677) hydrogen bonds : angle 4.21757 ( 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 125 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 97 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 830 MET cc_start: 0.7902 (ppp) cc_final: 0.7607 (ppp) REVERT: A 900 MET cc_start: 0.8950 (ttm) cc_final: 0.8359 (mtp) REVERT: A 993 MET cc_start: 0.7782 (pmm) cc_final: 0.7452 (pmm) REVERT: A 1051 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.6798 (m-10) REVERT: A 1154 LEU cc_start: 0.8920 (mm) cc_final: 0.8334 (tp) REVERT: B 576 ASN cc_start: 0.6931 (OUTLIER) cc_final: 0.6413 (t0) REVERT: B 900 MET cc_start: 0.8858 (ttm) cc_final: 0.8334 (mtp) REVERT: B 993 MET cc_start: 0.7295 (pmm) cc_final: 0.7014 (pmm) REVERT: B 1051 TYR cc_start: 0.6967 (OUTLIER) cc_final: 0.6516 (m-10) REVERT: B 1154 LEU cc_start: 0.9051 (mm) cc_final: 0.8433 (tp) REVERT: B 1188 ASP cc_start: 0.8916 (m-30) cc_final: 0.8634 (m-30) REVERT: B 1195 GLU cc_start: 0.8503 (pm20) cc_final: 0.8117 (mp0) outliers start: 28 outliers final: 19 residues processed: 114 average time/residue: 0.0801 time to fit residues: 14.6073 Evaluate side-chains 114 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 92 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 740 VAL 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 A residue 1176 LEU 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 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 Chi-restraints excluded: chain B residue 1176 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 107 optimal weight: 3.9990 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 8.9990 chunk 91 optimal weight: 0.2980 chunk 23 optimal weight: 6.9990 chunk 16 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 140 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 149 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.062521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.050351 restraints weight = 55682.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.052200 restraints weight = 27826.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.053493 restraints weight = 17254.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.054404 restraints weight = 12270.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.054974 restraints weight = 9607.725| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13420 Z= 0.155 Angle : 0.555 11.297 18342 Z= 0.292 Chirality : 0.038 0.183 2008 Planarity : 0.003 0.034 2148 Dihedral : 16.782 71.399 2306 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.72 % Allowed : 14.84 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.23), residues: 1452 helix: 2.00 (0.20), residues: 678 sheet: -1.66 (0.40), residues: 172 loop : -0.70 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B1047 TYR 0.013 0.001 TYR A 978 PHE 0.025 0.002 PHE A 674 TRP 0.011 0.001 TRP B 685 HIS 0.002 0.000 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00342 (13420) covalent geometry : angle 0.55520 (18342) hydrogen bonds : bond 0.03903 ( 677) hydrogen bonds : angle 4.15452 ( 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 120 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 830 MET cc_start: 0.7848 (ppp) cc_final: 0.7563 (ppp) REVERT: A 900 MET cc_start: 0.8976 (ttm) cc_final: 0.8367 (mtp) REVERT: A 993 MET cc_start: 0.7810 (pmm) cc_final: 0.7422 (pmm) REVERT: A 1051 TYR cc_start: 0.7858 (OUTLIER) cc_final: 0.6808 (m-10) REVERT: A 1154 LEU cc_start: 0.8918 (mm) cc_final: 0.8388 (tp) REVERT: B 576 ASN cc_start: 0.6900 (OUTLIER) cc_final: 0.6407 (t0) REVERT: B 900 MET cc_start: 0.8853 (ttm) cc_final: 0.8320 (mtp) REVERT: B 993 MET cc_start: 0.7292 (pmm) cc_final: 0.7021 (pmm) REVERT: B 1051 TYR cc_start: 0.6953 (OUTLIER) cc_final: 0.6498 (m-10) REVERT: B 1154 LEU cc_start: 0.8982 (mm) cc_final: 0.8348 (tp) REVERT: B 1188 ASP cc_start: 0.8863 (m-30) cc_final: 0.8597 (m-30) REVERT: B 1195 GLU cc_start: 0.8541 (pm20) cc_final: 0.8189 (mp0) outliers start: 22 outliers final: 17 residues processed: 112 average time/residue: 0.0869 time to fit residues: 15.3745 Evaluate side-chains 112 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 740 VAL 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 A residue 1176 LEU Chi-restraints excluded: chain B residue 523 MET 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 768 LEU Chi-restraints excluded: chain B residue 838 LEU 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 Chi-restraints excluded: chain B residue 1176 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 40 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 64 optimal weight: 1.9990 chunk 3 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.063776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.051609 restraints weight = 54119.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.053519 restraints weight = 26745.103| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.054788 restraints weight = 16438.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.055739 restraints weight = 11676.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.056326 restraints weight = 9113.070| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13420 Z= 0.117 Angle : 0.537 7.917 18342 Z= 0.281 Chirality : 0.037 0.172 2008 Planarity : 0.003 0.036 2148 Dihedral : 16.663 71.995 2306 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.56 % Allowed : 15.00 % Favored : 83.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.23), residues: 1452 helix: 2.16 (0.20), residues: 674 sheet: -1.57 (0.40), residues: 170 loop : -0.63 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1047 TYR 0.019 0.001 TYR A 978 PHE 0.022 0.001 PHE A 674 TRP 0.013 0.001 TRP B 685 HIS 0.001 0.000 HIS B 780 Details of bonding type rmsd covalent geometry : bond 0.00255 (13420) covalent geometry : angle 0.53744 (18342) hydrogen bonds : bond 0.03541 ( 677) hydrogen bonds : angle 4.03401 ( 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 120 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 100 time to evaluate : 0.301 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.8971 (ttm) cc_final: 0.8382 (mtp) REVERT: A 993 MET cc_start: 0.7782 (pmm) cc_final: 0.7404 (pmm) REVERT: A 1051 TYR cc_start: 0.7618 (OUTLIER) cc_final: 0.6596 (m-10) REVERT: A 1154 LEU cc_start: 0.8948 (mm) cc_final: 0.8357 (tp) REVERT: A 1188 ASP cc_start: 0.8864 (m-30) cc_final: 0.8389 (m-30) REVERT: B 576 ASN cc_start: 0.7084 (OUTLIER) cc_final: 0.6699 (t0) REVERT: B 900 MET cc_start: 0.8850 (ttm) cc_final: 0.8310 (mtp) REVERT: B 935 PHE cc_start: 0.8807 (m-10) cc_final: 0.8528 (m-10) REVERT: B 1051 TYR cc_start: 0.6798 (OUTLIER) cc_final: 0.6428 (m-10) REVERT: B 1154 LEU cc_start: 0.8952 (mm) cc_final: 0.8335 (tp) REVERT: B 1195 GLU cc_start: 0.8516 (pm20) cc_final: 0.8148 (mp0) outliers start: 20 outliers final: 16 residues processed: 112 average time/residue: 0.0778 time to fit residues: 13.9363 Evaluate side-chains 111 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.487 ------------------------------------------------------------------------------- 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 838 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain A residue 1176 LEU Chi-restraints excluded: chain B residue 523 MET 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 768 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 Chi-restraints excluded: chain B residue 1146 ILE Chi-restraints excluded: chain B residue 1176 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 117 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 44 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1072 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.060838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.048736 restraints weight = 56911.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.050523 restraints weight = 29017.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.051774 restraints weight = 18187.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.052616 restraints weight = 13063.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.053213 restraints weight = 10373.250| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.2133 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= 0.237 Angle : 0.656 11.998 18342 Z= 0.338 Chirality : 0.041 0.183 2008 Planarity : 0.004 0.033 2148 Dihedral : 16.872 71.815 2306 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.80 % Allowed : 15.94 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.23), residues: 1452 helix: 1.82 (0.20), residues: 678 sheet: -1.89 (0.38), residues: 176 loop : -0.77 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B1047 TYR 0.018 0.001 TYR A 978 PHE 0.030 0.002 PHE A 674 TRP 0.008 0.002 TRP B1152 HIS 0.003 0.001 HIS B 655 Details of bonding type rmsd covalent geometry : bond 0.00523 (13420) covalent geometry : angle 0.65577 (18342) hydrogen bonds : bond 0.04614 ( 677) hydrogen bonds : angle 4.30720 ( 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 110 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: A 993 MET cc_start: 0.7895 (pmm) cc_final: 0.7487 (pmm) REVERT: A 1051 TYR cc_start: 0.7972 (OUTLIER) cc_final: 0.6919 (m-10) REVERT: A 1154 LEU cc_start: 0.8963 (mm) cc_final: 0.8408 (tp) REVERT: B 576 ASN cc_start: 0.7114 (OUTLIER) cc_final: 0.6684 (t0) REVERT: B 900 MET cc_start: 0.8822 (ttm) cc_final: 0.8353 (mtp) REVERT: B 1051 TYR cc_start: 0.7017 (OUTLIER) cc_final: 0.6473 (m-10) REVERT: B 1154 LEU cc_start: 0.9003 (mm) cc_final: 0.8336 (tp) outliers start: 23 outliers final: 14 residues processed: 103 average time/residue: 0.0785 time to fit residues: 13.1822 Evaluate side-chains 102 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.446 ------------------------------------------------------------------------------- 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 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 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 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: 9.9990 chunk 21 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 133 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 77 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1072 GLN 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 = 0.061350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.049277 restraints weight = 56289.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.051097 restraints weight = 28444.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.052294 restraints weight = 17735.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.053194 restraints weight = 12767.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.053744 restraints weight = 10030.873| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13420 Z= 0.208 Angle : 0.645 11.857 18342 Z= 0.331 Chirality : 0.040 0.182 2008 Planarity : 0.004 0.036 2148 Dihedral : 16.896 73.031 2306 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.33 % Allowed : 16.41 % Favored : 82.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.23), residues: 1452 helix: 1.81 (0.20), residues: 676 sheet: -1.97 (0.38), residues: 176 loop : -0.79 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1047 TYR 0.017 0.001 TYR A 978 PHE 0.037 0.002 PHE A 674 TRP 0.010 0.002 TRP B1152 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00461 (13420) covalent geometry : angle 0.64456 (18342) hydrogen bonds : bond 0.04322 ( 677) hydrogen bonds : angle 4.28261 ( 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 104 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.494 Fit side-chains REVERT: A 830 MET cc_start: 0.7718 (ppp) cc_final: 0.7400 (ppp) REVERT: A 900 MET cc_start: 0.8703 (ttm) cc_final: 0.8434 (mtp) REVERT: A 993 MET cc_start: 0.7882 (pmm) cc_final: 0.7483 (pmm) REVERT: A 1051 TYR cc_start: 0.8100 (OUTLIER) cc_final: 0.7027 (m-10) REVERT: A 1154 LEU cc_start: 0.8954 (mm) cc_final: 0.8401 (tp) REVERT: A 1186 LYS cc_start: 0.9689 (mttt) cc_final: 0.9279 (mmtt) REVERT: B 576 ASN cc_start: 0.6904 (OUTLIER) cc_final: 0.6431 (t0) REVERT: B 900 MET cc_start: 0.8825 (ttm) cc_final: 0.8347 (mtp) REVERT: B 1051 TYR cc_start: 0.6823 (OUTLIER) cc_final: 0.6431 (m-10) REVERT: B 1154 LEU cc_start: 0.9002 (mm) cc_final: 0.8327 (tp) outliers start: 17 outliers final: 14 residues processed: 100 average time/residue: 0.0759 time to fit residues: 12.6416 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 : 0.486 ------------------------------------------------------------------------------- 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 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 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 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: 0.0370 chunk 54 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 148 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 39 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 5 optimal weight: 0.2980 overall best weight: 3.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS 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 = 0.061782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.049768 restraints weight = 55622.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.051573 restraints weight = 27902.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.052847 restraints weight = 17337.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.053660 restraints weight = 12327.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.054310 restraints weight = 9792.633| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13420 Z= 0.183 Angle : 0.624 11.735 18342 Z= 0.320 Chirality : 0.039 0.179 2008 Planarity : 0.003 0.034 2148 Dihedral : 16.899 73.336 2306 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.56 % Allowed : 16.02 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.45 (0.23), residues: 1452 helix: 1.88 (0.20), residues: 676 sheet: -1.97 (0.38), residues: 174 loop : -0.80 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1047 TYR 0.017 0.001 TYR A 978 PHE 0.034 0.002 PHE A 674 TRP 0.010 0.001 TRP B 685 HIS 0.002 0.001 HIS A 655 Details of bonding type rmsd covalent geometry : bond 0.00405 (13420) covalent geometry : angle 0.62391 (18342) hydrogen bonds : bond 0.04113 ( 677) hydrogen bonds : angle 4.22692 ( 1818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1587.63 seconds wall clock time: 28 minutes 24.22 seconds (1704.22 seconds total)