Starting phenix.real_space_refine on Mon Dec 30 14:46:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yq8_34022/12_2024/7yq8_34022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yq8_34022/12_2024/7yq8_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7yq8_34022/12_2024/7yq8_34022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yq8_34022/12_2024/7yq8_34022.map" model { file = "/net/cci-nas-00/data/ceres_data/7yq8_34022/12_2024/7yq8_34022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yq8_34022/12_2024/7yq8_34022.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 7.70, per 1000 atoms: 0.59 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: 3.45 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 5.21 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: 5.81 Time building geometry restraints manager: 3.90 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: 0.450 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 35.670 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.940 ------------------------------------------------------------------------------- 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= 0.229 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 : 13.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.017 0.002 TRP B 582 HIS 0.002 0.000 HIS B 569 PHE 0.026 0.002 PHE A 674 TYR 0.025 0.001 TYR B1051 ARG 0.006 0.000 ARG B1047 *********************** 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 : 1.420 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: 0.2492 time to fit residues: 39.2257 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 : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 20.0000 chunk 113 optimal weight: 0.1980 chunk 63 optimal weight: 0.1980 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 9.9990 chunk 60 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 87 optimal weight: 8.9990 chunk 136 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1072 GLN B 519 HIS B 806 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 13420 Z= 0.173 Angle : 0.542 7.329 18342 Z= 0.287 Chirality : 0.038 0.175 2008 Planarity : 0.003 0.032 2148 Dihedral : 16.384 64.338 2306 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.16 % Allowed : 6.72 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1452 helix: 1.99 (0.20), residues: 678 sheet: -1.16 (0.42), residues: 166 loop : -0.58 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1111 HIS 0.002 0.000 HIS A 579 PHE 0.020 0.001 PHE A 674 TYR 0.017 0.001 TYR A 978 ARG 0.008 0.000 ARG B 939 *********************** 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 99 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 97 time to evaluate : 1.398 Fit side-chains REVERT: A 674 PHE cc_start: 0.7753 (m-80) cc_final: 0.7510 (m-10) REVERT: A 830 MET cc_start: 0.7881 (ppp) cc_final: 0.7520 (ppp) REVERT: A 1055 LYS cc_start: 0.8929 (tttt) cc_final: 0.8684 (tmtt) REVERT: A 1154 LEU cc_start: 0.8884 (mm) cc_final: 0.8317 (tp) REVERT: A 1186 LYS cc_start: 0.9670 (mttt) cc_final: 0.9273 (mmmt) REVERT: B 560 MET cc_start: 0.6854 (ttp) cc_final: 0.6489 (ttp) REVERT: B 561 THR cc_start: 0.8028 (p) cc_final: 0.7777 (t) REVERT: B 900 MET cc_start: 0.8730 (mtp) cc_final: 0.8486 (mtp) REVERT: B 1149 MET cc_start: 0.8748 (mpp) cc_final: 0.8499 (mpp) REVERT: B 1154 LEU cc_start: 0.8915 (mm) cc_final: 0.8355 (tp) outliers start: 2 outliers final: 1 residues processed: 97 average time/residue: 0.2449 time to fit residues: 36.3958 Evaluate side-chains 88 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 9.9990 chunk 113 optimal weight: 0.4980 chunk 92 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 136 optimal weight: 0.9990 chunk 147 optimal weight: 7.9990 chunk 121 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 109 optimal weight: 10.0000 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13420 Z= 0.232 Angle : 0.549 6.155 18342 Z= 0.294 Chirality : 0.038 0.177 2008 Planarity : 0.003 0.034 2148 Dihedral : 16.673 68.802 2306 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.62 % Allowed : 9.38 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.23), residues: 1452 helix: 1.96 (0.20), residues: 684 sheet: -1.31 (0.41), residues: 170 loop : -0.63 (0.27), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 582 HIS 0.003 0.001 HIS B 655 PHE 0.021 0.002 PHE A 674 TYR 0.017 0.001 TYR A 978 ARG 0.003 0.000 ARG B 682 *********************** 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 101 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 1.486 Fit side-chains REVERT: A 993 MET cc_start: 0.7517 (pmm) cc_final: 0.7288 (pmm) REVERT: A 1154 LEU cc_start: 0.8962 (mm) cc_final: 0.8355 (tp) REVERT: A 1186 LYS cc_start: 0.9679 (mttt) cc_final: 0.9257 (mmmt) REVERT: B 900 MET cc_start: 0.8793 (mtp) cc_final: 0.8535 (mtp) REVERT: B 993 MET cc_start: 0.7251 (pmm) cc_final: 0.7038 (pmm) REVERT: B 1154 LEU cc_start: 0.8991 (mm) cc_final: 0.8379 (tp) outliers start: 8 outliers final: 3 residues processed: 95 average time/residue: 0.2428 time to fit residues: 36.7840 Evaluate side-chains 87 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 84 time to evaluate : 1.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 91 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 129 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 13420 Z= 0.378 Angle : 0.649 7.905 18342 Z= 0.347 Chirality : 0.042 0.181 2008 Planarity : 0.004 0.045 2148 Dihedral : 17.049 76.376 2306 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.41 % Allowed : 11.25 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.23), residues: 1452 helix: 1.47 (0.20), residues: 680 sheet: -1.75 (0.40), residues: 176 loop : -0.89 (0.26), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A1185 HIS 0.004 0.001 HIS A 655 PHE 0.028 0.002 PHE A 674 TYR 0.018 0.002 TYR A 978 ARG 0.003 0.000 ARG B 697 *********************** 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 108 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 1.535 Fit side-chains REVERT: A 830 MET cc_start: 0.7807 (ppp) cc_final: 0.7489 (ppp) REVERT: A 993 MET cc_start: 0.7298 (pmm) cc_final: 0.7046 (pmm) REVERT: A 1051 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7028 (m-10) REVERT: A 1154 LEU cc_start: 0.9034 (mm) cc_final: 0.8417 (tp) REVERT: B 576 ASN cc_start: 0.6962 (OUTLIER) cc_final: 0.6518 (t0) REVERT: B 775 MET cc_start: 0.7417 (ptm) cc_final: 0.7177 (ptm) REVERT: B 900 MET cc_start: 0.8726 (mtp) cc_final: 0.8473 (mtp) REVERT: B 993 MET cc_start: 0.7293 (pmm) cc_final: 0.6921 (pmm) REVERT: B 1051 TYR cc_start: 0.7122 (OUTLIER) cc_final: 0.6396 (m-10) outliers start: 18 outliers final: 8 residues processed: 102 average time/residue: 0.2154 time to fit residues: 35.5448 Evaluate side-chains 91 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 2 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 100 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 74 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 519 HIS A1072 GLN B1072 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1808 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= 0.163 Angle : 0.545 10.494 18342 Z= 0.285 Chirality : 0.038 0.169 2008 Planarity : 0.003 0.032 2148 Dihedral : 16.831 72.437 2306 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.86 % Allowed : 12.97 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.23), residues: 1452 helix: 1.96 (0.20), residues: 676 sheet: -1.71 (0.40), residues: 172 loop : -0.71 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 685 HIS 0.001 0.000 HIS B 579 PHE 0.023 0.001 PHE A 727 TYR 0.019 0.001 TYR A 978 ARG 0.002 0.000 ARG A1047 *********************** 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 109 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 1.563 Fit side-chains revert: symmetry clash REVERT: A 739 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8368 (tt) REVERT: A 830 MET cc_start: 0.7804 (ppp) cc_final: 0.7471 (ppp) REVERT: A 993 MET cc_start: 0.7643 (pmm) cc_final: 0.7365 (pmm) REVERT: A 1051 TYR cc_start: 0.7470 (OUTLIER) cc_final: 0.6480 (m-10) REVERT: A 1154 LEU cc_start: 0.8984 (mm) cc_final: 0.8391 (tp) REVERT: B 900 MET cc_start: 0.8795 (mtp) cc_final: 0.8560 (mtp) REVERT: B 935 PHE cc_start: 0.8840 (m-10) cc_final: 0.8554 (m-10) REVERT: B 993 MET cc_start: 0.7391 (pmm) cc_final: 0.6965 (pmm) REVERT: B 1051 TYR cc_start: 0.6277 (OUTLIER) cc_final: 0.6068 (m-10) REVERT: B 1149 MET cc_start: 0.8628 (mpp) cc_final: 0.8318 (mpp) REVERT: B 1154 LEU cc_start: 0.8628 (mt) cc_final: 0.8149 (tp) outliers start: 11 outliers final: 8 residues processed: 103 average time/residue: 0.2278 time to fit residues: 37.1075 Evaluate side-chains 97 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 739 LEU 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 8.9990 chunk 130 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 85 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 145 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 67 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 139 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1072 GLN ** A1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1072 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 13420 Z= 0.466 Angle : 0.706 7.766 18342 Z= 0.374 Chirality : 0.044 0.203 2008 Planarity : 0.004 0.053 2148 Dihedral : 17.145 75.830 2306 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.95 % Allowed : 15.23 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.22), residues: 1452 helix: 1.32 (0.20), residues: 678 sheet: -1.93 (0.38), residues: 176 loop : -1.03 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B1152 HIS 0.005 0.001 HIS B 569 PHE 0.039 0.003 PHE A 674 TYR 0.014 0.002 TYR A 978 ARG 0.004 0.001 ARG B1047 *********************** 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 109 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 1.468 Fit side-chains REVERT: A 993 MET cc_start: 0.7528 (pmm) cc_final: 0.7239 (pmm) REVERT: A 1051 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7137 (m-10) REVERT: B 576 ASN cc_start: 0.6933 (OUTLIER) cc_final: 0.6484 (t0) REVERT: B 775 MET cc_start: 0.7420 (ptm) cc_final: 0.7203 (ptm) REVERT: B 900 MET cc_start: 0.8727 (mtp) cc_final: 0.8486 (mtp) REVERT: B 993 MET cc_start: 0.7240 (pmm) cc_final: 0.6805 (pmm) REVERT: B 1051 TYR cc_start: 0.7216 (OUTLIER) cc_final: 0.6608 (m-10) outliers start: 25 outliers final: 19 residues processed: 102 average time/residue: 0.2022 time to fit residues: 33.6966 Evaluate side-chains 105 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 1.480 ------------------------------------------------------------------------------- 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 528 ILE Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 144 optimal weight: 0.8980 chunk 90 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 10.0000 chunk 57 optimal weight: 4.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1072 GLN B1072 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13420 Z= 0.239 Angle : 0.590 11.229 18342 Z= 0.309 Chirality : 0.039 0.169 2008 Planarity : 0.003 0.035 2148 Dihedral : 17.016 76.375 2306 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.80 % Allowed : 15.31 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.23), residues: 1452 helix: 1.70 (0.20), residues: 676 sheet: -1.92 (0.38), residues: 176 loop : -0.90 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 685 HIS 0.002 0.000 HIS B 655 PHE 0.034 0.002 PHE A 674 TYR 0.013 0.001 TYR A 928 ARG 0.002 0.000 ARG B 697 *********************** 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 113 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 90 time to evaluate : 1.469 Fit side-chains revert: symmetry clash REVERT: A 571 LYS cc_start: 0.8704 (mttp) cc_final: 0.8499 (mttp) REVERT: A 830 MET cc_start: 0.7800 (ppp) cc_final: 0.7473 (ppp) REVERT: A 993 MET cc_start: 0.7475 (pmm) cc_final: 0.7177 (pmm) REVERT: A 1051 TYR cc_start: 0.8016 (OUTLIER) cc_final: 0.7085 (m-10) REVERT: A 1154 LEU cc_start: 0.8691 (mt) cc_final: 0.8301 (tp) REVERT: B 576 ASN cc_start: 0.6915 (OUTLIER) cc_final: 0.6480 (t0) REVERT: B 900 MET cc_start: 0.8745 (mtp) cc_final: 0.8514 (mtp) REVERT: B 993 MET cc_start: 0.7166 (pmm) cc_final: 0.6747 (pmm) REVERT: B 1051 TYR cc_start: 0.6755 (OUTLIER) cc_final: 0.6481 (m-10) REVERT: B 1149 MET cc_start: 0.8785 (mpp) cc_final: 0.8541 (mpp) REVERT: B 1154 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8067 (tp) outliers start: 23 outliers final: 18 residues processed: 106 average time/residue: 0.2082 time to fit residues: 35.5341 Evaluate side-chains 107 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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 739 LEU 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 739 LEU Chi-restraints excluded: chain B residue 740 VAL 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 1154 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 91 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 138 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13420 Z= 0.237 Angle : 0.582 7.928 18342 Z= 0.306 Chirality : 0.039 0.168 2008 Planarity : 0.003 0.035 2148 Dihedral : 16.934 74.811 2306 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.34 % Allowed : 15.16 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.23), residues: 1452 helix: 1.85 (0.20), residues: 676 sheet: -1.93 (0.38), residues: 176 loop : -0.86 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 685 HIS 0.002 0.001 HIS A 655 PHE 0.030 0.002 PHE A 674 TYR 0.011 0.001 TYR A 928 ARG 0.003 0.000 ARG B 697 *********************** 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 119 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 89 time to evaluate : 1.439 Fit side-chains revert: symmetry clash REVERT: A 830 MET cc_start: 0.7799 (ppp) cc_final: 0.7478 (ppp) REVERT: A 993 MET cc_start: 0.7461 (pmm) cc_final: 0.7127 (pmm) REVERT: A 1051 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.6939 (m-10) REVERT: A 1154 LEU cc_start: 0.8716 (mt) cc_final: 0.8349 (tp) REVERT: B 576 ASN cc_start: 0.6886 (OUTLIER) cc_final: 0.6463 (t0) REVERT: B 900 MET cc_start: 0.8741 (mtp) cc_final: 0.8515 (mtp) REVERT: B 993 MET cc_start: 0.7208 (pmm) cc_final: 0.6795 (pmm) REVERT: B 1051 TYR cc_start: 0.6717 (OUTLIER) cc_final: 0.6429 (m-10) REVERT: B 1149 MET cc_start: 0.8806 (mpp) cc_final: 0.8530 (mpp) outliers start: 30 outliers final: 18 residues processed: 111 average time/residue: 0.2026 time to fit residues: 36.2330 Evaluate side-chains 106 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 85 time to evaluate : 1.329 ------------------------------------------------------------------------------- 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 842 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 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 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 Chi-restraints excluded: chain B residue 1154 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 9.9990 chunk 138 optimal weight: 0.9990 chunk 81 optimal weight: 10.0000 chunk 58 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 121 optimal weight: 6.9990 chunk 127 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 chunk 142 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13420 Z= 0.202 Angle : 0.578 11.784 18342 Z= 0.299 Chirality : 0.038 0.178 2008 Planarity : 0.003 0.036 2148 Dihedral : 16.860 72.079 2306 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.80 % Allowed : 15.70 % Favored : 82.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1452 helix: 2.01 (0.20), residues: 676 sheet: -1.90 (0.38), residues: 172 loop : -0.77 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 685 HIS 0.002 0.000 HIS A 622 PHE 0.027 0.002 PHE A 674 TYR 0.011 0.001 TYR A 978 ARG 0.002 0.000 ARG A 697 *********************** 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 116 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 830 MET cc_start: 0.7813 (ppp) cc_final: 0.7484 (ppp) REVERT: A 993 MET cc_start: 0.7798 (pmm) cc_final: 0.7421 (pmm) REVERT: A 1051 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.6844 (m-10) REVERT: A 1154 LEU cc_start: 0.8690 (mt) cc_final: 0.8348 (tp) REVERT: B 576 ASN cc_start: 0.6876 (OUTLIER) cc_final: 0.6449 (t0) REVERT: B 900 MET cc_start: 0.8797 (mtp) cc_final: 0.8569 (mtp) REVERT: B 993 MET cc_start: 0.7199 (pmm) cc_final: 0.6793 (pmm) REVERT: B 1051 TYR cc_start: 0.6616 (OUTLIER) cc_final: 0.6335 (m-10) REVERT: B 1149 MET cc_start: 0.8703 (mpp) cc_final: 0.8410 (mpp) REVERT: B 1154 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.7951 (tp) outliers start: 23 outliers final: 18 residues processed: 109 average time/residue: 0.2269 time to fit residues: 39.0913 Evaluate side-chains 110 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 1.806 ------------------------------------------------------------------------------- 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 842 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain 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 740 VAL 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 Chi-restraints excluded: chain B residue 1154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.8980 chunk 99 optimal weight: 0.5980 chunk 149 optimal weight: 6.9990 chunk 137 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 0.9980 chunk 72 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13420 Z= 0.158 Angle : 0.563 8.300 18342 Z= 0.291 Chirality : 0.038 0.166 2008 Planarity : 0.003 0.038 2148 Dihedral : 16.788 72.393 2306 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.64 % Allowed : 16.25 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.23), residues: 1452 helix: 2.17 (0.20), residues: 674 sheet: -1.76 (0.39), residues: 170 loop : -0.69 (0.27), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 685 HIS 0.001 0.000 HIS A 579 PHE 0.023 0.001 PHE A 674 TYR 0.011 0.001 TYR A 978 ARG 0.002 0.000 ARG A1047 ********************** 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 121 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 1.652 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 723 GLU cc_start: 0.9227 (mp0) cc_final: 0.8831 (mp0) REVERT: A 830 MET cc_start: 0.7864 (ppp) cc_final: 0.7522 (ppp) REVERT: A 993 MET cc_start: 0.7628 (pmm) cc_final: 0.7285 (pmm) REVERT: A 1051 TYR cc_start: 0.7718 (OUTLIER) cc_final: 0.6666 (m-10) REVERT: A 1149 MET cc_start: 0.8736 (ptp) cc_final: 0.8431 (mpp) REVERT: A 1154 LEU cc_start: 0.8691 (mt) cc_final: 0.8360 (tp) REVERT: A 1188 ASP cc_start: 0.8841 (m-30) cc_final: 0.8388 (m-30) REVERT: B 576 ASN cc_start: 0.6906 (OUTLIER) cc_final: 0.6501 (t0) REVERT: B 900 MET cc_start: 0.8766 (mtp) cc_final: 0.8554 (mtp) REVERT: B 993 MET cc_start: 0.7421 (pmm) cc_final: 0.7036 (pmm) REVERT: B 1051 TYR cc_start: 0.6493 (OUTLIER) cc_final: 0.6261 (m-10) REVERT: B 1149 MET cc_start: 0.8664 (mpp) cc_final: 0.8343 (mpp) REVERT: B 1154 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8027 (tp) outliers start: 21 outliers final: 16 residues processed: 114 average time/residue: 0.2509 time to fit residues: 44.1224 Evaluate side-chains 110 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 842 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain 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 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 1154 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 1.9990 chunk 17 optimal weight: 0.0770 chunk 33 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 122 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 6 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.3142 ------------------------------------------------------------------------------- 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 = 0.3513 r_free = 0.3513 target = 0.063676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.051532 restraints weight = 54355.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.053430 restraints weight = 26775.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.054778 restraints weight = 16462.940| |-----------------------------------------------------------------------------| r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13420 Z= 0.165 Angle : 0.572 12.047 18342 Z= 0.295 Chirality : 0.038 0.171 2008 Planarity : 0.004 0.051 2148 Dihedral : 16.765 72.242 2306 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.48 % Allowed : 16.64 % Favored : 81.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.23), residues: 1452 helix: 2.18 (0.20), residues: 674 sheet: -1.62 (0.39), residues: 166 loop : -0.67 (0.27), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 685 HIS 0.002 0.000 HIS A 780 PHE 0.023 0.001 PHE A 674 TYR 0.020 0.001 TYR A 978 ARG 0.004 0.000 ARG B 939 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1980.10 seconds wall clock time: 38 minutes 20.32 seconds (2300.32 seconds total)