Starting phenix.real_space_refine on Fri Jul 3 09:17:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7yq8_34022/07_2026/7yq8_34022.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yq8_34022/07_2026/7yq8_34022.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yq8_34022/07_2026/7yq8_34022.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yq8_34022/07_2026/7yq8_34022.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7yq8_34022/07_2026/7yq8_34022.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7yq8_34022/07_2026/7yq8_34022.cif" model { file = "/net/cci-nas-00/data/ceres_data/7yq8_34022/07_2026/7yq8_34022.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yq8_34022/07_2026/7yq8_34022.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 56 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 8123 2.51 5 N 2247 2.21 5 O 2560 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13036 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 5901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5901 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 25, 'TRANS': 704} Chain breaks: 1 Chain: "B" Number of atoms: 5901 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5901 Classifications: {'peptide': 730} Link IDs: {'PTRANS': 25, 'TRANS': 704} Chain breaks: 1 Chain: "C" Number of atoms: 245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 245 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "E" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 243 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "F" Number of atoms: 328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 328 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'EVP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.14, per 1000 atoms: 0.24 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: 1.39 Conformation dependent library (CDL) restraints added in 626.0 milliseconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2736 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 16 sheets defined 54.6% alpha, 11.2% beta 28 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 1.57 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: 2.64 Time building geometry restraints manager: 1.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3928 1.34 - 1.46: 2544 1.46 - 1.58: 6754 1.58 - 1.70: 108 1.70 - 1.82: 86 Bond restraints: 13420 Sorted by residual: bond pdb=" C7 EVP D 101 " pdb=" O4 EVP D 101 " ideal model delta sigma weight residual 1.200 1.296 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" C7 EVP F 101 " pdb=" O4 EVP F 101 " ideal model delta sigma weight residual 1.200 1.295 -0.095 2.00e-02 2.50e+03 2.25e+01 bond pdb=" C3' DT F 38 " pdb=" C2' DT F 38 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DC E 14 " pdb=" C2' DC E 14 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.53e+00 bond pdb=" C3' DT D 30 " pdb=" C2' DT D 30 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.73e+00 ... (remaining 13415 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 17893 1.82 - 3.64: 357 3.64 - 5.45: 53 5.45 - 7.27: 26 7.27 - 9.09: 13 Bond angle restraints: 18342 Sorted by residual: angle pdb=" N3 DT D 30 " pdb=" C4 DT D 30 " pdb=" O4 DT D 30 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT F 33 " pdb=" C4 DT F 33 " pdb=" O4 DT F 33 " ideal model delta sigma weight residual 119.90 122.51 -2.61 6.00e-01 2.78e+00 1.90e+01 angle pdb=" N3 DT E 23 " pdb=" C4 DT E 23 " pdb=" O4 DT E 23 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT C 14 " pdb=" C4 DT C 14 " pdb=" O4 DT C 14 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT F 38 " pdb=" C4 DT F 38 " pdb=" O4 DT F 38 " ideal model delta sigma weight residual 119.90 122.44 -2.54 6.00e-01 2.78e+00 1.79e+01 ... (remaining 18337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 6893 17.65 - 35.29: 819 35.29 - 52.94: 262 52.94 - 70.59: 53 70.59 - 88.23: 19 Dihedral angle restraints: 8046 sinusoidal: 3802 harmonic: 4244 Sorted by residual: dihedral pdb=" CA ALA A 673 " pdb=" C ALA A 673 " pdb=" N PHE A 674 " pdb=" CA PHE A 674 " ideal model delta harmonic sigma weight residual -180.00 -164.37 -15.63 0 5.00e+00 4.00e-02 9.77e+00 dihedral pdb=" CA ALA B 673 " pdb=" C ALA B 673 " pdb=" N PHE B 674 " pdb=" CA PHE B 674 " ideal model delta harmonic sigma weight residual 180.00 -164.40 -15.60 0 5.00e+00 4.00e-02 9.74e+00 dihedral pdb=" N LYS B 540 " pdb=" CA LYS B 540 " pdb=" CB LYS B 540 " pdb=" CG LYS B 540 " ideal model delta sinusoidal sigma weight residual -60.00 -118.10 58.10 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 8043 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.110: 1959 0.110 - 0.220: 45 0.220 - 0.330: 2 0.330 - 0.441: 0 0.441 - 0.551: 2 Chirality restraints: 2008 Sorted by residual: chirality pdb=" C6 EVP D 101 " pdb=" C5 EVP D 101 " pdb=" C7 EVP D 101 " pdb=" C9 EVP D 101 " both_signs ideal model delta sigma weight residual False -2.41 -1.86 -0.55 2.00e-01 2.50e+01 7.58e+00 chirality pdb=" C6 EVP F 101 " pdb=" C5 EVP F 101 " pdb=" C7 EVP F 101 " pdb=" C9 EVP F 101 " both_signs ideal model delta sigma weight residual False -2.41 -1.87 -0.54 2.00e-01 2.50e+01 7.33e+00 chirality pdb=" CA GLU B 723 " pdb=" N GLU B 723 " pdb=" C GLU B 723 " pdb=" CB GLU B 723 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.00e+00 ... (remaining 2005 not shown) Planarity restraints: 2148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 723 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.73e+00 pdb=" CD GLU B 723 " -0.045 2.00e-02 2.50e+03 pdb=" OE1 GLU B 723 " 0.016 2.00e-02 2.50e+03 pdb=" OE2 GLU B 723 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B1051 " 0.019 2.00e-02 2.50e+03 1.15e-02 2.62e+00 pdb=" CG TYR B1051 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR B1051 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR B1051 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B1051 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B1051 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B1051 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR B1051 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 482 " -0.008 2.00e-02 2.50e+03 1.55e-02 2.39e+00 pdb=" C GLU A 482 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU A 482 " -0.010 2.00e-02 2.50e+03 pdb=" N GLY A 483 " -0.009 2.00e-02 2.50e+03 ... (remaining 2145 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 188 2.61 - 3.18: 11391 3.18 - 3.76: 21704 3.76 - 4.33: 29009 4.33 - 4.90: 45737 Nonbonded interactions: 108029 Sorted by model distance: nonbonded pdb=" OD2 ASP A 564 " pdb="MG MG A1701 " model vdw 2.038 2.170 nonbonded pdb=" OD2 ASP B 564 " pdb="MG MG B1701 " model vdw 2.045 2.170 nonbonded pdb=" OD2 ASP A 562 " pdb="MG MG A1701 " model vdw 2.053 2.170 nonbonded pdb=" OD2 ASP B 562 " pdb="MG MG B1701 " model vdw 2.056 2.170 nonbonded pdb=" O VAL B 772 " pdb=" OG SER B 776 " model vdw 2.205 3.040 ... (remaining 108024 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.590 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: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.030 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.040 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.096 13420 Z= 0.285 Angle : 0.678 9.090 18342 Z= 0.398 Chirality : 0.047 0.551 2008 Planarity : 0.003 0.032 2148 Dihedral : 17.079 88.235 5310 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.24), residues: 1452 helix: 1.92 (0.20), residues: 678 sheet: -1.08 (0.43), residues: 166 loop : -0.63 (0.28), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B1047 TYR 0.025 0.001 TYR B1051 PHE 0.026 0.002 PHE A 674 TRP 0.017 0.002 TRP B 582 HIS 0.002 0.000 HIS B 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.29 (13420) covalent geometry : angle 0.67834 / 0.40 (18342) hydrogen bonds : bond 0.15371 / 9.75 ( 677) hydrogen bonds : angle 5.29969 / 3.67 ( 1818) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.497 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: 0.1014 time to fit residues: 16.0141 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 : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 519 HIS ** B 806 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.061082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.049147 restraints weight = 57700.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.050907 restraints weight = 29471.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.052112 restraints weight = 18524.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.052998 restraints weight = 13393.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.053595 restraints weight = 10581.165| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.1144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 13420 Z= 0.304 Angle : 0.719 8.515 18342 Z= 0.385 Chirality : 0.045 0.201 2008 Planarity : 0.005 0.081 2148 Dihedral : 16.759 63.649 2306 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 0.55 % Allowed : 7.81 % Favored : 91.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.23), residues: 1452 helix: 1.42 (0.19), residues: 682 sheet: -1.57 (0.40), residues: 170 loop : -0.82 (0.27), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 501 TYR 0.018 0.002 TYR B1051 PHE 0.026 0.003 PHE A 674 TRP 0.012 0.002 TRP A1185 HIS 0.004 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00647 / 0.30 (13420) covalent geometry : angle 0.71892 / 0.39 (18342) hydrogen bonds : bond 0.05583 / 3.65 ( 677) hydrogen bonds : angle 4.79840 / 3.37 ( 1818) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.354 Fit side-chains REVERT: A 481 THR cc_start: 0.7248 (p) cc_final: 0.7025 (p) REVERT: A 560 MET cc_start: 0.6292 (ppp) cc_final: 0.5972 (ppp) REVERT: A 830 MET cc_start: 0.7766 (ppp) cc_final: 0.7395 (ppp) REVERT: A 1154 LEU cc_start: 0.8875 (mm) cc_final: 0.8346 (tp) REVERT: B 561 THR cc_start: 0.8052 (p) cc_final: 0.7845 (t) REVERT: B 1149 MET cc_start: 0.8768 (mpp) cc_final: 0.8550 (mpp) outliers start: 7 outliers final: 5 residues processed: 93 average time/residue: 0.0967 time to fit residues: 13.8896 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 : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 149 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 117 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1072 GLN B 806 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.062888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.050568 restraints weight = 56293.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.052485 restraints weight = 27935.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.053709 restraints weight = 17238.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.054704 restraints weight = 12443.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.055245 restraints weight = 9665.288| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 13420 Z= 0.138 Angle : 0.555 8.442 18342 Z= 0.305 Chirality : 0.039 0.169 2008 Planarity : 0.004 0.044 2148 Dihedral : 16.706 64.651 2306 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.39 % Allowed : 9.38 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.23), residues: 1452 helix: 1.78 (0.20), residues: 670 sheet: -1.57 (0.40), residues: 168 loop : -0.79 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 939 TYR 0.015 0.001 TYR B 978 PHE 0.027 0.002 PHE A 674 TRP 0.013 0.002 TRP B 582 HIS 0.002 0.000 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (13420) covalent geometry : angle 0.55524 / 0.30 (18342) hydrogen bonds : bond 0.04341 / 2.85 ( 677) hydrogen bonds : angle 4.40247 / 3.09 ( 1818) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.498 Fit side-chains REVERT: A 481 THR cc_start: 0.7693 (p) cc_final: 0.7367 (p) REVERT: A 560 MET cc_start: 0.6237 (ppp) cc_final: 0.5968 (ppp) REVERT: A 900 MET cc_start: 0.8954 (ttm) cc_final: 0.8397 (mtp) REVERT: A 993 MET cc_start: 0.6919 (pmm) cc_final: 0.6692 (pmm) REVERT: A 1154 LEU cc_start: 0.8847 (mm) cc_final: 0.8320 (tp) REVERT: B 830 MET cc_start: 0.6936 (ppp) cc_final: 0.6718 (ppp) REVERT: B 900 MET cc_start: 0.8946 (ttm) cc_final: 0.8395 (mtp) REVERT: B 993 MET cc_start: 0.7219 (pmm) cc_final: 0.6924 (pmm) REVERT: B 1154 LEU cc_start: 0.9016 (mm) cc_final: 0.8309 (tp) outliers start: 5 outliers final: 3 residues processed: 93 average time/residue: 0.0893 time to fit residues: 13.7333 Evaluate side-chains 89 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 86 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain B residue 591 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 145 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 86 optimal weight: 6.9990 chunk 143 optimal weight: 8.9990 chunk 65 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 38 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3517 r_free = 0.3517 target = 0.063861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.051740 restraints weight = 55397.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.053637 restraints weight = 27803.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.054919 restraints weight = 17191.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.055857 restraints weight = 12250.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.056502 restraints weight = 9615.978| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.1333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 13420 Z= 0.123 Angle : 0.527 6.548 18342 Z= 0.288 Chirality : 0.039 0.166 2008 Planarity : 0.003 0.033 2148 Dihedral : 16.681 64.549 2306 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.55 % Allowed : 11.02 % Favored : 88.44 % 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 are not related in a simple way. whole: 0.60 (0.23), residues: 1452 helix: 1.95 (0.20), residues: 672 sheet: -1.52 (0.40), residues: 168 loop : -0.77 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 508 TYR 0.021 0.001 TYR A 978 PHE 0.027 0.001 PHE A 674 TRP 0.011 0.001 TRP B 582 HIS 0.002 0.000 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (13420) covalent geometry : angle 0.52710 / 0.29 (18342) hydrogen bonds : bond 0.03965 / 2.62 ( 677) hydrogen bonds : angle 4.21084 / 2.96 ( 1818) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 0.520 Fit side-chains REVERT: A 830 MET cc_start: 0.7659 (ppp) cc_final: 0.7337 (ppp) REVERT: A 900 MET cc_start: 0.8942 (ttm) cc_final: 0.8369 (mtp) REVERT: A 1154 LEU cc_start: 0.8848 (mm) cc_final: 0.8303 (tp) REVERT: A 1186 LYS cc_start: 0.9704 (mttt) cc_final: 0.9273 (mmmt) REVERT: B 900 MET cc_start: 0.8962 (ttm) cc_final: 0.8364 (mtp) REVERT: B 1149 MET cc_start: 0.8975 (mpp) cc_final: 0.8733 (mpp) REVERT: B 1154 LEU cc_start: 0.9003 (mm) cc_final: 0.8322 (tp) outliers start: 7 outliers final: 4 residues processed: 101 average time/residue: 0.0992 time to fit residues: 15.7413 Evaluate side-chains 92 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 1048 LEU Chi-restraints excluded: chain B residue 667 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 118 optimal weight: 0.0040 chunk 146 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 109 optimal weight: 0.0570 chunk 84 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 120 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 overall best weight: 1.2116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3527 r_free = 0.3527 target = 0.064119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.051959 restraints weight = 55280.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.053890 restraints weight = 27227.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.055185 restraints weight = 16649.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.056150 restraints weight = 11789.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.056801 restraints weight = 9157.236| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7916 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 13420 Z= 0.116 Angle : 0.532 7.923 18342 Z= 0.286 Chirality : 0.038 0.174 2008 Planarity : 0.003 0.034 2148 Dihedral : 16.659 64.876 2306 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.25 % Allowed : 11.17 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.23), residues: 1452 helix: 2.04 (0.20), residues: 670 sheet: -1.44 (0.41), residues: 168 loop : -0.74 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 939 TYR 0.021 0.001 TYR A 978 PHE 0.022 0.001 PHE A 674 TRP 0.011 0.001 TRP A 685 HIS 0.001 0.000 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.12 (13420) covalent geometry : angle 0.53170 / 0.29 (18342) hydrogen bonds : bond 0.03794 / 2.51 ( 677) hydrogen bonds : angle 4.11032 / 2.88 ( 1818) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.517 Fit side-chains REVERT: A 561 THR cc_start: 0.8000 (p) cc_final: 0.7728 (t) REVERT: A 900 MET cc_start: 0.8974 (ttm) cc_final: 0.8370 (mtp) REVERT: A 1051 TYR cc_start: 0.7466 (OUTLIER) cc_final: 0.6246 (m-10) REVERT: A 1154 LEU cc_start: 0.8851 (mm) cc_final: 0.8321 (tp) REVERT: A 1186 LYS cc_start: 0.9684 (mttt) cc_final: 0.9241 (mmmt) REVERT: B 900 MET cc_start: 0.8958 (ttm) cc_final: 0.8350 (mtp) REVERT: B 1051 TYR cc_start: 0.6467 (OUTLIER) cc_final: 0.5663 (m-10) REVERT: B 1154 LEU cc_start: 0.8928 (mm) cc_final: 0.8308 (tp) REVERT: B 1188 ASP cc_start: 0.8343 (m-30) cc_final: 0.8006 (m-30) outliers start: 16 outliers final: 10 residues processed: 110 average time/residue: 0.0843 time to fit residues: 15.0770 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 : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 121 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 98 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 147 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 135 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 overall best weight: 5.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1072 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.060632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.048483 restraints weight = 57524.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.050278 restraints weight = 29069.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.051525 restraints weight = 18222.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.052420 restraints weight = 13031.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.052967 restraints weight = 10251.530| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 13420 Z= 0.290 Angle : 0.682 9.729 18342 Z= 0.362 Chirality : 0.043 0.238 2008 Planarity : 0.004 0.037 2148 Dihedral : 17.008 67.751 2306 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.95 % Allowed : 13.05 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.23), residues: 1452 helix: 1.66 (0.20), residues: 686 sheet: -1.67 (0.39), residues: 172 loop : -1.01 (0.26), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 939 TYR 0.020 0.002 TYR A 978 PHE 0.025 0.003 PHE B 674 TRP 0.012 0.002 TRP A1185 HIS 0.004 0.001 HIS A 569 Details of bonding type rmsd/Z covalent geometry : bond 0.00608 / 0.29 (13420) covalent geometry : angle 0.68181 / 0.36 (18342) hydrogen bonds : bond 0.05300 / 3.47 ( 677) hydrogen bonds : angle 4.46098 / 3.15 ( 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 112 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 87 time to evaluate : 0.506 Fit side-chains REVERT: A 561 THR cc_start: 0.8062 (p) cc_final: 0.7830 (t) REVERT: A 993 MET cc_start: 0.7254 (pmm) cc_final: 0.7037 (pmm) REVERT: A 1051 TYR cc_start: 0.7742 (OUTLIER) cc_final: 0.6498 (m-10) REVERT: A 1154 LEU cc_start: 0.8921 (mm) cc_final: 0.8317 (tp) REVERT: B 576 ASN cc_start: 0.6855 (OUTLIER) cc_final: 0.6434 (t0) REVERT: B 768 LEU cc_start: 0.9457 (mt) cc_final: 0.9227 (tp) REVERT: B 993 MET cc_start: 0.7403 (pmm) cc_final: 0.7085 (pmm) REVERT: B 1051 TYR cc_start: 0.7122 (OUTLIER) cc_final: 0.6247 (m-10) REVERT: B 1154 LEU cc_start: 0.9029 (mm) cc_final: 0.8387 (tp) outliers start: 25 outliers final: 20 residues processed: 103 average time/residue: 0.0800 time to fit residues: 13.4247 Evaluate side-chains 104 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 504 VAL Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 739 LEU Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 753 THR Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 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 504 VAL Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 107 optimal weight: 0.9980 chunk 75 optimal weight: 0.9990 chunk 113 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 86 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 149 optimal weight: 20.0000 chunk 141 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1072 GLN ** B1148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.062811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.050609 restraints weight = 55376.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.052481 restraints weight = 27711.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.053774 restraints weight = 17227.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.054704 restraints weight = 12236.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.055236 restraints weight = 9615.801| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13420 Z= 0.126 Angle : 0.558 8.752 18342 Z= 0.300 Chirality : 0.039 0.169 2008 Planarity : 0.003 0.035 2148 Dihedral : 16.897 67.141 2306 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.64 % Allowed : 13.36 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.23), residues: 1452 helix: 1.94 (0.20), residues: 674 sheet: -1.57 (0.40), residues: 168 loop : -0.90 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 939 TYR 0.019 0.001 TYR A 978 PHE 0.027 0.002 PHE A 674 TRP 0.013 0.001 TRP B 582 HIS 0.002 0.000 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 (13420) covalent geometry : angle 0.55796 / 0.30 (18342) hydrogen bonds : bond 0.04017 / 2.66 ( 677) hydrogen bonds : angle 4.20978 / 2.96 ( 1818) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.546 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.8646 (ttm) cc_final: 0.8440 (mtp) REVERT: A 993 MET cc_start: 0.7188 (pmm) cc_final: 0.6985 (pmm) REVERT: A 1051 TYR cc_start: 0.7571 (OUTLIER) cc_final: 0.6409 (m-10) REVERT: A 1154 LEU cc_start: 0.8891 (mm) cc_final: 0.8311 (tp) REVERT: B 768 LEU cc_start: 0.9431 (mt) cc_final: 0.9170 (tt) REVERT: B 830 MET cc_start: 0.6867 (ppp) cc_final: 0.6605 (ppp) REVERT: B 900 MET cc_start: 0.8932 (ttm) cc_final: 0.8345 (mtp) REVERT: B 993 MET cc_start: 0.7307 (pmm) cc_final: 0.6954 (pmm) REVERT: B 1051 TYR cc_start: 0.6647 (OUTLIER) cc_final: 0.5906 (m-10) REVERT: B 1154 LEU cc_start: 0.9013 (mm) cc_final: 0.8390 (tp) REVERT: B 1188 ASP cc_start: 0.8396 (m-30) cc_final: 0.8070 (m-30) outliers start: 21 outliers final: 14 residues processed: 111 average time/residue: 0.0930 time to fit residues: 16.8056 Evaluate side-chains 103 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 93 optimal weight: 0.2980 chunk 58 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 64 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 131 optimal weight: 1.9990 chunk 28 optimal weight: 7.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3492 r_free = 0.3492 target = 0.062797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.050703 restraints weight = 55591.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.052565 restraints weight = 27902.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.053819 restraints weight = 17355.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.054752 restraints weight = 12414.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.055397 restraints weight = 9726.535| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1707 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= 0.135 Angle : 0.570 12.944 18342 Z= 0.302 Chirality : 0.039 0.168 2008 Planarity : 0.003 0.038 2148 Dihedral : 16.873 67.323 2306 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.41 % Allowed : 14.45 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.23), residues: 1452 helix: 2.01 (0.20), residues: 672 sheet: -1.53 (0.41), residues: 168 loop : -0.86 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 939 TYR 0.024 0.001 TYR A 978 PHE 0.032 0.002 PHE A 674 TRP 0.011 0.001 TRP B 582 HIS 0.002 0.000 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (13420) covalent geometry : angle 0.56965 / 0.30 (18342) hydrogen bonds : bond 0.03980 / 2.64 ( 677) hydrogen bonds : angle 4.19329 / 2.96 ( 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 110 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 92 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 900 MET cc_start: 0.8736 (ttm) cc_final: 0.8444 (mtp) REVERT: A 993 MET cc_start: 0.7207 (pmm) cc_final: 0.7004 (pmm) REVERT: A 1051 TYR cc_start: 0.7494 (OUTLIER) cc_final: 0.6301 (m-10) REVERT: A 1154 LEU cc_start: 0.8881 (mm) cc_final: 0.8306 (tp) REVERT: B 571 LYS cc_start: 0.8444 (mptt) cc_final: 0.8213 (mmtt) REVERT: B 830 MET cc_start: 0.6779 (ppp) cc_final: 0.6542 (ppp) REVERT: B 900 MET cc_start: 0.8968 (ttm) cc_final: 0.8365 (mtp) REVERT: B 993 MET cc_start: 0.7323 (pmm) cc_final: 0.6962 (pmm) REVERT: B 1051 TYR cc_start: 0.6521 (OUTLIER) cc_final: 0.5855 (m-10) REVERT: B 1154 LEU cc_start: 0.9005 (mm) cc_final: 0.8388 (tp) REVERT: B 1188 ASP cc_start: 0.8411 (m-30) cc_final: 0.8128 (m-30) outliers start: 18 outliers final: 15 residues processed: 105 average time/residue: 0.0920 time to fit residues: 15.6360 Evaluate side-chains 106 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 7.9990 chunk 88 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 117 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 122 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1072 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.061209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.049038 restraints weight = 57325.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.050877 restraints weight = 28665.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.052074 restraints weight = 17898.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.052979 restraints weight = 12877.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.053601 restraints weight = 10163.188| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13420 Z= 0.224 Angle : 0.637 8.254 18342 Z= 0.337 Chirality : 0.041 0.182 2008 Planarity : 0.004 0.033 2148 Dihedral : 17.018 68.299 2306 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.56 % Allowed : 14.84 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.23), residues: 1452 helix: 1.76 (0.20), residues: 676 sheet: -1.83 (0.39), residues: 176 loop : -0.90 (0.26), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 939 TYR 0.021 0.002 TYR A 978 PHE 0.034 0.002 PHE A 674 TRP 0.009 0.002 TRP B1152 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.22 (13420) covalent geometry : angle 0.63689 / 0.34 (18342) hydrogen bonds : bond 0.04720 / 3.10 ( 677) hydrogen bonds : angle 4.36109 / 3.08 ( 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 109 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 89 time to evaluate : 0.521 Fit side-chains REVERT: A 900 MET cc_start: 0.8733 (ttm) cc_final: 0.8348 (mtp) REVERT: A 993 MET cc_start: 0.7294 (pmm) cc_final: 0.7083 (pmm) REVERT: A 1051 TYR cc_start: 0.7766 (OUTLIER) cc_final: 0.6585 (m-10) REVERT: A 1154 LEU cc_start: 0.8919 (mm) cc_final: 0.8317 (tp) REVERT: A 1186 LYS cc_start: 0.9728 (mttt) cc_final: 0.9315 (mmmt) REVERT: B 571 LYS cc_start: 0.8453 (mptt) cc_final: 0.8193 (mmtt) REVERT: B 576 ASN cc_start: 0.6704 (OUTLIER) cc_final: 0.6352 (t0) REVERT: B 993 MET cc_start: 0.7384 (pmm) cc_final: 0.7018 (pmm) REVERT: B 1051 TYR cc_start: 0.6750 (OUTLIER) cc_final: 0.5985 (m-10) REVERT: B 1154 LEU cc_start: 0.9040 (mm) cc_final: 0.8393 (tp) REVERT: B 1188 ASP cc_start: 0.8539 (m-30) cc_final: 0.8238 (m-30) outliers start: 20 outliers final: 17 residues processed: 105 average time/residue: 0.0952 time to fit residues: 16.3619 Evaluate side-chains 106 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 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 842 VAL Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 122 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 133 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 53 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 147 optimal weight: 20.0000 chunk 22 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1072 GLN ** A1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1096 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.060630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.048649 restraints weight = 57517.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.050383 restraints weight = 29064.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.051539 restraints weight = 18214.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.052418 restraints weight = 13188.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.053026 restraints weight = 10431.130| |-----------------------------------------------------------------------------| r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 13420 Z= 0.249 Angle : 0.670 9.036 18342 Z= 0.355 Chirality : 0.042 0.180 2008 Planarity : 0.004 0.032 2148 Dihedral : 17.170 69.558 2306 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % 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 are not related in a simple way. whole: 0.07 (0.23), residues: 1452 helix: 1.50 (0.20), residues: 678 sheet: -1.88 (0.39), residues: 176 loop : -1.01 (0.26), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 939 TYR 0.021 0.002 TYR A 978 PHE 0.036 0.002 PHE A 674 TRP 0.011 0.002 TRP B1152 HIS 0.003 0.001 HIS A 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.25 (13420) covalent geometry : angle 0.66980 / 0.36 (18342) hydrogen bonds : bond 0.04922 / 3.23 ( 677) hydrogen bonds : angle 4.49645 / 3.17 ( 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 106 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 84 time to evaluate : 0.532 Fit side-chains REVERT: A 993 MET cc_start: 0.7558 (pmm) cc_final: 0.7272 (pmm) REVERT: A 1051 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.6896 (m-10) REVERT: A 1154 LEU cc_start: 0.8955 (mm) cc_final: 0.8331 (tp) REVERT: A 1186 LYS cc_start: 0.9728 (mttt) cc_final: 0.9328 (mmmt) REVERT: B 571 LYS cc_start: 0.8541 (mptt) cc_final: 0.8315 (mmtt) REVERT: B 576 ASN cc_start: 0.6996 (OUTLIER) cc_final: 0.6576 (t0) REVERT: B 900 MET cc_start: 0.8735 (ttm) cc_final: 0.8428 (mtp) REVERT: B 993 MET cc_start: 0.7403 (pmm) cc_final: 0.6900 (pmm) REVERT: B 1051 TYR cc_start: 0.6887 (OUTLIER) cc_final: 0.6125 (m-10) outliers start: 22 outliers final: 18 residues processed: 101 average time/residue: 0.0959 time to fit residues: 15.9438 Evaluate side-chains 105 residues out of total 1280 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 481 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 667 ASP Chi-restraints excluded: chain A residue 715 THR Chi-restraints excluded: chain A residue 740 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 842 VAL Chi-restraints excluded: chain A residue 869 VAL Chi-restraints excluded: chain A residue 1048 LEU Chi-restraints excluded: chain A residue 1051 TYR Chi-restraints excluded: chain B residue 576 ASN Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 667 ASP Chi-restraints excluded: chain B residue 715 THR Chi-restraints excluded: chain B residue 739 LEU Chi-restraints excluded: chain B residue 838 LEU Chi-restraints excluded: chain B residue 842 VAL Chi-restraints excluded: chain B residue 869 VAL Chi-restraints excluded: chain B residue 1048 LEU Chi-restraints excluded: chain B residue 1051 TYR Chi-restraints excluded: chain B residue 1146 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 117 optimal weight: 0.0000 chunk 54 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 chunk 30 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3483 r_free = 0.3483 target = 0.062747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.050735 restraints weight = 55468.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.052556 restraints weight = 27474.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.053798 restraints weight = 17005.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.054729 restraints weight = 12157.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.055237 restraints weight = 9506.408| |-----------------------------------------------------------------------------| r_work (final): 0.3258 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.1898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13420 Z= 0.138 Angle : 0.596 8.888 18342 Z= 0.316 Chirality : 0.040 0.161 2008 Planarity : 0.003 0.033 2148 Dihedral : 17.019 70.269 2306 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.48 % Allowed : 15.31 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.23), residues: 1452 helix: 1.89 (0.20), residues: 676 sheet: -1.84 (0.40), residues: 172 loop : -0.88 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 939 TYR 0.021 0.001 TYR A 978 PHE 0.030 0.002 PHE A 674 TRP 0.011 0.002 TRP B 582 HIS 0.003 0.001 HIS B 655 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (13420) covalent geometry : angle 0.59577 / 0.32 (18342) hydrogen bonds : bond 0.04042 / 2.68 ( 677) hydrogen bonds : angle 4.27264 / 3.01 ( 1818) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1797.03 seconds wall clock time: 32 minutes 10.32 seconds (1930.32 seconds total)