Starting phenix.real_space_refine on Thu Mar 5 14:15:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vq2_32083/03_2026/7vq2_32083.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vq2_32083/03_2026/7vq2_32083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vq2_32083/03_2026/7vq2_32083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vq2_32083/03_2026/7vq2_32083.map" model { file = "/net/cci-nas-00/data/ceres_data/7vq2_32083/03_2026/7vq2_32083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vq2_32083/03_2026/7vq2_32083.cif" } resolution = 3.68 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= 0.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 76 5.16 5 C 7732 2.51 5 N 1872 2.21 5 O 1896 1.98 5 H 11764 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23340 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 5835 Classifications: {'peptide': 354} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 21, 'TRANS': 332} Restraints were copied for chains: B, C, D Time building chain proxies: 5.99, per 1000 atoms: 0.26 Number of scatterers: 23340 At special positions: 0 Unit cell: (137.655, 137.655, 73.53, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 O 1896 8.00 N 1872 7.00 C 7732 6.00 H 11764 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 996 " - pdb=" SG CYS A1008 " distance=2.03 Simple disulfide: pdb=" SG CYS B 996 " - pdb=" SG CYS B1008 " distance=2.03 Simple disulfide: pdb=" SG CYS C 996 " - pdb=" SG CYS C1008 " distance=2.03 Simple disulfide: pdb=" SG CYS D 996 " - pdb=" SG CYS D1008 " distance=2.03 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: 2.16 Conformation dependent library (CDL) restraints added in 886.5 milliseconds 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2704 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 76.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'A' and resid 753 through 762 removed outlier: 3.527A pdb=" N LEU A 761 " --> pdb=" O THR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 768 removed outlier: 3.842A pdb=" N LEU A 766 " --> pdb=" O ALA A 762 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU A 767 " --> pdb=" O PHE A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 780 removed outlier: 3.659A pdb=" N GLN A 779 " --> pdb=" O GLU A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 794 removed outlier: 3.572A pdb=" N ALA A 794 " --> pdb=" O ALA A 790 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 819 Processing helix chain 'A' and resid 826 through 846 Processing helix chain 'A' and resid 855 through 866 Processing helix chain 'A' and resid 866 through 888 removed outlier: 3.881A pdb=" N THR A 884 " --> pdb=" O VAL A 880 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 908 Processing helix chain 'A' and resid 909 through 917 removed outlier: 3.596A pdb=" N ILE A 916 " --> pdb=" O ILE A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 920 through 956 removed outlier: 4.741A pdb=" N LYS A 932 " --> pdb=" O LYS A 928 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASP A 933 " --> pdb=" O ARG A 929 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE A 936 " --> pdb=" O LYS A 932 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A 940 " --> pdb=" O PHE A 936 " (cutoff:3.500A) Processing helix chain 'A' and resid 962 through 978 removed outlier: 3.804A pdb=" N LEU A 966 " --> pdb=" O ARG A 962 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR A 972 " --> pdb=" O ARG A 968 " (cutoff:3.500A) Processing helix chain 'A' and resid 1021 through 1036 removed outlier: 3.558A pdb=" N PHE A1035 " --> pdb=" O LEU A1031 " (cutoff:3.500A) Processing helix chain 'A' and resid 1038 through 1056 removed outlier: 3.871A pdb=" N GLN A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A1054 " --> pdb=" O TYR A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1077 removed outlier: 4.371A pdb=" N HIS A1068 " --> pdb=" O LYS A1064 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP A1069 " --> pdb=" O PHE A1065 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU A1070 " --> pdb=" O GLN A1066 " (cutoff:3.500A) Processing helix chain 'A' and resid 1081 through 1098 removed outlier: 4.054A pdb=" N LEU A1086 " --> pdb=" O PRO A1082 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU A1087 " --> pdb=" O PRO A1083 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER A1088 " --> pdb=" O PHE A1084 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 762 removed outlier: 3.527A pdb=" N LEU B 761 " --> pdb=" O THR B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 768 removed outlier: 3.843A pdb=" N LEU B 766 " --> pdb=" O ALA B 762 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU B 767 " --> pdb=" O PHE B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 removed outlier: 3.659A pdb=" N GLN B 779 " --> pdb=" O GLU B 775 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 794 removed outlier: 3.572A pdb=" N ALA B 794 " --> pdb=" O ALA B 790 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 819 Processing helix chain 'B' and resid 826 through 846 Processing helix chain 'B' and resid 855 through 866 Processing helix chain 'B' and resid 866 through 888 removed outlier: 3.881A pdb=" N THR B 884 " --> pdb=" O VAL B 880 " (cutoff:3.500A) Processing helix chain 'B' and resid 891 through 908 Processing helix chain 'B' and resid 909 through 917 removed outlier: 3.596A pdb=" N ILE B 916 " --> pdb=" O ILE B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 920 through 956 removed outlier: 4.741A pdb=" N LYS B 932 " --> pdb=" O LYS B 928 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASP B 933 " --> pdb=" O ARG B 929 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N PHE B 936 " --> pdb=" O LYS B 932 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU B 940 " --> pdb=" O PHE B 936 " (cutoff:3.500A) Processing helix chain 'B' and resid 962 through 978 removed outlier: 3.804A pdb=" N LEU B 966 " --> pdb=" O ARG B 962 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR B 972 " --> pdb=" O ARG B 968 " (cutoff:3.500A) Processing helix chain 'B' and resid 1021 through 1036 removed outlier: 3.558A pdb=" N PHE B1035 " --> pdb=" O LEU B1031 " (cutoff:3.500A) Processing helix chain 'B' and resid 1038 through 1056 removed outlier: 3.871A pdb=" N GLN B1053 " --> pdb=" O ASN B1049 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN B1054 " --> pdb=" O TYR B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1058 through 1077 removed outlier: 4.371A pdb=" N HIS B1068 " --> pdb=" O LYS B1064 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP B1069 " --> pdb=" O PHE B1065 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU B1070 " --> pdb=" O GLN B1066 " (cutoff:3.500A) Processing helix chain 'B' and resid 1081 through 1098 removed outlier: 4.055A pdb=" N LEU B1086 " --> pdb=" O PRO B1082 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU B1087 " --> pdb=" O PRO B1083 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N SER B1088 " --> pdb=" O PHE B1084 " (cutoff:3.500A) Processing helix chain 'C' and resid 753 through 762 removed outlier: 3.527A pdb=" N LEU C 761 " --> pdb=" O THR C 757 " (cutoff:3.500A) Processing helix chain 'C' and resid 762 through 768 removed outlier: 3.841A pdb=" N LEU C 766 " --> pdb=" O ALA C 762 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU C 767 " --> pdb=" O PHE C 763 " (cutoff:3.500A) Processing helix chain 'C' and resid 775 through 780 removed outlier: 3.659A pdb=" N GLN C 779 " --> pdb=" O GLU C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 783 through 794 removed outlier: 3.573A pdb=" N ALA C 794 " --> pdb=" O ALA C 790 " (cutoff:3.500A) Processing helix chain 'C' and resid 794 through 819 Processing helix chain 'C' and resid 826 through 846 Processing helix chain 'C' and resid 855 through 866 Processing helix chain 'C' and resid 866 through 888 removed outlier: 3.881A pdb=" N THR C 884 " --> pdb=" O VAL C 880 " (cutoff:3.500A) Processing helix chain 'C' and resid 891 through 908 Processing helix chain 'C' and resid 909 through 917 removed outlier: 3.596A pdb=" N ILE C 916 " --> pdb=" O ILE C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 956 removed outlier: 4.741A pdb=" N LYS C 932 " --> pdb=" O LYS C 928 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASP C 933 " --> pdb=" O ARG C 929 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE C 936 " --> pdb=" O LYS C 932 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU C 940 " --> pdb=" O PHE C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 962 through 978 removed outlier: 3.804A pdb=" N LEU C 966 " --> pdb=" O ARG C 962 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR C 972 " --> pdb=" O ARG C 968 " (cutoff:3.500A) Processing helix chain 'C' and resid 1021 through 1036 removed outlier: 3.558A pdb=" N PHE C1035 " --> pdb=" O LEU C1031 " (cutoff:3.500A) Processing helix chain 'C' and resid 1038 through 1056 removed outlier: 3.871A pdb=" N GLN C1053 " --> pdb=" O ASN C1049 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN C1054 " --> pdb=" O TYR C1050 " (cutoff:3.500A) Processing helix chain 'C' and resid 1058 through 1077 removed outlier: 4.372A pdb=" N HIS C1068 " --> pdb=" O LYS C1064 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP C1069 " --> pdb=" O PHE C1065 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU C1070 " --> pdb=" O GLN C1066 " (cutoff:3.500A) Processing helix chain 'C' and resid 1081 through 1098 removed outlier: 4.054A pdb=" N LEU C1086 " --> pdb=" O PRO C1082 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU C1087 " --> pdb=" O PRO C1083 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER C1088 " --> pdb=" O PHE C1084 " (cutoff:3.500A) Processing helix chain 'D' and resid 753 through 762 removed outlier: 3.527A pdb=" N LEU D 761 " --> pdb=" O THR D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 768 removed outlier: 3.842A pdb=" N LEU D 766 " --> pdb=" O ALA D 762 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU D 767 " --> pdb=" O PHE D 763 " (cutoff:3.500A) Processing helix chain 'D' and resid 775 through 780 removed outlier: 3.659A pdb=" N GLN D 779 " --> pdb=" O GLU D 775 " (cutoff:3.500A) Processing helix chain 'D' and resid 783 through 794 removed outlier: 3.572A pdb=" N ALA D 794 " --> pdb=" O ALA D 790 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 819 Processing helix chain 'D' and resid 826 through 846 Processing helix chain 'D' and resid 855 through 866 Processing helix chain 'D' and resid 866 through 888 removed outlier: 3.880A pdb=" N THR D 884 " --> pdb=" O VAL D 880 " (cutoff:3.500A) Processing helix chain 'D' and resid 891 through 908 Processing helix chain 'D' and resid 909 through 917 removed outlier: 3.597A pdb=" N ILE D 916 " --> pdb=" O ILE D 913 " (cutoff:3.500A) Processing helix chain 'D' and resid 920 through 956 removed outlier: 4.741A pdb=" N LYS D 932 " --> pdb=" O LYS D 928 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N ASP D 933 " --> pdb=" O ARG D 929 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N PHE D 936 " --> pdb=" O LYS D 932 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 940 " --> pdb=" O PHE D 936 " (cutoff:3.500A) Processing helix chain 'D' and resid 962 through 978 removed outlier: 3.804A pdb=" N LEU D 966 " --> pdb=" O ARG D 962 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR D 972 " --> pdb=" O ARG D 968 " (cutoff:3.500A) Processing helix chain 'D' and resid 1021 through 1036 removed outlier: 3.559A pdb=" N PHE D1035 " --> pdb=" O LEU D1031 " (cutoff:3.500A) Processing helix chain 'D' and resid 1038 through 1056 removed outlier: 3.870A pdb=" N GLN D1053 " --> pdb=" O ASN D1049 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN D1054 " --> pdb=" O TYR D1050 " (cutoff:3.500A) Processing helix chain 'D' and resid 1058 through 1077 removed outlier: 4.371A pdb=" N HIS D1068 " --> pdb=" O LYS D1064 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASP D1069 " --> pdb=" O PHE D1065 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LEU D1070 " --> pdb=" O GLN D1066 " (cutoff:3.500A) Processing helix chain 'D' and resid 1081 through 1098 removed outlier: 4.054A pdb=" N LEU D1086 " --> pdb=" O PRO D1082 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU D1087 " --> pdb=" O PRO D1083 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N SER D1088 " --> pdb=" O PHE D1084 " (cutoff:3.500A) 744 hydrogen bonds defined for protein. 2172 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.66 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 11728 1.13 - 1.30: 1736 1.30 - 1.47: 4966 1.47 - 1.64: 5162 1.64 - 1.81: 108 Bond restraints: 23700 Sorted by residual: bond pdb=" N PRO A1021 " pdb=" CD PRO A1021 " ideal model delta sigma weight residual 1.473 1.614 -0.141 1.40e-02 5.10e+03 1.02e+02 bond pdb=" N PRO C1021 " pdb=" CD PRO C1021 " ideal model delta sigma weight residual 1.473 1.614 -0.141 1.40e-02 5.10e+03 1.02e+02 bond pdb=" N PRO D1021 " pdb=" CD PRO D1021 " ideal model delta sigma weight residual 1.473 1.614 -0.141 1.40e-02 5.10e+03 1.01e+02 bond pdb=" N PRO B1021 " pdb=" CD PRO B1021 " ideal model delta sigma weight residual 1.473 1.613 -0.140 1.40e-02 5.10e+03 1.00e+02 bond pdb=" CE1 PHE A 809 " pdb=" HE1 PHE A 809 " ideal model delta sigma weight residual 0.930 1.094 -0.164 2.00e-02 2.50e+03 6.69e+01 ... (remaining 23695 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.63: 39314 2.63 - 5.26: 3172 5.26 - 7.89: 408 7.89 - 10.52: 6 10.52 - 13.15: 40 Bond angle restraints: 42940 Sorted by residual: angle pdb=" CA ALA A1013 " pdb=" C ALA A1013 " pdb=" N THR A1014 " ideal model delta sigma weight residual 117.96 110.03 7.93 1.23e+00 6.61e-01 4.16e+01 angle pdb=" CA ALA C1013 " pdb=" C ALA C1013 " pdb=" N THR C1014 " ideal model delta sigma weight residual 117.96 110.05 7.91 1.23e+00 6.61e-01 4.13e+01 angle pdb=" CA ALA B1013 " pdb=" C ALA B1013 " pdb=" N THR B1014 " ideal model delta sigma weight residual 117.96 110.08 7.88 1.23e+00 6.61e-01 4.10e+01 angle pdb=" CA ALA D1013 " pdb=" C ALA D1013 " pdb=" N THR D1014 " ideal model delta sigma weight residual 117.96 110.10 7.86 1.23e+00 6.61e-01 4.09e+01 angle pdb=" N GLY B1000 " pdb=" CA GLY B1000 " pdb=" C GLY B1000 " ideal model delta sigma weight residual 115.08 110.03 5.05 1.19e+00 7.06e-01 1.80e+01 ... (remaining 42935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.93: 10445 16.93 - 33.87: 427 33.87 - 50.80: 228 50.80 - 67.73: 84 67.73 - 84.66: 12 Dihedral angle restraints: 11196 sinusoidal: 5880 harmonic: 5316 Sorted by residual: dihedral pdb=" CA ALA C1013 " pdb=" C ALA C1013 " pdb=" N THR C1014 " pdb=" CA THR C1014 " ideal model delta harmonic sigma weight residual -180.00 -147.80 -32.20 0 5.00e+00 4.00e-02 4.15e+01 dihedral pdb=" CA ALA A1013 " pdb=" C ALA A1013 " pdb=" N THR A1014 " pdb=" CA THR A1014 " ideal model delta harmonic sigma weight residual -180.00 -147.81 -32.19 0 5.00e+00 4.00e-02 4.14e+01 dihedral pdb=" CA ALA D1013 " pdb=" C ALA D1013 " pdb=" N THR D1014 " pdb=" CA THR D1014 " ideal model delta harmonic sigma weight residual -180.00 -147.87 -32.13 0 5.00e+00 4.00e-02 4.13e+01 ... (remaining 11193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1203 0.036 - 0.072: 186 0.072 - 0.108: 376 0.108 - 0.144: 55 0.144 - 0.180: 8 Chirality restraints: 1828 Sorted by residual: chirality pdb=" CA VAL C 824 " pdb=" N VAL C 824 " pdb=" C VAL C 824 " pdb=" CB VAL C 824 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CA VAL A 824 " pdb=" N VAL A 824 " pdb=" C VAL A 824 " pdb=" CB VAL A 824 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CA VAL B 824 " pdb=" N VAL B 824 " pdb=" C VAL B 824 " pdb=" CB VAL B 824 " both_signs ideal model delta sigma weight residual False 2.44 2.62 -0.18 2.00e-01 2.50e+01 8.13e-01 ... (remaining 1825 not shown) Planarity restraints: 3348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D1013 " 0.022 2.00e-02 2.50e+03 4.94e-02 2.44e+01 pdb=" C ALA D1013 " -0.085 2.00e-02 2.50e+03 pdb=" O ALA D1013 " 0.033 2.00e-02 2.50e+03 pdb=" N THR D1014 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B1013 " -0.022 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C ALA B1013 " 0.085 2.00e-02 2.50e+03 pdb=" O ALA B1013 " -0.033 2.00e-02 2.50e+03 pdb=" N THR B1014 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C1013 " -0.022 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C ALA C1013 " 0.085 2.00e-02 2.50e+03 pdb=" O ALA C1013 " -0.033 2.00e-02 2.50e+03 pdb=" N THR C1014 " -0.030 2.00e-02 2.50e+03 ... (remaining 3345 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.01: 759 2.01 - 2.66: 29813 2.66 - 3.31: 71466 3.31 - 3.95: 87738 3.95 - 4.60: 130925 Nonbonded interactions: 320701 Sorted by model distance: nonbonded pdb="HE22 GLN C1056 " pdb="HE21 GLN D1054 " model vdw 1.364 2.100 nonbonded pdb="HE22 GLN A1056 " pdb="HE21 GLN B1054 " model vdw 1.364 2.100 nonbonded pdb="HE22 GLN B1056 " pdb="HE21 GLN C1054 " model vdw 1.364 2.100 nonbonded pdb="HE21 GLN A1054 " pdb="HE22 GLN D1056 " model vdw 1.364 2.100 nonbonded pdb=" H GLU B 994 " pdb=" H GLU B1022 " model vdw 1.402 2.100 ... (remaining 320696 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.960 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: 0.130 Extract box with map and model: 0.330 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 25.390 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3835 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.141 11940 Z= 0.549 Angle : 0.836 7.935 16268 Z= 0.541 Chirality : 0.051 0.180 1828 Planarity : 0.004 0.049 2020 Dihedral : 12.144 84.663 4256 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 1.42 % Allowed : 4.83 % Favored : 93.75 % Rotamer: Outliers : 1.27 % Allowed : 1.27 % Favored : 97.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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: -3.35 (0.18), residues: 1408 helix: -1.74 (0.14), residues: 968 sheet: None (None), residues: 0 loop : -3.04 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1096 TYR 0.002 0.000 TYR D 893 PHE 0.002 0.001 PHE B 939 TRP 0.002 0.001 TRP C1063 HIS 0.002 0.000 HIS B 958 Details of bonding type rmsd covalent geometry : bond 0.00902 (11936) covalent geometry : angle 0.83415 (16260) SS BOND : bond 0.00485 ( 4) SS BOND : angle 2.36529 ( 8) hydrogen bonds : bond 0.19987 ( 744) hydrogen bonds : angle 7.31301 ( 2172) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 270 time to evaluate : 0.664 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 12 residues processed: 286 average time/residue: 0.2725 time to fit residues: 106.7908 Evaluate side-chains 174 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 893 TYR Chi-restraints excluded: chain A residue 979 PHE Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 893 TYR Chi-restraints excluded: chain B residue 979 PHE Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 893 TYR Chi-restraints excluded: chain C residue 979 PHE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 893 TYR Chi-restraints excluded: chain D residue 979 PHE Chi-restraints excluded: chain D residue 1048 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 GLN A 869 ASN A1053 GLN B 746 GLN B1053 GLN B1054 GLN C 746 GLN C1053 GLN D 746 GLN D 869 ASN D1053 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.141155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.113593 restraints weight = 129227.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.120635 restraints weight = 61606.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.125722 restraints weight = 38153.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.129005 restraints weight = 27516.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.131114 restraints weight = 21728.757| |-----------------------------------------------------------------------------| r_work (final): 0.4588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6147 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11940 Z= 0.214 Angle : 0.660 5.681 16268 Z= 0.358 Chirality : 0.038 0.172 1828 Planarity : 0.005 0.056 2020 Dihedral : 7.131 72.038 1560 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.19 % Allowed : 7.22 % Favored : 91.59 % 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: -1.36 (0.21), residues: 1408 helix: -0.16 (0.16), residues: 964 sheet: None (None), residues: 0 loop : -2.45 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B1077 TYR 0.016 0.001 TYR B 806 PHE 0.025 0.002 PHE A 809 TRP 0.013 0.001 TRP C 944 HIS 0.009 0.002 HIS C1068 Details of bonding type rmsd covalent geometry : bond 0.00454 (11936) covalent geometry : angle 0.66028 (16260) SS BOND : bond 0.00076 ( 4) SS BOND : angle 0.45201 ( 8) hydrogen bonds : bond 0.06543 ( 744) hydrogen bonds : angle 5.37972 ( 2172) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 818 MET cc_start: 0.7915 (mmm) cc_final: 0.7555 (tpt) REVERT: B 1064 LYS cc_start: 0.4989 (tttt) cc_final: 0.4267 (tptt) REVERT: C 1064 LYS cc_start: 0.5023 (tttt) cc_final: 0.4292 (tptt) REVERT: D 818 MET cc_start: 0.7933 (mmm) cc_final: 0.7609 (tpt) outliers start: 15 outliers final: 11 residues processed: 175 average time/residue: 0.2767 time to fit residues: 66.4043 Evaluate side-chains 151 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 778 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1049 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 115 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 0.0570 chunk 120 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 9.9990 overall best weight: 0.7302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.142603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.116051 restraints weight = 125485.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.123048 restraints weight = 60666.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.127986 restraints weight = 37644.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4579 r_free = 0.4579 target = 0.131295 restraints weight = 26959.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 54)----------------| | r_work = 0.4608 r_free = 0.4608 target = 0.133461 restraints weight = 21001.535| |-----------------------------------------------------------------------------| r_work (final): 0.4611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6061 moved from start: 0.5081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11940 Z= 0.126 Angle : 0.551 6.221 16268 Z= 0.281 Chirality : 0.035 0.118 1828 Planarity : 0.005 0.066 2020 Dihedral : 6.096 67.666 1544 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.71 % Allowed : 9.21 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.22), residues: 1408 helix: 0.93 (0.16), residues: 964 sheet: None (None), residues: 0 loop : -2.25 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 777 TYR 0.009 0.001 TYR A1074 PHE 0.015 0.001 PHE C 939 TRP 0.015 0.001 TRP A 944 HIS 0.004 0.001 HIS B1068 Details of bonding type rmsd covalent geometry : bond 0.00262 (11936) covalent geometry : angle 0.55092 (16260) SS BOND : bond 0.00102 ( 4) SS BOND : angle 0.36432 ( 8) hydrogen bonds : bond 0.05223 ( 744) hydrogen bonds : angle 4.72462 ( 2172) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.636 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 797 VAL cc_start: 0.8524 (t) cc_final: 0.8296 (p) REVERT: A 818 MET cc_start: 0.7979 (mmm) cc_final: 0.7577 (tpt) REVERT: B 914 PHE cc_start: 0.8004 (m-10) cc_final: 0.7624 (m-10) REVERT: B 1064 LYS cc_start: 0.4995 (tttt) cc_final: 0.4258 (tptt) REVERT: C 1064 LYS cc_start: 0.5096 (tttt) cc_final: 0.4427 (tptt) REVERT: D 818 MET cc_start: 0.8004 (mmm) cc_final: 0.7579 (tpt) outliers start: 9 outliers final: 7 residues processed: 154 average time/residue: 0.2753 time to fit residues: 58.0889 Evaluate side-chains 141 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 134 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1049 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 122 optimal weight: 0.6980 chunk 77 optimal weight: 6.9990 chunk 65 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 958 HIS A1037 ASN A1091 GLN ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 HIS ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1091 GLN D1091 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.137123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.107469 restraints weight = 122502.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.113271 restraints weight = 65916.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.117626 restraints weight = 43902.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.120849 restraints weight = 33202.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.123103 restraints weight = 27047.263| |-----------------------------------------------------------------------------| r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.6068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 11940 Z= 0.242 Angle : 0.658 6.721 16268 Z= 0.364 Chirality : 0.038 0.181 1828 Planarity : 0.006 0.050 2020 Dihedral : 6.353 72.941 1544 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.67 % Allowed : 8.97 % Favored : 89.37 % 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: -0.39 (0.22), residues: 1408 helix: 0.59 (0.16), residues: 956 sheet: None (None), residues: 0 loop : -2.06 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 909 TYR 0.029 0.002 TYR B 806 PHE 0.033 0.002 PHE D 813 TRP 0.016 0.002 TRP A 944 HIS 0.010 0.002 HIS A1068 Details of bonding type rmsd covalent geometry : bond 0.00522 (11936) covalent geometry : angle 0.65821 (16260) SS BOND : bond 0.00116 ( 4) SS BOND : angle 0.68364 ( 8) hydrogen bonds : bond 0.05631 ( 744) hydrogen bonds : angle 5.17067 ( 2172) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 818 MET cc_start: 0.7890 (mmm) cc_final: 0.7527 (tpt) REVERT: A 1040 LEU cc_start: 0.8838 (mt) cc_final: 0.8594 (mp) REVERT: B 1064 LYS cc_start: 0.4895 (tttt) cc_final: 0.3608 (tptt) REVERT: C 858 LYS cc_start: 0.9141 (tttt) cc_final: 0.8920 (mmtt) REVERT: C 1064 LYS cc_start: 0.5019 (tttt) cc_final: 0.3807 (tptt) REVERT: D 818 MET cc_start: 0.7748 (mmm) cc_final: 0.7274 (tpt) outliers start: 21 outliers final: 18 residues processed: 148 average time/residue: 0.2391 time to fit residues: 50.8767 Evaluate side-chains 142 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 803 ILE Chi-restraints excluded: chain B residue 810 LEU Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 933 ASP Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1048 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 19 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 137 optimal weight: 0.4980 chunk 127 optimal weight: 30.0000 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 869 ASN ** C 869 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 = 0.4672 r_free = 0.4672 target = 0.138204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.108744 restraints weight = 121184.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.114978 restraints weight = 62852.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.119625 restraints weight = 40819.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.122962 restraints weight = 30480.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.125171 restraints weight = 24600.305| |-----------------------------------------------------------------------------| r_work (final): 0.4486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.6403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11940 Z= 0.153 Angle : 0.562 6.365 16268 Z= 0.295 Chirality : 0.036 0.158 1828 Planarity : 0.005 0.041 2020 Dihedral : 6.141 73.543 1544 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.06 % Allowed : 10.16 % Favored : 87.78 % 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: 0.12 (0.22), residues: 1408 helix: 1.02 (0.16), residues: 960 sheet: None (None), residues: 0 loop : -2.03 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 777 TYR 0.017 0.001 TYR B1074 PHE 0.018 0.001 PHE D 809 TRP 0.014 0.001 TRP A 944 HIS 0.007 0.001 HIS A1068 Details of bonding type rmsd covalent geometry : bond 0.00331 (11936) covalent geometry : angle 0.56231 (16260) SS BOND : bond 0.00100 ( 4) SS BOND : angle 0.66180 ( 8) hydrogen bonds : bond 0.04864 ( 744) hydrogen bonds : angle 4.70439 ( 2172) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 132 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 818 MET cc_start: 0.7968 (mmm) cc_final: 0.7701 (tpt) REVERT: A 1040 LEU cc_start: 0.8851 (mt) cc_final: 0.8585 (mp) REVERT: B 912 HIS cc_start: 0.7630 (t-90) cc_final: 0.7345 (t-90) REVERT: B 931 MET cc_start: 0.7273 (tmm) cc_final: 0.7006 (tmm) REVERT: B 1064 LYS cc_start: 0.4761 (tttt) cc_final: 0.3649 (tptt) REVERT: C 858 LYS cc_start: 0.9122 (tttt) cc_final: 0.8882 (mmtt) REVERT: C 1064 LYS cc_start: 0.4833 (tttt) cc_final: 0.3795 (tptt) REVERT: D 818 MET cc_start: 0.7858 (mmm) cc_final: 0.7362 (tpt) outliers start: 26 outliers final: 19 residues processed: 155 average time/residue: 0.2469 time to fit residues: 54.4471 Evaluate side-chains 146 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 127 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 803 ILE Chi-restraints excluded: chain C residue 857 MET Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1049 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 0 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 98 optimal weight: 20.0000 chunk 92 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 103 optimal weight: 0.0040 chunk 117 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 69 optimal weight: 6.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1091 GLN ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 958 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4679 r_free = 0.4679 target = 0.139175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.110127 restraints weight = 118095.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.116445 restraints weight = 60848.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.121095 restraints weight = 39426.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.124377 restraints weight = 29324.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.126588 restraints weight = 23590.366| |-----------------------------------------------------------------------------| r_work (final): 0.4502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6268 moved from start: 0.6695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11940 Z= 0.128 Angle : 0.550 7.188 16268 Z= 0.283 Chirality : 0.036 0.124 1828 Planarity : 0.005 0.045 2020 Dihedral : 5.960 71.401 1544 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.14 % Allowed : 11.11 % Favored : 86.75 % 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: 0.55 (0.23), residues: 1408 helix: 1.38 (0.17), residues: 960 sheet: None (None), residues: 0 loop : -1.95 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 777 TYR 0.014 0.001 TYR A1074 PHE 0.016 0.001 PHE B 813 TRP 0.014 0.001 TRP A 944 HIS 0.006 0.001 HIS A1068 Details of bonding type rmsd covalent geometry : bond 0.00280 (11936) covalent geometry : angle 0.55025 (16260) SS BOND : bond 0.00103 ( 4) SS BOND : angle 0.52989 ( 8) hydrogen bonds : bond 0.04418 ( 744) hydrogen bonds : angle 4.42329 ( 2172) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 134 time to evaluate : 0.599 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 818 MET cc_start: 0.7909 (mmm) cc_final: 0.7596 (tpt) REVERT: B 931 MET cc_start: 0.7270 (tmm) cc_final: 0.6973 (tmm) REVERT: B 1064 LYS cc_start: 0.4808 (tttt) cc_final: 0.3636 (tptt) REVERT: C 810 LEU cc_start: 0.7844 (tp) cc_final: 0.7612 (tt) REVERT: C 1064 LYS cc_start: 0.4779 (tttt) cc_final: 0.3696 (tptt) REVERT: D 818 MET cc_start: 0.7822 (mmm) cc_final: 0.7327 (tpt) outliers start: 27 outliers final: 20 residues processed: 155 average time/residue: 0.2334 time to fit residues: 52.5011 Evaluate side-chains 142 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 835 TRP Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1048 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 137 optimal weight: 0.5980 chunk 28 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 27 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 94 optimal weight: 20.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 800 HIS D 912 HIS ** D1054 GLN ** 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 = 0.4672 r_free = 0.4672 target = 0.138302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.109813 restraints weight = 115645.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.115601 restraints weight = 60434.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.121854 restraints weight = 38536.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.122702 restraints weight = 30151.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.123968 restraints weight = 25398.839| |-----------------------------------------------------------------------------| r_work (final): 0.4454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6408 moved from start: 0.6998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11940 Z= 0.155 Angle : 0.570 7.365 16268 Z= 0.299 Chirality : 0.036 0.142 1828 Planarity : 0.005 0.040 2020 Dihedral : 6.016 71.562 1544 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.54 % Allowed : 11.35 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.49 (0.22), residues: 1408 helix: 1.43 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -2.12 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 909 TYR 0.016 0.001 TYR C1074 PHE 0.021 0.001 PHE D 809 TRP 0.013 0.001 TRP A 944 HIS 0.007 0.001 HIS A1068 Details of bonding type rmsd covalent geometry : bond 0.00335 (11936) covalent geometry : angle 0.56972 (16260) SS BOND : bond 0.00417 ( 4) SS BOND : angle 0.83239 ( 8) hydrogen bonds : bond 0.04449 ( 744) hydrogen bonds : angle 4.49396 ( 2172) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 1064 LYS cc_start: 0.4850 (tttt) cc_final: 0.3539 (tptt) REVERT: C 810 LEU cc_start: 0.7789 (tp) cc_final: 0.7410 (tt) REVERT: C 1064 LYS cc_start: 0.4915 (tttt) cc_final: 0.3695 (tptt) REVERT: D 800 HIS cc_start: 0.7542 (OUTLIER) cc_final: 0.7086 (m-70) REVERT: D 818 MET cc_start: 0.7914 (mmm) cc_final: 0.7423 (tpt) outliers start: 32 outliers final: 27 residues processed: 149 average time/residue: 0.2209 time to fit residues: 47.8573 Evaluate side-chains 149 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 835 TRP Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 835 TRP Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 800 HIS Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 912 HIS Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1049 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 20 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 128 optimal weight: 10.0000 chunk 101 optimal weight: 3.9990 chunk 121 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 60 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 43 optimal weight: 0.6980 chunk 57 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 800 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4667 r_free = 0.4667 target = 0.137910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.107776 restraints weight = 115173.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.113553 restraints weight = 61064.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.117975 restraints weight = 40352.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.121192 restraints weight = 30259.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.123493 restraints weight = 24632.944| |-----------------------------------------------------------------------------| r_work (final): 0.4459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.7164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11940 Z= 0.167 Angle : 0.574 8.259 16268 Z= 0.302 Chirality : 0.036 0.145 1828 Planarity : 0.005 0.044 2020 Dihedral : 6.019 72.514 1544 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 2.54 % Allowed : 11.83 % Favored : 85.63 % 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: 0.54 (0.22), residues: 1408 helix: 1.47 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -2.09 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 909 TYR 0.015 0.001 TYR A1074 PHE 0.046 0.002 PHE C 813 TRP 0.012 0.001 TRP A 944 HIS 0.010 0.001 HIS D 912 Details of bonding type rmsd covalent geometry : bond 0.00359 (11936) covalent geometry : angle 0.57350 (16260) SS BOND : bond 0.00172 ( 4) SS BOND : angle 0.74979 ( 8) hydrogen bonds : bond 0.04482 ( 744) hydrogen bonds : angle 4.51257 ( 2172) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1040 LEU cc_start: 0.8870 (mt) cc_final: 0.8611 (mp) REVERT: B 1064 LYS cc_start: 0.4704 (tttt) cc_final: 0.3375 (tptt) REVERT: C 810 LEU cc_start: 0.7718 (tp) cc_final: 0.7463 (tt) REVERT: C 1064 LYS cc_start: 0.4834 (tttt) cc_final: 0.3568 (tptt) REVERT: D 800 HIS cc_start: 0.7670 (OUTLIER) cc_final: 0.7088 (m-70) REVERT: D 818 MET cc_start: 0.7899 (mmm) cc_final: 0.7411 (tpt) outliers start: 32 outliers final: 29 residues processed: 149 average time/residue: 0.2074 time to fit residues: 45.1463 Evaluate side-chains 149 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 806 TYR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 835 TRP Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 835 TRP Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 800 HIS Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1049 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 42 optimal weight: 7.9990 chunk 47 optimal weight: 0.9990 chunk 33 optimal weight: 0.2980 chunk 118 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 53 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 131 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 overall best weight: 0.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 800 HIS D 912 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.139283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.109714 restraints weight = 114195.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.115834 restraints weight = 58923.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.120508 restraints weight = 38093.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.123849 restraints weight = 28194.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.126085 restraints weight = 22668.273| |-----------------------------------------------------------------------------| r_work (final): 0.4497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6275 moved from start: 0.7234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11940 Z= 0.117 Angle : 0.545 8.011 16268 Z= 0.277 Chirality : 0.036 0.140 1828 Planarity : 0.005 0.040 2020 Dihedral : 5.865 69.754 1544 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.54 % Allowed : 12.54 % Favored : 84.92 % 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: 0.90 (0.23), residues: 1408 helix: 1.77 (0.16), residues: 948 sheet: None (None), residues: 0 loop : -2.02 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 961 TYR 0.014 0.001 TYR D1074 PHE 0.034 0.001 PHE C 813 TRP 0.011 0.001 TRP A 944 HIS 0.014 0.001 HIS D 800 Details of bonding type rmsd covalent geometry : bond 0.00255 (11936) covalent geometry : angle 0.54469 (16260) SS BOND : bond 0.00146 ( 4) SS BOND : angle 0.85742 ( 8) hydrogen bonds : bond 0.04201 ( 744) hydrogen bonds : angle 4.22393 ( 2172) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1040 LEU cc_start: 0.8813 (mt) cc_final: 0.8553 (mp) REVERT: B 1064 LYS cc_start: 0.4784 (tttt) cc_final: 0.3486 (tptt) REVERT: C 810 LEU cc_start: 0.7717 (tp) cc_final: 0.7444 (tt) REVERT: C 1064 LYS cc_start: 0.4774 (tttt) cc_final: 0.3551 (tptt) REVERT: D 800 HIS cc_start: 0.7711 (OUTLIER) cc_final: 0.7159 (m-70) REVERT: D 818 MET cc_start: 0.7874 (mmm) cc_final: 0.7393 (tpt) outliers start: 32 outliers final: 29 residues processed: 149 average time/residue: 0.2090 time to fit residues: 46.5058 Evaluate side-chains 154 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 124 time to evaluate : 0.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 806 TYR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 806 TYR Chi-restraints excluded: chain B residue 835 TRP Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1034 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 800 HIS Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1049 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 74 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 126 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 21 optimal weight: 5.9990 chunk 100 optimal weight: 6.9990 chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 800 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.137083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.107374 restraints weight = 114122.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.112664 restraints weight = 64290.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.116741 restraints weight = 43714.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.119644 restraints weight = 33451.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.121655 restraints weight = 27646.930| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6421 moved from start: 0.7450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11940 Z= 0.221 Angle : 0.627 7.940 16268 Z= 0.339 Chirality : 0.038 0.175 1828 Planarity : 0.005 0.042 2020 Dihedral : 6.061 74.260 1544 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 2.54 % Allowed : 12.94 % Favored : 84.52 % 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: 0.38 (0.22), residues: 1408 helix: 1.41 (0.17), residues: 940 sheet: None (None), residues: 0 loop : -2.25 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 909 TYR 0.018 0.002 TYR C1074 PHE 0.032 0.002 PHE C 813 TRP 0.013 0.002 TRP B 868 HIS 0.017 0.002 HIS D 800 Details of bonding type rmsd covalent geometry : bond 0.00472 (11936) covalent geometry : angle 0.62688 (16260) SS BOND : bond 0.00221 ( 4) SS BOND : angle 0.89374 ( 8) hydrogen bonds : bond 0.04678 ( 744) hydrogen bonds : angle 4.68534 ( 2172) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 123 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 806 TYR cc_start: 0.6127 (OUTLIER) cc_final: 0.4361 (m-10) REVERT: A 1040 LEU cc_start: 0.8853 (mt) cc_final: 0.8605 (mp) REVERT: B 806 TYR cc_start: 0.5870 (OUTLIER) cc_final: 0.4213 (m-10) REVERT: C 810 LEU cc_start: 0.7717 (tp) cc_final: 0.7455 (tt) REVERT: C 858 LYS cc_start: 0.9109 (tttt) cc_final: 0.8887 (mmtt) REVERT: C 931 MET cc_start: 0.7287 (tmm) cc_final: 0.7032 (tmm) REVERT: D 800 HIS cc_start: 0.7592 (OUTLIER) cc_final: 0.7297 (m-70) REVERT: D 818 MET cc_start: 0.7846 (mmm) cc_final: 0.7383 (tpt) outliers start: 32 outliers final: 29 residues processed: 148 average time/residue: 0.2119 time to fit residues: 46.8550 Evaluate side-chains 153 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 121 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 802 ASN Chi-restraints excluded: chain A residue 806 TYR Chi-restraints excluded: chain A residue 877 LEU Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1048 PHE Chi-restraints excluded: chain B residue 747 LEU Chi-restraints excluded: chain B residue 806 TYR Chi-restraints excluded: chain B residue 835 TRP Chi-restraints excluded: chain B residue 877 LEU Chi-restraints excluded: chain B residue 907 CYS Chi-restraints excluded: chain B residue 913 ILE Chi-restraints excluded: chain B residue 941 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1040 LEU Chi-restraints excluded: chain B residue 1048 PHE Chi-restraints excluded: chain C residue 747 LEU Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 904 ILE Chi-restraints excluded: chain C residue 941 LEU Chi-restraints excluded: chain C residue 1040 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU Chi-restraints excluded: chain D residue 800 HIS Chi-restraints excluded: chain D residue 817 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1043 LEU Chi-restraints excluded: chain D residue 1048 PHE Chi-restraints excluded: chain D residue 1049 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 52 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 137 optimal weight: 0.8980 chunk 95 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 114 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 800 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.139445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.110330 restraints weight = 112589.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.116283 restraints weight = 59255.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.120800 restraints weight = 38745.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.123993 restraints weight = 29006.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.126140 restraints weight = 23501.137| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6257 moved from start: 0.7480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11940 Z= 0.115 Angle : 0.555 7.714 16268 Z= 0.279 Chirality : 0.036 0.131 1828 Planarity : 0.005 0.040 2020 Dihedral : 5.865 71.681 1544 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.89 % Favored : 94.03 % Rotamer: Outliers : 2.46 % Allowed : 13.25 % Favored : 84.29 % 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: 0.87 (0.23), residues: 1408 helix: 1.73 (0.17), residues: 952 sheet: None (None), residues: 0 loop : -2.03 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 777 TYR 0.017 0.001 TYR D1074 PHE 0.027 0.001 PHE C 813 TRP 0.013 0.001 TRP B 868 HIS 0.012 0.001 HIS D 800 Details of bonding type rmsd covalent geometry : bond 0.00252 (11936) covalent geometry : angle 0.55451 (16260) SS BOND : bond 0.00196 ( 4) SS BOND : angle 0.73818 ( 8) hydrogen bonds : bond 0.04159 ( 744) hydrogen bonds : angle 4.18450 ( 2172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4788.98 seconds wall clock time: 81 minutes 55.13 seconds (4915.13 seconds total)