Starting phenix.real_space_refine on Thu May 22 15:47:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vq2_32083/05_2025/7vq2_32083.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vq2_32083/05_2025/7vq2_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_32083/05_2025/7vq2_32083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vq2_32083/05_2025/7vq2_32083.map" model { file = "/net/cci-nas-00/data/ceres_data/7vq2_32083/05_2025/7vq2_32083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vq2_32083/05_2025/7vq2_32083.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.000 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: C, B, D Time building chain proxies: 14.67, per 1000 atoms: 0.63 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 C 996 " - pdb=" SG CYS C1008 " distance=2.03 Simple disulfide: pdb=" SG CYS B 996 " - pdb=" SG CYS B1008 " 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: 6.36 Conformation dependent library (CDL) restraints added in 1.9 seconds 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: 1.64 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: 8.15 Time building geometry restraints manager: 7.59 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' 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: 4.870 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: 0.390 Extract box with map and model: 0.970 Check model and map are aligned: 0.160 Set scattering table: 0.240 Process input model: 52.540 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3834 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.002 0.001 TRP C1063 HIS 0.002 0.000 HIS B 958 PHE 0.002 0.001 PHE B 939 TYR 0.002 0.000 TYR D 893 ARG 0.002 0.000 ARG C1096 Details of bonding type rmsd hydrogen bonds : bond 0.19987 ( 744) hydrogen bonds : angle 7.31301 ( 2172) SS BOND : bond 0.00485 ( 4) SS BOND : angle 2.36529 ( 8) covalent geometry : bond 0.00902 (11936) covalent geometry : angle 0.83415 (16260) *********************** 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 : 1.831 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: 0.6043 time to fit residues: 236.5859 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 : 1.871 ------------------------------------------------------------------------------- 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 118 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 109 optimal weight: 1.9990 chunk 42 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 81 optimal weight: 5.9990 chunk 127 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 GLN A1054 GLN B 746 GLN B1053 GLN B1054 GLN C 746 GLN C1053 GLN C1054 GLN D 746 GLN ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1053 GLN D1054 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.140638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.112763 restraints weight = 127982.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.119676 restraints weight = 61866.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.124724 restraints weight = 38644.915| |-----------------------------------------------------------------------------| r_work (final): 0.4500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6382 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11940 Z= 0.249 Angle : 0.686 5.972 16268 Z= 0.375 Chirality : 0.039 0.184 1828 Planarity : 0.006 0.057 2020 Dihedral : 7.213 73.434 1560 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.21), residues: 1408 helix: -0.27 (0.16), residues: 964 sheet: None (None), residues: 0 loop : -2.50 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 944 HIS 0.010 0.002 HIS B1068 PHE 0.028 0.002 PHE A 809 TYR 0.018 0.002 TYR B 806 ARG 0.004 0.001 ARG D1067 Details of bonding type rmsd hydrogen bonds : bond 0.06753 ( 744) hydrogen bonds : angle 5.54148 ( 2172) SS BOND : bond 0.00109 ( 4) SS BOND : angle 0.47506 ( 8) covalent geometry : bond 0.00537 (11936) covalent geometry : angle 0.68614 (16260) *********************** 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 170 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 1.747 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: A 818 MET cc_start: 0.7925 (mmm) cc_final: 0.7577 (tpt) REVERT: B 1064 LYS cc_start: 0.5071 (tttt) cc_final: 0.4337 (tptt) REVERT: C 1064 LYS cc_start: 0.5122 (tttt) cc_final: 0.4372 (tptt) REVERT: D 818 MET cc_start: 0.7980 (mmm) cc_final: 0.7641 (tpt) outliers start: 15 outliers final: 10 residues processed: 168 average time/residue: 0.5989 time to fit residues: 138.2475 Evaluate side-chains 143 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 1.693 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 107 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 61 optimal weight: 0.3980 chunk 124 optimal weight: 0.6980 chunk 11 optimal weight: 0.8980 chunk 96 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 136 optimal weight: 6.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4733 r_free = 0.4733 target = 0.142485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.115895 restraints weight = 125170.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.122790 restraints weight = 60436.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.127690 restraints weight = 37608.397| |-----------------------------------------------------------------------------| r_work (final): 0.4536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6282 moved from start: 0.5009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11940 Z= 0.128 Angle : 0.552 6.251 16268 Z= 0.282 Chirality : 0.035 0.122 1828 Planarity : 0.005 0.039 2020 Dihedral : 6.171 69.463 1544 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.71 % Allowed : 9.13 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.22), residues: 1408 helix: 0.86 (0.16), residues: 964 sheet: None (None), residues: 0 loop : -2.24 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 944 HIS 0.004 0.001 HIS B1068 PHE 0.015 0.001 PHE D1052 TYR 0.011 0.001 TYR D1074 ARG 0.008 0.000 ARG B 961 Details of bonding type rmsd hydrogen bonds : bond 0.05254 ( 744) hydrogen bonds : angle 4.77838 ( 2172) SS BOND : bond 0.00118 ( 4) SS BOND : angle 0.36551 ( 8) covalent geometry : bond 0.00265 (11936) covalent geometry : angle 0.55188 (16260) *********************** 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 157 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 148 time to evaluate : 1.895 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: B 914 PHE cc_start: 0.8049 (m-10) cc_final: 0.7672 (m-10) REVERT: B 1064 LYS cc_start: 0.5053 (tttt) cc_final: 0.4334 (tptt) REVERT: C 1064 LYS cc_start: 0.5151 (tttt) cc_final: 0.4472 (tptt) REVERT: D 818 MET cc_start: 0.7962 (mmm) cc_final: 0.7534 (tpt) outliers start: 9 outliers final: 5 residues processed: 155 average time/residue: 0.6084 time to fit residues: 129.5948 Evaluate side-chains 141 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 136 time to evaluate : 1.738 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 136 optimal weight: 6.9990 chunk 7 optimal weight: 0.0980 chunk 51 optimal weight: 0.7980 chunk 24 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 107 optimal weight: 0.7980 chunk 125 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 958 HIS ** A1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1091 GLN ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1037 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1091 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.140059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.110344 restraints weight = 124854.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.117058 restraints weight = 63023.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.121866 restraints weight = 40631.358| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6500 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11940 Z= 0.189 Angle : 0.591 7.037 16268 Z= 0.319 Chirality : 0.037 0.159 1828 Planarity : 0.005 0.049 2020 Dihedral : 5.976 70.550 1542 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 1.51 % Allowed : 8.97 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.22), residues: 1408 helix: 0.85 (0.16), residues: 960 sheet: None (None), residues: 0 loop : -1.98 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 944 HIS 0.007 0.001 HIS C1068 PHE 0.032 0.002 PHE A 813 TYR 0.019 0.002 TYR A1074 ARG 0.003 0.000 ARG D1077 Details of bonding type rmsd hydrogen bonds : bond 0.05235 ( 744) hydrogen bonds : angle 4.93735 ( 2172) SS BOND : bond 0.00086 ( 4) SS BOND : angle 0.54872 ( 8) covalent geometry : bond 0.00411 (11936) covalent geometry : angle 0.59138 (16260) *********************** 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 151 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 2.026 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: B 912 HIS cc_start: 0.7515 (t-90) cc_final: 0.7199 (t-90) REVERT: B 1064 LYS cc_start: 0.4912 (tttt) cc_final: 0.3829 (tptt) REVERT: C 858 LYS cc_start: 0.9223 (tttt) cc_final: 0.8939 (mmtt) REVERT: C 1064 LYS cc_start: 0.5081 (tttt) cc_final: 0.4082 (tptt) REVERT: D 818 MET cc_start: 0.7912 (mmm) cc_final: 0.7479 (tpt) outliers start: 19 outliers final: 14 residues processed: 147 average time/residue: 0.5905 time to fit residues: 120.7267 Evaluate side-chains 137 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.739 ------------------------------------------------------------------------------- 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 877 LEU Chi-restraints excluded: chain B residue 1034 LEU Chi-restraints excluded: chain B residue 1048 PHE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 42 optimal weight: 0.8980 chunk 101 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 96 optimal weight: 7.9990 chunk 34 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 73 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1037 ASN ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1037 ASN ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1091 GLN ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4709 r_free = 0.4709 target = 0.140799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.111892 restraints weight = 124237.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.118646 restraints weight = 62019.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.123486 restraints weight = 39868.095| |-----------------------------------------------------------------------------| r_work (final): 0.4463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6444 moved from start: 0.6235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11940 Z= 0.134 Angle : 0.542 6.783 16268 Z= 0.280 Chirality : 0.036 0.135 1828 Planarity : 0.005 0.039 2020 Dihedral : 5.730 67.477 1542 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.90 % Allowed : 9.13 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.22), residues: 1408 helix: 1.23 (0.17), residues: 960 sheet: None (None), residues: 0 loop : -1.91 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 944 HIS 0.006 0.001 HIS C1068 PHE 0.018 0.001 PHE A 813 TYR 0.018 0.001 TYR B1074 ARG 0.001 0.000 ARG A 777 Details of bonding type rmsd hydrogen bonds : bond 0.04647 ( 744) hydrogen bonds : angle 4.54289 ( 2172) SS BOND : bond 0.00120 ( 4) SS BOND : angle 0.46018 ( 8) covalent geometry : bond 0.00287 (11936) covalent geometry : angle 0.54230 (16260) *********************** 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 164 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.905 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: B 1064 LYS cc_start: 0.4891 (tttt) cc_final: 0.3727 (tptt) REVERT: C 1064 LYS cc_start: 0.4956 (tttt) cc_final: 0.3839 (tptt) REVERT: D 818 MET cc_start: 0.7894 (mmm) cc_final: 0.7415 (tpt) outliers start: 24 outliers final: 18 residues processed: 159 average time/residue: 0.5523 time to fit residues: 126.1057 Evaluate side-chains 148 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 130 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 907 CYS Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1040 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 1040 LEU Chi-restraints excluded: chain B residue 1048 PHE 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 1043 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 73 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 57 optimal weight: 20.0000 chunk 126 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 958 HIS B1091 GLN ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 912 HIS D 958 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4656 r_free = 0.4656 target = 0.137320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.107626 restraints weight = 118875.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.113354 restraints weight = 64397.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.117705 restraints weight = 43027.713| |-----------------------------------------------------------------------------| r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6595 moved from start: 0.6780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 11940 Z= 0.222 Angle : 0.615 6.744 16268 Z= 0.337 Chirality : 0.038 0.174 1828 Planarity : 0.005 0.050 2020 Dihedral : 5.946 71.492 1542 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.10 % Favored : 92.90 % Rotamer: Outliers : 2.46 % Allowed : 10.24 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.22), residues: 1408 helix: 0.95 (0.16), residues: 960 sheet: None (None), residues: 0 loop : -2.08 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 944 HIS 0.008 0.001 HIS A1068 PHE 0.031 0.002 PHE D 813 TYR 0.021 0.002 TYR C1074 ARG 0.005 0.000 ARG C 777 Details of bonding type rmsd hydrogen bonds : bond 0.04996 ( 744) hydrogen bonds : angle 4.87592 ( 2172) SS BOND : bond 0.00097 ( 4) SS BOND : angle 0.60327 ( 8) covalent geometry : bond 0.00481 (11936) covalent geometry : angle 0.61527 (16260) *********************** 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 159 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 1.808 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 931 MET cc_start: 0.7162 (tmm) cc_final: 0.6874 (tmm) REVERT: B 1064 LYS cc_start: 0.4935 (tttt) cc_final: 0.3649 (tptt) REVERT: C 858 LYS cc_start: 0.9219 (tttt) cc_final: 0.8933 (mmtt) REVERT: C 1064 LYS cc_start: 0.4954 (tttt) cc_final: 0.3738 (tptt) REVERT: D 818 MET cc_start: 0.7812 (mmm) cc_final: 0.7346 (tpt) outliers start: 31 outliers final: 25 residues processed: 151 average time/residue: 0.5485 time to fit residues: 117.1356 Evaluate side-chains 149 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 124 time to evaluate : 1.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 LEU 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 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 835 TRP Chi-restraints excluded: chain C residue 877 LEU Chi-restraints excluded: chain C residue 933 ASP 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 904 ILE Chi-restraints excluded: chain D residue 910 LEU Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1040 LEU Chi-restraints excluded: chain D residue 1043 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 58 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 125 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 132 optimal weight: 30.0000 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.138291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.108711 restraints weight = 117332.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.114700 restraints weight = 61719.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.119307 restraints weight = 40310.893| |-----------------------------------------------------------------------------| r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6534 moved from start: 0.6982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11940 Z= 0.153 Angle : 0.566 6.996 16268 Z= 0.297 Chirality : 0.036 0.135 1828 Planarity : 0.005 0.045 2020 Dihedral : 5.816 71.666 1542 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.38 % Allowed : 11.43 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.22), residues: 1408 helix: 1.20 (0.17), residues: 960 sheet: None (None), residues: 0 loop : -2.10 (0.28), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 944 HIS 0.007 0.001 HIS A1068 PHE 0.023 0.001 PHE A 813 TYR 0.017 0.001 TYR B1074 ARG 0.006 0.000 ARG D 961 Details of bonding type rmsd hydrogen bonds : bond 0.04571 ( 744) hydrogen bonds : angle 4.54997 ( 2172) SS BOND : bond 0.00094 ( 4) SS BOND : angle 0.56346 ( 8) covalent geometry : bond 0.00334 (11936) covalent geometry : angle 0.56584 (16260) *********************** 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 162 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 132 time to evaluate : 1.787 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 931 MET cc_start: 0.7405 (tmm) cc_final: 0.7129 (tmm) REVERT: B 1064 LYS cc_start: 0.4926 (tttt) cc_final: 0.3604 (tptt) REVERT: C 810 LEU cc_start: 0.7700 (tp) cc_final: 0.7369 (tt) REVERT: C 1064 LYS cc_start: 0.4887 (tttt) cc_final: 0.3658 (tptt) REVERT: D 818 MET cc_start: 0.7850 (mmm) cc_final: 0.7388 (tpt) outliers start: 30 outliers final: 24 residues processed: 152 average time/residue: 0.5478 time to fit residues: 118.3367 Evaluate side-chains 152 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 128 time to evaluate : 2.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 1034 LEU Chi-restraints excluded: chain A residue 1040 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 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 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 817 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 939 PHE Chi-restraints excluded: chain D residue 941 LEU Chi-restraints excluded: chain D residue 1034 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 29 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 137 optimal weight: 0.9980 chunk 78 optimal weight: 0.4980 chunk 66 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 869 ASN ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 869 ASN ** 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 = 0.4689 r_free = 0.4689 target = 0.139679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.110700 restraints weight = 115671.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.116889 restraints weight = 59446.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.121699 restraints weight = 38277.293| |-----------------------------------------------------------------------------| r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.7121 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= 0.116 Angle : 0.545 8.225 16268 Z= 0.276 Chirality : 0.036 0.127 1828 Planarity : 0.005 0.044 2020 Dihedral : 5.568 66.473 1542 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.90 % Allowed : 12.22 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.23), residues: 1408 helix: 1.61 (0.17), residues: 960 sheet: None (None), residues: 0 loop : -1.91 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 944 HIS 0.005 0.001 HIS A1068 PHE 0.024 0.001 PHE C 813 TYR 0.011 0.001 TYR B1074 ARG 0.003 0.000 ARG A 777 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 744) hydrogen bonds : angle 4.24293 ( 2172) SS BOND : bond 0.00081 ( 4) SS BOND : angle 0.81081 ( 8) covalent geometry : bond 0.00256 (11936) covalent geometry : angle 0.54532 (16260) *********************** 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: 24 poor density : 131 time to evaluate : 1.980 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: B 931 MET cc_start: 0.7367 (tmm) cc_final: 0.7095 (tmm) REVERT: B 1064 LYS cc_start: 0.4855 (tttt) cc_final: 0.3628 (tptt) REVERT: C 810 LEU cc_start: 0.7802 (tp) cc_final: 0.7564 (tt) REVERT: C 1064 LYS cc_start: 0.4954 (tttt) cc_final: 0.3754 (tptt) REVERT: D 818 MET cc_start: 0.7857 (mmm) cc_final: 0.7384 (tpt) outliers start: 24 outliers final: 21 residues processed: 145 average time/residue: 0.5346 time to fit residues: 110.5874 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 : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 747 LEU Chi-restraints excluded: chain A residue 877 LEU 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 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 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 1040 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU 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 1043 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 32 optimal weight: 0.9980 chunk 75 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 68 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 40 optimal weight: 0.1980 chunk 54 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.138529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.108881 restraints weight = 114947.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.114774 restraints weight = 60482.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.119368 restraints weight = 39510.932| |-----------------------------------------------------------------------------| r_work (final): 0.4393 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.7275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11940 Z= 0.139 Angle : 0.562 8.230 16268 Z= 0.290 Chirality : 0.036 0.130 1828 Planarity : 0.005 0.042 2020 Dihedral : 5.568 63.052 1542 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.67 % Allowed : 12.38 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.23), residues: 1408 helix: 1.63 (0.17), residues: 956 sheet: None (None), residues: 0 loop : -1.94 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 944 HIS 0.006 0.001 HIS A1068 PHE 0.024 0.001 PHE C 813 TYR 0.013 0.001 TYR B1074 ARG 0.003 0.000 ARG A 961 Details of bonding type rmsd hydrogen bonds : bond 0.04156 ( 744) hydrogen bonds : angle 4.32622 ( 2172) SS BOND : bond 0.00271 ( 4) SS BOND : angle 0.69819 ( 8) covalent geometry : bond 0.00306 (11936) covalent geometry : angle 0.56190 (16260) *********************** 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 152 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 1.810 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: B 1064 LYS cc_start: 0.4845 (tttt) cc_final: 0.3521 (tptt) REVERT: C 810 LEU cc_start: 0.7773 (tp) cc_final: 0.7552 (tt) REVERT: C 1064 LYS cc_start: 0.4858 (tttt) cc_final: 0.3618 (tptt) REVERT: D 818 MET cc_start: 0.7863 (mmm) cc_final: 0.7395 (tpt) outliers start: 21 outliers final: 20 residues processed: 144 average time/residue: 0.5020 time to fit residues: 104.7412 Evaluate side-chains 149 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.701 ------------------------------------------------------------------------------- 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 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 877 LEU Chi-restraints excluded: chain C residue 904 ILE 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 817 LEU Chi-restraints excluded: chain D residue 904 ILE Chi-restraints excluded: chain D residue 1034 LEU Chi-restraints excluded: chain D residue 1043 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 137 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 127 optimal weight: 20.0000 chunk 119 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 128 optimal weight: 4.9990 chunk 117 optimal weight: 0.7980 chunk 80 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1054 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.139292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.109899 restraints weight = 114671.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.115994 restraints weight = 59654.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.120658 restraints weight = 38657.300| |-----------------------------------------------------------------------------| r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6464 moved from start: 0.7411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11940 Z= 0.122 Angle : 0.548 8.535 16268 Z= 0.278 Chirality : 0.036 0.128 1828 Planarity : 0.005 0.041 2020 Dihedral : 5.441 58.684 1542 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 1.75 % Allowed : 12.62 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.23), residues: 1408 helix: 1.78 (0.17), residues: 952 sheet: None (None), residues: 0 loop : -1.97 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 944 HIS 0.005 0.001 HIS A1068 PHE 0.021 0.001 PHE C 813 TYR 0.012 0.001 TYR B1074 ARG 0.002 0.000 ARG A 961 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 744) hydrogen bonds : angle 4.18959 ( 2172) SS BOND : bond 0.00263 ( 4) SS BOND : angle 0.73398 ( 8) covalent geometry : bond 0.00270 (11936) covalent geometry : angle 0.54781 (16260) ********************** 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: 22 poor density : 133 time to evaluate : 1.794 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: B 1064 LYS cc_start: 0.4798 (tttt) cc_final: 0.3493 (tptt) REVERT: C 810 LEU cc_start: 0.7776 (tp) cc_final: 0.7563 (tt) REVERT: C 1064 LYS cc_start: 0.4856 (tttt) cc_final: 0.3581 (tptt) REVERT: D 818 MET cc_start: 0.7879 (mmm) cc_final: 0.7416 (tpt) outliers start: 22 outliers final: 21 residues processed: 145 average time/residue: 0.5203 time to fit residues: 109.8778 Evaluate side-chains 151 residues out of total 1260 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 1.843 ------------------------------------------------------------------------------- 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 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 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 1040 LEU Chi-restraints excluded: chain C residue 1048 PHE Chi-restraints excluded: chain D residue 747 LEU 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 1043 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.6567 > 50: distance: 33 - 201: 21.863 distance: 105 - 117: 3.149 distance: 117 - 118: 7.108 distance: 117 - 129: 10.821 distance: 118 - 119: 9.389 distance: 118 - 121: 8.551 distance: 118 - 130: 10.860 distance: 119 - 120: 9.226 distance: 119 - 138: 7.869 distance: 121 - 122: 9.623 distance: 121 - 131: 7.792 distance: 121 - 132: 13.218 distance: 122 - 123: 7.793 distance: 122 - 124: 3.364 distance: 123 - 125: 4.276 distance: 123 - 133: 5.165 distance: 124 - 126: 4.223 distance: 124 - 134: 8.468 distance: 125 - 127: 5.294 distance: 126 - 127: 5.142 distance: 127 - 128: 6.192 distance: 128 - 137: 5.737 distance: 138 - 147: 18.105 distance: 139 - 140: 9.469 distance: 139 - 148: 3.710 distance: 140 - 141: 6.861 distance: 140 - 160: 6.304 distance: 142 - 143: 11.408 distance: 142 - 149: 5.536 distance: 142 - 150: 5.628 distance: 143 - 151: 6.758 distance: 143 - 152: 8.385 distance: 144 - 145: 7.697 distance: 144 - 153: 5.773 distance: 144 - 154: 7.254 distance: 145 - 146: 4.974 distance: 145 - 155: 5.846 distance: 145 - 156: 8.330 distance: 146 - 157: 3.825 distance: 146 - 159: 3.004 distance: 160 - 161: 3.684 distance: 160 - 166: 3.703 distance: 161 - 162: 22.637 distance: 161 - 164: 6.805 distance: 161 - 167: 6.085 distance: 162 - 163: 19.236 distance: 162 - 174: 58.657 distance: 164 - 165: 12.365 distance: 164 - 168: 12.031 distance: 164 - 169: 23.758 distance: 165 - 166: 7.054 distance: 165 - 170: 6.473 distance: 165 - 171: 11.753 distance: 166 - 172: 8.542 distance: 166 - 173: 8.830 distance: 174 - 175: 29.432 distance: 174 - 183: 40.226 distance: 175 - 176: 21.113 distance: 175 - 178: 36.148 distance: 175 - 184: 25.291 distance: 176 - 177: 14.762 distance: 176 - 196: 12.323 distance: 178 - 179: 24.170 distance: 178 - 185: 27.771 distance: 178 - 186: 26.204 distance: 179 - 180: 9.784 distance: 179 - 187: 8.869 distance: 179 - 188: 18.036 distance: 180 - 181: 5.764 distance: 180 - 189: 13.831 distance: 180 - 190: 9.313 distance: 181 - 182: 6.015 distance: 181 - 191: 12.009 distance: 181 - 192: 7.090 distance: 182 - 194: 5.788 distance: 182 - 195: 4.434 distance: 196 - 197: 8.224 distance: 196 - 202: 13.319 distance: 197 - 198: 9.544 distance: 197 - 200: 10.042 distance: 197 - 203: 29.954 distance: 198 - 199: 17.725 distance: 198 - 206: 13.911 distance: 200 - 201: 17.151 distance: 200 - 204: 38.147 distance: 200 - 205: 17.644 distance: 206 - 207: 9.524 distance: 206 - 212: 21.265 distance: 207 - 210: 8.968 distance: 207 - 213: 16.618 distance: 208 - 209: 3.877 distance: 208 - 220: 7.450 distance: 210 - 211: 23.326 distance: 210 - 214: 25.104 distance: 210 - 215: 18.857 distance: 211 - 212: 33.774 distance: 211 - 216: 26.428 distance: 211 - 217: 24.614 distance: 212 - 218: 26.503 distance: 212 - 219: 43.064 distance: 220 - 221: 7.575 distance: 220 - 229: 17.715 distance: 221 - 222: 6.751 distance: 221 - 224: 19.715 distance: 221 - 230: 9.152 distance: 222 - 223: 31.938 distance: 224 - 225: 25.061 distance: 224 - 231: 18.373 distance: 224 - 232: 17.842 distance: 225 - 226: 9.946 distance: 225 - 233: 17.799 distance: 225 - 234: 12.706 distance: 226 - 227: 11.892 distance: 226 - 228: 12.219 distance: 235 - 236: 5.139 distance: 235 - 241: 5.289 distance: 236 - 237: 11.646 distance: 236 - 239: 7.038 distance: 236 - 242: 10.680 distance: 237 - 238: 21.669 distance: 237 - 246: 16.904 distance: 239 - 240: 13.368 distance: 239 - 243: 14.778 distance: 239 - 244: 9.217 distance: 246 - 247: 4.828 distance: 246 - 254: 16.408 distance: 247 - 248: 5.482 distance: 247 - 250: 3.375 distance: 247 - 255: 6.731 distance: 248 - 249: 13.682 distance: 248 - 258: 5.895 distance: 250 - 251: 8.274 distance: 250 - 256: 9.534 distance: 250 - 257: 12.839 distance: 251 - 252: 8.824 distance: 251 - 253: 23.128 distance: 258 - 259: 10.516 distance: 258 - 263: 15.019 distance: 259 - 260: 9.225 distance: 259 - 262: 5.395 distance: 259 - 264: 13.498 distance: 260 - 261: 7.047 distance: 260 - 268: 9.371 distance: 262 - 265: 20.920 distance: 262 - 266: 18.950 distance: 262 - 267: 16.482 distance: 346 - 370: 3.259 distance: 356 - 383: 3.042