Starting phenix.real_space_refine on Sat Sep 12 16:01:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6iy2_9748/09_2026/6iy2_9748.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iy2_9748/09_2026/6iy2_9748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.47 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6iy2_9748/09_2026/6iy2_9748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iy2_9748/09_2026/6iy2_9748.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6iy2_9748/09_2026/6iy2_9748.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6iy2_9748/09_2026/6iy2_9748.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6iy2_9748/09_2026/6iy2_9748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iy2_9748/09_2026/6iy2_9748.map" } resolution = 3.47 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 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 P 296 5.49 5 S 27 5.16 5 C 9843 2.51 5 N 3171 2.21 5 O 3751 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 17088 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "B" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 708 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 859 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 789 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "E" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 816 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 859 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "H" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "J" Number of atoms: 2971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2971 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "I" Number of atoms: 3057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3057 Classifications: {'DNA': 147} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 146} Chain: "O" Number of atoms: 4764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 580, 4764 Classifications: {'peptide': 580} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 563} Chain breaks: 6 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "O" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.70, per 1000 atoms: 0.22 Number of scatterers: 17088 At special positions: 0 Unit cell: (142.56, 128.04, 126.72, 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 27 16.00 P 296 15.00 O 3751 8.00 N 3171 7.00 C 9843 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 670.3 milliseconds 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2592 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 9 sheets defined 62.1% alpha, 3.7% beta 110 base pairs and 251 stacking pairs defined. Time for finding SS restraints: 2.12 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.827A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 77 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.872A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 removed outlier: 3.627A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 68 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.661A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 85 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'O' and resid 671 through 682 Processing helix chain 'O' and resid 684 through 689 Processing helix chain 'O' and resid 744 through 748 Processing helix chain 'O' and resid 768 through 784 Processing helix chain 'O' and resid 797 through 812 removed outlier: 4.041A pdb=" N GLN O 801 " --> pdb=" O GLY O 797 " (cutoff:3.500A) Processing helix chain 'O' and resid 824 through 826 No H-bonds generated for 'chain 'O' and resid 824 through 826' Processing helix chain 'O' and resid 827 through 839 Processing helix chain 'O' and resid 850 through 862 Processing helix chain 'O' and resid 873 through 879 removed outlier: 4.362A pdb=" N ILE O 877 " --> pdb=" O PHE O 873 " (cutoff:3.500A) Processing helix chain 'O' and resid 881 through 886 removed outlier: 3.889A pdb=" N VAL O 886 " --> pdb=" O LEU O 882 " (cutoff:3.500A) Processing helix chain 'O' and resid 895 through 900 removed outlier: 4.082A pdb=" N MET O 899 " --> pdb=" O GLU O 895 " (cutoff:3.500A) Processing helix chain 'O' and resid 904 through 912 Processing helix chain 'O' and resid 933 through 938 removed outlier: 3.763A pdb=" N LEU O 937 " --> pdb=" O GLU O 933 " (cutoff:3.500A) Processing helix chain 'O' and resid 943 through 948 removed outlier: 3.980A pdb=" N ASN O 947 " --> pdb=" O PRO O 943 " (cutoff:3.500A) Processing helix chain 'O' and resid 952 through 957 Processing helix chain 'O' and resid 976 through 987 Processing helix chain 'O' and resid 1020 through 1031 removed outlier: 3.625A pdb=" N MET O1026 " --> pdb=" O MET O1022 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS O1028 " --> pdb=" O GLN O1024 " (cutoff:3.500A) Processing helix chain 'O' and resid 1050 through 1061 removed outlier: 3.734A pdb=" N GLN O1054 " --> pdb=" O ASN O1050 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS O1056 " --> pdb=" O ILE O1052 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS O1057 " --> pdb=" O MET O1053 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N CYS O1059 " --> pdb=" O LEU O1055 " (cutoff:3.500A) Processing helix chain 'O' and resid 1068 through 1073 Processing helix chain 'O' and resid 1086 through 1103 Proline residue: O1097 - end of helix Processing helix chain 'O' and resid 1112 through 1126 removed outlier: 3.646A pdb=" N MET O1116 " --> pdb=" O MET O1112 " (cutoff:3.500A) Processing helix chain 'O' and resid 1139 through 1150 removed outlier: 4.613A pdb=" N LEU O1146 " --> pdb=" O ARG O1142 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N ARG O1147 " --> pdb=" O SER O1143 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU O1148 " --> pdb=" O GLU O1144 " (cutoff:3.500A) Processing helix chain 'O' and resid 1187 through 1198 removed outlier: 5.104A pdb=" N ASP O1195 " --> pdb=" O LEU O1191 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA O1197 " --> pdb=" O ALA O1193 " (cutoff:3.500A) Processing helix chain 'O' and resid 1216 through 1229 removed outlier: 4.191A pdb=" N VAL O1220 " --> pdb=" O SER O1216 " (cutoff:3.500A) Processing helix chain 'O' and resid 1232 through 1239 Processing helix chain 'O' and resid 1240 through 1243 Processing helix chain 'O' and resid 1251 through 1259 Processing helix chain 'O' and resid 1263 through 1269 Processing helix chain 'O' and resid 1279 through 1287 removed outlier: 3.639A pdb=" N LEU O1287 " --> pdb=" O ILE O1283 " (cutoff:3.500A) Processing helix chain 'O' and resid 1290 through 1307 removed outlier: 3.756A pdb=" N LYS O1307 " --> pdb=" O ASP O1303 " (cutoff:3.500A) Processing helix chain 'O' and resid 1337 through 1346 removed outlier: 4.156A pdb=" N ALA O1344 " --> pdb=" O SER O1340 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL O1345 " --> pdb=" O GLU O1341 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N TYR O1346 " --> pdb=" O SER O1342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.224A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA5, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA6, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.822A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA8, first strand: chain 'O' and resid 789 through 790 removed outlier: 3.682A pdb=" N LEU O 790 " --> pdb=" O ILE O 921 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL O 869 " --> pdb=" O TYR O 819 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'O' and resid 1007 through 1013 removed outlier: 3.608A pdb=" N ARG O1210 " --> pdb=" O LYS O1009 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL O1178 " --> pdb=" O LEU O1209 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N LEU O1211 " --> pdb=" O VAL O1178 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N ILE O1180 " --> pdb=" O LEU O1211 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N THR O1213 " --> pdb=" O ILE O1180 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N PHE O1109 " --> pdb=" O ILE O1179 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL O1106 " --> pdb=" O PHE O1159 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU O1131 " --> pdb=" O ILE O1160 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 285 hydrogen bonds 550 hydrogen bond angles 0 basepair planarities 110 basepair parallelities 251 stacking parallelities Total time for adding SS restraints: 4.50 Time building geometry restraints manager: 1.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3006 1.33 - 1.45: 5543 1.45 - 1.57: 8790 1.57 - 1.69: 589 1.69 - 1.80: 51 Bond restraints: 17979 Sorted by residual: bond pdb=" C3' DA I 26 " pdb=" O3' DA I 26 " ideal model delta sigma weight residual 1.435 1.373 0.062 1.30e-02 5.92e+03 2.30e+01 bond pdb=" C3' DC J 123 " pdb=" O3' DC J 123 " ideal model delta sigma weight residual 1.435 1.374 0.061 1.30e-02 5.92e+03 2.18e+01 bond pdb=" C3' DA I 70 " pdb=" O3' DA I 70 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.04e+01 bond pdb=" C3' DG I 80 " pdb=" O3' DG I 80 " ideal model delta sigma weight residual 1.435 1.377 0.058 1.30e-02 5.92e+03 2.02e+01 bond pdb=" C3' DG J 56 " pdb=" O3' DG J 56 " ideal model delta sigma weight residual 1.435 1.377 0.058 1.30e-02 5.92e+03 2.01e+01 ... (remaining 17974 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 23996 2.38 - 4.75: 1372 4.75 - 7.13: 115 7.13 - 9.51: 17 9.51 - 11.88: 7 Bond angle restraints: 25507 Sorted by residual: angle pdb=" O4' DC I 24 " pdb=" C1' DC I 24 " pdb=" N1 DC I 24 " ideal model delta sigma weight residual 108.00 112.96 -4.96 7.00e-01 2.04e+00 5.03e+01 angle pdb=" N PRO O 959 " pdb=" CA PRO O 959 " pdb=" CB PRO O 959 " ideal model delta sigma weight residual 103.52 110.39 -6.87 1.06e+00 8.90e-01 4.20e+01 angle pdb=" O5' DG J 121 " pdb=" C5' DG J 121 " pdb=" C4' DG J 121 " ideal model delta sigma weight residual 109.40 114.55 -5.15 8.00e-01 1.56e+00 4.14e+01 angle pdb=" O4' DA I 17 " pdb=" C4' DA I 17 " pdb=" C3' DA I 17 " ideal model delta sigma weight residual 106.00 102.17 3.83 6.00e-01 2.78e+00 4.08e+01 angle pdb=" O4' DA J 19 " pdb=" C4' DA J 19 " pdb=" C3' DA J 19 " ideal model delta sigma weight residual 106.00 102.39 3.61 6.00e-01 2.78e+00 3.62e+01 ... (remaining 25502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 8520 35.43 - 70.86: 1596 70.86 - 106.29: 32 106.29 - 141.72: 4 141.72 - 177.15: 1 Dihedral angle restraints: 10153 sinusoidal: 6163 harmonic: 3990 Sorted by residual: dihedral pdb=" CA PHE O1110 " pdb=" C PHE O1110 " pdb=" N GLN O1111 " pdb=" CA GLN O1111 " ideal model delta harmonic sigma weight residual 180.00 144.71 35.29 0 5.00e+00 4.00e-02 4.98e+01 dihedral pdb=" O2A ADP O2000 " pdb=" O3A ADP O2000 " pdb=" PA ADP O2000 " pdb=" PB ADP O2000 " ideal model delta sinusoidal sigma weight residual -60.00 80.97 -140.97 1 2.00e+01 2.50e-03 4.26e+01 dihedral pdb=" O1B ADP O2000 " pdb=" O3A ADP O2000 " pdb=" PB ADP O2000 " pdb=" PA ADP O2000 " ideal model delta sinusoidal sigma weight residual -60.00 73.65 -133.65 1 2.00e+01 2.50e-03 4.06e+01 ... (remaining 10150 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1956 0.058 - 0.117: 747 0.117 - 0.175: 165 0.175 - 0.234: 19 0.234 - 0.292: 5 Chirality restraints: 2892 Sorted by residual: chirality pdb=" CA ASN O1050 " pdb=" N ASN O1050 " pdb=" C ASN O1050 " pdb=" CB ASN O1050 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.13e+00 chirality pdb=" CB ILE H 54 " pdb=" CA ILE H 54 " pdb=" CG1 ILE H 54 " pdb=" CG2 ILE H 54 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CG LEU O1123 " pdb=" CB LEU O1123 " pdb=" CD1 LEU O1123 " pdb=" CD2 LEU O1123 " both_signs ideal model delta sigma weight residual False -2.59 -2.86 0.27 2.00e-01 2.50e+01 1.83e+00 ... (remaining 2889 not shown) Planarity restraints: 2206 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 30 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.07e+00 pdb=" C ARG D 30 " -0.049 2.00e-02 2.50e+03 pdb=" O ARG D 30 " 0.019 2.00e-02 2.50e+03 pdb=" N LYS D 31 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER O1139 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.85e+00 pdb=" C SER O1139 " 0.048 2.00e-02 2.50e+03 pdb=" O SER O1139 " -0.018 2.00e-02 2.50e+03 pdb=" N ASP O1140 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 120 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO A 121 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 121 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 121 " -0.037 5.00e-02 4.00e+02 ... (remaining 2203 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3476 2.78 - 3.31: 14765 3.31 - 3.84: 32498 3.84 - 4.37: 36918 4.37 - 4.90: 54713 Nonbonded interactions: 142370 Sorted by model distance: nonbonded pdb=" N2 DG J 32 " pdb=" O2 DC I 116 " model vdw 2.248 2.496 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.269 3.040 nonbonded pdb=" OG1 THR C 76 " pdb=" OP1 DA I 133 " model vdw 2.271 3.040 nonbonded pdb=" OD2 ASP E 106 " pdb=" NH2 ARG E 131 " model vdw 2.290 3.120 nonbonded pdb=" OP1 DT I 97 " pdb=" ND2 ASN O1186 " model vdw 2.291 3.120 ... (remaining 142365 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 37 through 135) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 22 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 11 through 119) selection = (chain 'G' and resid 11 through 119) } ncs_group { reference = (chain 'D' and resid 29 through 125) selection = chain 'H' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.020 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 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 : 0.011 0.110 17979 Z= 0.770 Angle : 1.183 11.882 25507 Z= 0.877 Chirality : 0.063 0.292 2892 Planarity : 0.007 0.065 2206 Dihedral : 25.750 177.154 7561 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.55 % Favored : 92.22 % Rotamer: Outliers : 0.59 % Allowed : 2.04 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.13 (0.18), residues: 1337 helix: -2.25 (0.14), residues: 797 sheet: -3.70 (0.51), residues: 66 loop : -3.23 (0.23), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 55 TYR 0.042 0.004 TYR B 51 PHE 0.038 0.005 PHE C 25 TRP 0.030 0.004 TRP O1083 HIS 0.017 0.003 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.01090 / 0.77 (17979) covalent geometry : angle 1.18311 / 0.88 (25507) hydrogen bonds : bond 0.12484 / 8.18 ( 872) hydrogen bonds : angle 5.93182 / 4.22 ( 2302) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 276 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8254 (tp30) cc_final: 0.8039 (tp30) REVERT: B 59 LYS cc_start: 0.8798 (tttt) cc_final: 0.8475 (tttm) REVERT: C 95 LYS cc_start: 0.8990 (tttp) cc_final: 0.8751 (ttpt) REVERT: D 30 ARG cc_start: 0.7230 (ttm-80) cc_final: 0.6744 (tpm170) REVERT: D 68 ASP cc_start: 0.8085 (t0) cc_final: 0.7774 (t0) REVERT: E 79 LYS cc_start: 0.8353 (tptt) cc_final: 0.8052 (tttp) REVERT: H 59 MET cc_start: 0.8056 (tpp) cc_final: 0.7689 (tpp) REVERT: H 122 THR cc_start: 0.9069 (m) cc_final: 0.8725 (p) REVERT: O 800 ILE cc_start: 0.7524 (mt) cc_final: 0.7223 (mp) REVERT: O 1309 GLU cc_start: 0.6802 (tp30) cc_final: 0.5828 (pm20) outliers start: 7 outliers final: 4 residues processed: 281 average time/residue: 0.1833 time to fit residues: 71.3980 Evaluate side-chains 162 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 158 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain O residue 886 VAL Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 949 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.0030 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 30.0000 chunk 77 optimal weight: 30.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 30.0000 chunk 149 optimal weight: 7.9990 overall best weight: 5.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN C 24 GLN C 31 HIS C 73 ASN C 104 GLN D 82 HIS E 113 HIS F 64 ASN F 93 GLN G 68 ASN O 681 HIS O 687 ASN O 749 HIS O 776 GLN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O1104 HIS ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O1347 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.130909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.092246 restraints weight = 36205.954| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.55 r_work: 0.3000 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 17979 Z= 0.350 Angle : 0.897 10.683 25507 Z= 0.485 Chirality : 0.056 0.281 2892 Planarity : 0.007 0.067 2206 Dihedral : 31.089 178.928 4739 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.40 % Favored : 92.52 % Rotamer: Outliers : 3.74 % Allowed : 7.39 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.59 (0.21), residues: 1337 helix: -0.76 (0.17), residues: 813 sheet: -3.39 (0.53), residues: 66 loop : -3.12 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG O1142 TYR 0.024 0.002 TYR B 51 PHE 0.024 0.003 PHE O1063 TRP 0.018 0.002 TRP O1083 HIS 0.008 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00771 / 0.35 (17979) covalent geometry : angle 0.89736 / 0.49 (25507) hydrogen bonds : bond 0.07527 / 5.17 ( 872) hydrogen bonds : angle 4.86269 / 3.45 ( 2302) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 161 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9142 (tttt) cc_final: 0.8815 (tttm) REVERT: C 95 LYS cc_start: 0.9072 (tttp) cc_final: 0.8722 (ttpt) REVERT: D 30 ARG cc_start: 0.7491 (ttm-80) cc_final: 0.6537 (tpm170) REVERT: E 79 LYS cc_start: 0.8525 (tptt) cc_final: 0.8121 (tttp) REVERT: G 56 GLU cc_start: 0.8887 (tt0) cc_final: 0.8603 (tt0) REVERT: G 92 GLU cc_start: 0.8086 (pm20) cc_final: 0.7565 (pm20) REVERT: G 93 LEU cc_start: 0.9482 (OUTLIER) cc_final: 0.9149 (mm) REVERT: G 112 GLN cc_start: 0.8929 (mm110) cc_final: 0.8596 (mm110) REVERT: H 34 LYS cc_start: 0.8399 (ptpp) cc_final: 0.7940 (mmtt) REVERT: H 59 MET cc_start: 0.8814 (tpp) cc_final: 0.8424 (tpp) REVERT: H 122 THR cc_start: 0.9231 (m) cc_final: 0.8826 (p) REVERT: O 1309 GLU cc_start: 0.7337 (tp30) cc_final: 0.6225 (pm20) outliers start: 44 outliers final: 28 residues processed: 190 average time/residue: 0.1386 time to fit residues: 39.7672 Evaluate side-chains 174 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 145 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 72 ASP Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 831 TRP Chi-restraints excluded: chain O residue 886 VAL Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1082 ILE Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1214 THR Chi-restraints excluded: chain O residue 1231 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 87 optimal weight: 20.0000 chunk 142 optimal weight: 5.9990 chunk 89 optimal weight: 30.0000 chunk 137 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 24 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 140 optimal weight: 10.0000 chunk 126 optimal weight: 8.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 109 HIS F 25 ASN O 776 GLN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 984 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.133125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.094479 restraints weight = 36444.600| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.44 r_work: 0.3042 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 17979 Z= 0.207 Angle : 0.717 10.399 25507 Z= 0.402 Chirality : 0.048 0.260 2892 Planarity : 0.005 0.042 2206 Dihedral : 30.673 179.995 4738 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.96 % Favored : 92.97 % Rotamer: Outliers : 3.14 % Allowed : 10.19 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.41 (0.22), residues: 1337 helix: 0.26 (0.18), residues: 813 sheet: -2.91 (0.56), residues: 66 loop : -2.83 (0.26), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 92 TYR 0.018 0.002 TYR B 51 PHE 0.019 0.002 PHE O1063 TRP 0.014 0.002 TRP O 935 HIS 0.007 0.001 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.21 (17979) covalent geometry : angle 0.71688 / 0.40 (25507) hydrogen bonds : bond 0.06154 / 4.23 ( 872) hydrogen bonds : angle 4.38407 / 3.12 ( 2302) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 163 time to evaluate : 0.488 Fit side-chains revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9027 (tttt) cc_final: 0.8707 (tttm) REVERT: C 95 LYS cc_start: 0.9105 (tttp) cc_final: 0.8766 (ttpt) REVERT: D 30 ARG cc_start: 0.7414 (ttm-80) cc_final: 0.6526 (tpm170) REVERT: E 79 LYS cc_start: 0.8581 (tptt) cc_final: 0.8221 (tttp) REVERT: E 120 MET cc_start: 0.8301 (mtt) cc_final: 0.7990 (mtt) REVERT: F 84 MET cc_start: 0.8869 (mmm) cc_final: 0.8613 (mmt) REVERT: G 92 GLU cc_start: 0.8139 (pm20) cc_final: 0.7782 (pm20) REVERT: H 34 LYS cc_start: 0.8404 (ptpp) cc_final: 0.7923 (mmtt) REVERT: H 59 MET cc_start: 0.8586 (tpp) cc_final: 0.8198 (tpp) REVERT: H 122 THR cc_start: 0.9134 (m) cc_final: 0.8721 (p) REVERT: O 1268 ARG cc_start: 0.4017 (ttt180) cc_final: 0.3229 (ptp-170) REVERT: O 1309 GLU cc_start: 0.7212 (tp30) cc_final: 0.5849 (pm20) outliers start: 37 outliers final: 29 residues processed: 187 average time/residue: 0.1285 time to fit residues: 36.7738 Evaluate side-chains 177 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 831 TRP Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 886 VAL Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1082 ILE Chi-restraints excluded: chain O residue 1137 THR Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1231 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 129 optimal weight: 9.9990 chunk 73 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 97 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 59 optimal weight: 2.9990 chunk 161 optimal weight: 0.8980 chunk 140 optimal weight: 0.0070 chunk 115 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 24 GLN C 84 GLN O 776 GLN ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 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 = 0.4060 r_free = 0.4060 target = 0.135320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096802 restraints weight = 36492.821| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.47 r_work: 0.3087 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17979 Z= 0.141 Angle : 0.653 9.182 25507 Z= 0.369 Chirality : 0.044 0.259 2892 Planarity : 0.004 0.046 2206 Dihedral : 30.330 177.600 4736 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.03 % Favored : 92.89 % Rotamer: Outliers : 3.23 % Allowed : 11.54 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.23), residues: 1337 helix: 0.97 (0.18), residues: 803 sheet: -2.26 (0.61), residues: 66 loop : -2.61 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O1196 TYR 0.019 0.001 TYR D 83 PHE 0.019 0.002 PHE O1063 TRP 0.018 0.002 TRP O 838 HIS 0.007 0.001 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.14 (17979) covalent geometry : angle 0.65306 / 0.37 (25507) hydrogen bonds : bond 0.05257 / 3.63 ( 872) hydrogen bonds : angle 4.07000 / 2.89 ( 2302) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.4657 (OUTLIER) cc_final: 0.4452 (pt) REVERT: B 59 LYS cc_start: 0.8976 (tttt) cc_final: 0.8656 (tttm) REVERT: C 95 LYS cc_start: 0.9165 (tttp) cc_final: 0.8834 (ttpt) REVERT: D 30 ARG cc_start: 0.7306 (ttm-80) cc_final: 0.6504 (tpm170) REVERT: D 93 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: E 79 LYS cc_start: 0.8409 (tptt) cc_final: 0.8034 (tttp) REVERT: F 88 TYR cc_start: 0.8900 (m-10) cc_final: 0.8244 (m-10) REVERT: G 92 GLU cc_start: 0.8287 (pm20) cc_final: 0.7779 (pm20) REVERT: G 93 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9148 (mm) REVERT: H 34 LYS cc_start: 0.8339 (ptpp) cc_final: 0.7862 (mmtt) REVERT: H 59 MET cc_start: 0.8487 (tpp) cc_final: 0.8096 (tpp) REVERT: H 83 TYR cc_start: 0.8637 (m-10) cc_final: 0.8245 (m-10) REVERT: H 122 THR cc_start: 0.9076 (m) cc_final: 0.8703 (p) REVERT: O 675 LYS cc_start: 0.6832 (mttt) cc_final: 0.6392 (mmtt) REVERT: O 882 LEU cc_start: 0.8138 (tp) cc_final: 0.7902 (tp) REVERT: O 1119 MET cc_start: 0.8468 (tpp) cc_final: 0.8209 (tpt) REVERT: O 1268 ARG cc_start: 0.3991 (ttt180) cc_final: 0.3207 (ptp-170) REVERT: O 1293 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6383 (mm-30) REVERT: O 1309 GLU cc_start: 0.7142 (tp30) cc_final: 0.5648 (pm20) outliers start: 38 outliers final: 25 residues processed: 183 average time/residue: 0.1343 time to fit residues: 37.7362 Evaluate side-chains 175 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 147 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 858 GLN Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1137 THR Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1231 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 20 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 145 optimal weight: 8.9990 chunk 151 optimal weight: 7.9990 chunk 69 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 155 optimal weight: 20.0000 chunk 100 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN O 749 HIS O 776 GLN O 911 ASN ** O 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.136467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.096830 restraints weight = 36522.653| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 2.33 r_work: 0.3117 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17979 Z= 0.133 Angle : 0.623 7.985 25507 Z= 0.353 Chirality : 0.043 0.259 2892 Planarity : 0.004 0.045 2206 Dihedral : 30.028 176.725 4735 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 3.74 % Allowed : 12.39 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.24), residues: 1337 helix: 1.32 (0.19), residues: 805 sheet: -2.34 (0.60), residues: 77 loop : -2.35 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.014 0.001 TYR F 51 PHE 0.019 0.002 PHE O1063 TRP 0.014 0.002 TRP O 838 HIS 0.007 0.001 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (17979) covalent geometry : angle 0.62315 / 0.35 (25507) hydrogen bonds : bond 0.04870 / 3.36 ( 872) hydrogen bonds : angle 3.92243 / 2.78 ( 2302) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 160 time to evaluate : 0.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8972 (tttt) cc_final: 0.8662 (tttm) REVERT: C 95 LYS cc_start: 0.9164 (tttp) cc_final: 0.8828 (ttpt) REVERT: D 30 ARG cc_start: 0.7263 (ttm-80) cc_final: 0.6559 (tpm170) REVERT: D 93 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: D 123 SER cc_start: 0.8392 (OUTLIER) cc_final: 0.8025 (m) REVERT: E 79 LYS cc_start: 0.8386 (tptt) cc_final: 0.7975 (tttp) REVERT: F 88 TYR cc_start: 0.8896 (m-10) cc_final: 0.8211 (m-10) REVERT: G 92 GLU cc_start: 0.8218 (pm20) cc_final: 0.7862 (pm20) REVERT: H 34 LYS cc_start: 0.8261 (ptpp) cc_final: 0.7814 (mmtt) REVERT: H 59 MET cc_start: 0.8463 (tpp) cc_final: 0.8049 (tpp) REVERT: H 83 TYR cc_start: 0.8622 (m-10) cc_final: 0.8249 (m-10) REVERT: H 122 THR cc_start: 0.9009 (m) cc_final: 0.8672 (p) REVERT: O 675 LYS cc_start: 0.6844 (mttt) cc_final: 0.6452 (mmtt) REVERT: O 794 MET cc_start: 0.6610 (tpp) cc_final: 0.6245 (tmm) REVERT: O 990 PHE cc_start: 0.7309 (m-10) cc_final: 0.6969 (m-80) REVERT: O 1268 ARG cc_start: 0.4012 (ttt180) cc_final: 0.3421 (ptp-170) REVERT: O 1293 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6593 (mm-30) REVERT: O 1309 GLU cc_start: 0.6893 (tp30) cc_final: 0.5622 (pm20) REVERT: O 1337 ARG cc_start: 0.7210 (mmt-90) cc_final: 0.6209 (mmm160) outliers start: 44 outliers final: 27 residues processed: 190 average time/residue: 0.1403 time to fit residues: 40.5738 Evaluate side-chains 179 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 858 GLN Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 886 VAL Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1137 THR Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1157 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1231 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 76 optimal weight: 50.0000 chunk 121 optimal weight: 6.9990 chunk 86 optimal weight: 30.0000 chunk 137 optimal weight: 10.0000 chunk 82 optimal weight: 20.0000 chunk 73 optimal weight: 1.9990 chunk 18 optimal weight: 20.0000 chunk 6 optimal weight: 0.5980 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 39 HIS H 84 ASN O 749 HIS O 776 GLN ** O 890 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.133011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.094740 restraints weight = 36365.016| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.80 r_work: 0.3000 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 17979 Z= 0.247 Angle : 0.726 11.711 25507 Z= 0.395 Chirality : 0.047 0.298 2892 Planarity : 0.005 0.045 2206 Dihedral : 30.148 176.545 4735 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.18 % Favored : 92.74 % Rotamer: Outliers : 4.24 % Allowed : 12.31 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.43 (0.23), residues: 1337 helix: 1.06 (0.18), residues: 803 sheet: -2.53 (0.58), residues: 77 loop : -2.37 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 86 TYR 0.024 0.002 TYR G 57 PHE 0.023 0.002 PHE O1063 TRP 0.010 0.002 TRP O 935 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.25 (17979) covalent geometry : angle 0.72611 / 0.40 (25507) hydrogen bonds : bond 0.05964 / 4.12 ( 872) hydrogen bonds : angle 4.21999 / 3.00 ( 2302) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 149 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9095 (tttt) cc_final: 0.8784 (tttm) REVERT: C 95 LYS cc_start: 0.9144 (tttp) cc_final: 0.8785 (ttpt) REVERT: D 30 ARG cc_start: 0.7361 (ttm-80) cc_final: 0.6446 (tpm170) REVERT: D 93 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.7760 (mp0) REVERT: E 79 LYS cc_start: 0.8609 (tptt) cc_final: 0.8198 (tttp) REVERT: G 56 GLU cc_start: 0.8917 (tt0) cc_final: 0.8690 (tt0) REVERT: G 92 GLU cc_start: 0.8283 (pm20) cc_final: 0.8009 (pm20) REVERT: H 59 MET cc_start: 0.8746 (tpp) cc_final: 0.8338 (tpp) REVERT: H 83 TYR cc_start: 0.8785 (m-10) cc_final: 0.8312 (m-10) REVERT: H 122 THR cc_start: 0.9117 (m) cc_final: 0.8714 (p) REVERT: O 675 LYS cc_start: 0.6765 (mttt) cc_final: 0.6325 (mmtt) REVERT: O 794 MET cc_start: 0.6608 (tpp) cc_final: 0.5758 (tmm) REVERT: O 1293 GLU cc_start: 0.7299 (mt-10) cc_final: 0.6651 (mm-30) REVERT: O 1337 ARG cc_start: 0.7227 (mmt-90) cc_final: 0.6261 (mmm160) outliers start: 50 outliers final: 37 residues processed: 183 average time/residue: 0.1403 time to fit residues: 38.6693 Evaluate side-chains 184 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 146 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 776 GLN Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 858 GLN Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 886 VAL Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 931 LEU Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1082 ILE Chi-restraints excluded: chain O residue 1137 THR Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1213 THR Chi-restraints excluded: chain O residue 1231 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 76 optimal weight: 50.0000 chunk 97 optimal weight: 20.0000 chunk 6 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 75 optimal weight: 3.9990 chunk 161 optimal weight: 40.0000 chunk 57 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 749 HIS ** O 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.135034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.096207 restraints weight = 36448.817| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 2.36 r_work: 0.3077 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 17979 Z= 0.147 Angle : 0.639 12.713 25507 Z= 0.357 Chirality : 0.044 0.384 2892 Planarity : 0.004 0.043 2206 Dihedral : 29.981 176.794 4735 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 3.40 % Allowed : 13.92 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.24), residues: 1337 helix: 1.38 (0.19), residues: 805 sheet: -2.33 (0.60), residues: 77 loop : -2.29 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.016 0.001 TYR D 83 PHE 0.020 0.002 PHE O1063 TRP 0.011 0.002 TRP O 831 HIS 0.005 0.001 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (17979) covalent geometry : angle 0.63908 / 0.36 (25507) hydrogen bonds : bond 0.05151 / 3.57 ( 872) hydrogen bonds : angle 3.99119 / 2.83 ( 2302) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9007 (tttt) cc_final: 0.8690 (tttm) REVERT: C 95 LYS cc_start: 0.9207 (tttp) cc_final: 0.8862 (ttpt) REVERT: D 30 ARG cc_start: 0.7324 (ttm-80) cc_final: 0.6516 (tpm170) REVERT: D 83 TYR cc_start: 0.8172 (m-80) cc_final: 0.7850 (m-80) REVERT: D 93 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7666 (mp0) REVERT: E 79 LYS cc_start: 0.8502 (tptt) cc_final: 0.8094 (tttp) REVERT: F 88 TYR cc_start: 0.8924 (m-10) cc_final: 0.8133 (m-10) REVERT: G 56 GLU cc_start: 0.8803 (tt0) cc_final: 0.8576 (tt0) REVERT: G 85 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8367 (mp) REVERT: G 92 GLU cc_start: 0.8288 (pm20) cc_final: 0.7982 (pm20) REVERT: H 59 MET cc_start: 0.8547 (tpp) cc_final: 0.8181 (tpp) REVERT: H 83 TYR cc_start: 0.8694 (m-10) cc_final: 0.8243 (m-10) REVERT: H 122 THR cc_start: 0.9059 (m) cc_final: 0.8674 (p) REVERT: O 675 LYS cc_start: 0.6742 (mttt) cc_final: 0.6325 (mmtt) REVERT: O 794 MET cc_start: 0.6597 (tpp) cc_final: 0.5831 (tmm) REVERT: O 1293 GLU cc_start: 0.6895 (mt-10) cc_final: 0.6353 (mm-30) REVERT: O 1337 ARG cc_start: 0.7246 (mmt-90) cc_final: 0.6257 (mmm160) outliers start: 40 outliers final: 28 residues processed: 175 average time/residue: 0.1377 time to fit residues: 36.5335 Evaluate side-chains 171 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 141 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 858 GLN Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 886 VAL Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1137 THR Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1157 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1231 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 74 optimal weight: 0.4980 chunk 49 optimal weight: 1.9990 chunk 158 optimal weight: 0.0770 chunk 26 optimal weight: 2.9990 chunk 136 optimal weight: 0.0000 chunk 91 optimal weight: 30.0000 chunk 145 optimal weight: 0.1980 chunk 54 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 89 optimal weight: 30.0000 overall best weight: 0.5544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 749 HIS O 776 GLN O 890 HIS O 928 GLN ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.137245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.098648 restraints weight = 36814.588| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.40 r_work: 0.3128 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 17979 Z= 0.127 Angle : 0.619 13.929 25507 Z= 0.346 Chirality : 0.042 0.349 2892 Planarity : 0.004 0.045 2206 Dihedral : 29.748 176.015 4735 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.23 % Allowed : 14.60 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.24), residues: 1337 helix: 1.64 (0.19), residues: 807 sheet: -2.23 (0.59), residues: 77 loop : -2.17 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.012 0.001 TYR F 51 PHE 0.019 0.001 PHE O1063 TRP 0.022 0.003 TRP O 831 HIS 0.006 0.001 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.13 (17979) covalent geometry : angle 0.61861 / 0.35 (25507) hydrogen bonds : bond 0.04620 / 3.18 ( 872) hydrogen bonds : angle 3.80041 / 2.69 ( 2302) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 156 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8997 (tttt) cc_final: 0.8682 (tttm) REVERT: C 95 LYS cc_start: 0.9194 (tttp) cc_final: 0.8862 (ttpt) REVERT: D 30 ARG cc_start: 0.7214 (ttm-80) cc_final: 0.6426 (tpm170) REVERT: D 93 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7602 (mp0) REVERT: E 79 LYS cc_start: 0.8385 (tptt) cc_final: 0.7967 (tttp) REVERT: F 88 TYR cc_start: 0.8906 (m-10) cc_final: 0.8128 (m-10) REVERT: G 85 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8265 (mp) REVERT: G 92 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7971 (pm20) REVERT: H 47 GLN cc_start: 0.8576 (mt0) cc_final: 0.8255 (tt0) REVERT: H 59 MET cc_start: 0.8481 (tpp) cc_final: 0.8123 (tpp) REVERT: H 83 TYR cc_start: 0.8563 (m-10) cc_final: 0.8165 (m-10) REVERT: H 122 THR cc_start: 0.8926 (m) cc_final: 0.8647 (p) REVERT: O 675 LYS cc_start: 0.6735 (mttt) cc_final: 0.6422 (mmtt) REVERT: O 769 ASP cc_start: 0.7970 (m-30) cc_final: 0.7524 (p0) REVERT: O 794 MET cc_start: 0.6557 (tpp) cc_final: 0.5827 (tmm) REVERT: O 990 PHE cc_start: 0.7552 (m-10) cc_final: 0.7210 (m-80) REVERT: O 1268 ARG cc_start: 0.4034 (ttt180) cc_final: 0.3395 (ptp-170) REVERT: O 1293 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6467 (mm-30) outliers start: 38 outliers final: 26 residues processed: 181 average time/residue: 0.1394 time to fit residues: 38.3056 Evaluate side-chains 177 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 148 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 858 GLN Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 886 VAL Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1081 ASP Chi-restraints excluded: chain O residue 1137 THR Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1157 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1188 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 142 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 133 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 100 optimal weight: 20.0000 chunk 70 optimal weight: 0.7980 chunk 47 optimal weight: 0.6980 chunk 10 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 749 HIS ** O 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.135415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.096801 restraints weight = 36860.822| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.48 r_work: 0.3081 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17979 Z= 0.175 Angle : 0.652 13.641 25507 Z= 0.357 Chirality : 0.043 0.383 2892 Planarity : 0.004 0.049 2206 Dihedral : 29.838 175.774 4735 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.89 % Allowed : 14.86 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.24), residues: 1337 helix: 1.52 (0.18), residues: 806 sheet: -2.18 (0.60), residues: 77 loop : -2.19 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 92 TYR 0.023 0.002 TYR G 50 PHE 0.021 0.002 PHE O1063 TRP 0.016 0.002 TRP O 831 HIS 0.005 0.001 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 (17979) covalent geometry : angle 0.65156 / 0.36 (25507) hydrogen bonds : bond 0.05059 / 3.49 ( 872) hydrogen bonds : angle 3.93860 / 2.79 ( 2302) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 145 time to evaluate : 0.509 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9040 (tttt) cc_final: 0.8738 (tttm) REVERT: C 95 LYS cc_start: 0.9226 (tttp) cc_final: 0.8905 (ttpt) REVERT: D 30 ARG cc_start: 0.7250 (ttm-80) cc_final: 0.6449 (tpm170) REVERT: D 93 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: E 79 LYS cc_start: 0.8470 (tptt) cc_final: 0.8072 (tttp) REVERT: F 88 TYR cc_start: 0.8951 (m-10) cc_final: 0.8141 (m-10) REVERT: G 85 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8342 (mp) REVERT: G 92 GLU cc_start: 0.8168 (pm20) cc_final: 0.7875 (pm20) REVERT: H 47 GLN cc_start: 0.8607 (mt0) cc_final: 0.8271 (tt0) REVERT: H 59 MET cc_start: 0.8576 (tpp) cc_final: 0.8170 (tpp) REVERT: H 83 TYR cc_start: 0.8605 (m-10) cc_final: 0.8212 (m-10) REVERT: H 122 THR cc_start: 0.8996 (m) cc_final: 0.8698 (p) REVERT: O 675 LYS cc_start: 0.6739 (mttt) cc_final: 0.6400 (mmtt) REVERT: O 769 ASP cc_start: 0.7882 (m-30) cc_final: 0.7478 (p0) REVERT: O 794 MET cc_start: 0.6416 (tpp) cc_final: 0.5735 (tmm) REVERT: O 929 ASN cc_start: 0.6103 (OUTLIER) cc_final: 0.5408 (t0) REVERT: O 1190 ASP cc_start: 0.8442 (t0) cc_final: 0.7769 (t0) REVERT: O 1268 ARG cc_start: 0.4009 (ttt180) cc_final: 0.3415 (ptp-170) REVERT: O 1293 GLU cc_start: 0.6969 (mt-10) cc_final: 0.6474 (mm-30) REVERT: O 1337 ARG cc_start: 0.7315 (mmt-90) cc_final: 0.6166 (mmm160) outliers start: 34 outliers final: 28 residues processed: 168 average time/residue: 0.1361 time to fit residues: 34.9735 Evaluate side-chains 175 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 144 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 858 GLN Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 886 VAL Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1081 ASP Chi-restraints excluded: chain O residue 1137 THR Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1157 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1231 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 50 optimal weight: 0.0970 chunk 100 optimal weight: 20.0000 chunk 127 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 0.0010 chunk 145 optimal weight: 2.9990 chunk 97 optimal weight: 20.0000 chunk 62 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 150 optimal weight: 10.0000 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 749 HIS O 776 GLN ** O 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** 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 = 0.4086 r_free = 0.4086 target = 0.137008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.097374 restraints weight = 36445.720| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.30 r_work: 0.3129 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 17979 Z= 0.132 Angle : 0.626 14.955 25507 Z= 0.346 Chirality : 0.042 0.375 2892 Planarity : 0.004 0.050 2206 Dihedral : 29.724 175.530 4735 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.66 % Favored : 93.34 % Rotamer: Outliers : 2.72 % Allowed : 15.37 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.24), residues: 1337 helix: 1.63 (0.19), residues: 809 sheet: -2.05 (0.60), residues: 77 loop : -2.17 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O1337 TYR 0.031 0.002 TYR D 83 PHE 0.020 0.002 PHE O1063 TRP 0.021 0.002 TRP O 831 HIS 0.005 0.001 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.13 (17979) covalent geometry : angle 0.62627 / 0.35 (25507) hydrogen bonds : bond 0.04685 / 3.22 ( 872) hydrogen bonds : angle 3.83930 / 2.72 ( 2302) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2674 Ramachandran restraints generated. 1337 Oldfield, 0 Emsley, 1337 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.505 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8988 (tttt) cc_final: 0.8696 (tttm) REVERT: C 95 LYS cc_start: 0.9214 (tttp) cc_final: 0.8897 (ttpt) REVERT: D 30 ARG cc_start: 0.7167 (ttm-80) cc_final: 0.6436 (tpm170) REVERT: D 93 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: E 79 LYS cc_start: 0.8390 (tptt) cc_final: 0.7994 (tttp) REVERT: F 88 TYR cc_start: 0.8891 (m-10) cc_final: 0.8123 (m-10) REVERT: G 85 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8286 (mp) REVERT: G 92 GLU cc_start: 0.8218 (pm20) cc_final: 0.7878 (pm20) REVERT: H 47 GLN cc_start: 0.8589 (mt0) cc_final: 0.8268 (tt0) REVERT: H 59 MET cc_start: 0.8500 (tpp) cc_final: 0.8133 (tpp) REVERT: H 83 TYR cc_start: 0.8610 (m-10) cc_final: 0.8207 (m-10) REVERT: H 122 THR cc_start: 0.8951 (m) cc_final: 0.8667 (p) REVERT: O 675 LYS cc_start: 0.6708 (mttt) cc_final: 0.6400 (mmtt) REVERT: O 769 ASP cc_start: 0.7864 (m-30) cc_final: 0.7506 (p0) REVERT: O 794 MET cc_start: 0.6363 (tpp) cc_final: 0.5639 (tmm) REVERT: O 929 ASN cc_start: 0.6288 (OUTLIER) cc_final: 0.5762 (t0) REVERT: O 1190 ASP cc_start: 0.8454 (t0) cc_final: 0.7931 (t0) REVERT: O 1268 ARG cc_start: 0.3960 (ttt180) cc_final: 0.3357 (ptp-170) REVERT: O 1293 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6353 (mm-30) outliers start: 32 outliers final: 25 residues processed: 170 average time/residue: 0.1285 time to fit residues: 33.7549 Evaluate side-chains 174 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain C residue 110 ASN Chi-restraints excluded: chain D residue 93 GLU Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 95 ARG Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 113 GLU Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 815 ILE Chi-restraints excluded: chain O residue 858 GLN Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 886 VAL Chi-restraints excluded: chain O residue 891 MET Chi-restraints excluded: chain O residue 893 ILE Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1068 VAL Chi-restraints excluded: chain O residue 1081 ASP Chi-restraints excluded: chain O residue 1137 THR Chi-restraints excluded: chain O residue 1148 LEU Chi-restraints excluded: chain O residue 1157 LEU Chi-restraints excluded: chain O residue 1161 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 6 optimal weight: 0.7980 chunk 137 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 132 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... O 749 HIS ** O 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.137361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.098596 restraints weight = 36830.482| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 2.39 r_work: 0.3130 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.3515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17979 Z= 0.132 Angle : 0.623 14.660 25507 Z= 0.343 Chirality : 0.041 0.398 2892 Planarity : 0.004 0.052 2206 Dihedral : 29.665 175.045 4735 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 2.80 % Allowed : 15.28 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.24), residues: 1337 helix: 1.66 (0.19), residues: 806 sheet: -1.97 (0.60), residues: 77 loop : -2.12 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 92 TYR 0.066 0.002 TYR B 88 PHE 0.020 0.001 PHE O1063 TRP 0.025 0.002 TRP O 831 HIS 0.005 0.001 HIS O 984 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.13 (17979) covalent geometry : angle 0.62284 / 0.34 (25507) hydrogen bonds : bond 0.04645 / 3.19 ( 872) hydrogen bonds : angle 3.84603 / 2.72 ( 2302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3796.43 seconds wall clock time: 65 minutes 49.27 seconds (3949.27 seconds total)