Starting phenix.real_space_refine on Wed Mar 4 22:19:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6iy2_9748/03_2026/6iy2_9748.cif Found real_map, /net/cci-nas-00/data/ceres_data/6iy2_9748/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6iy2_9748/03_2026/6iy2_9748.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6iy2_9748/03_2026/6iy2_9748.map" model { file = "/net/cci-nas-00/data/ceres_data/6iy2_9748/03_2026/6iy2_9748.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6iy2_9748/03_2026/6iy2_9748.cif" } 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-dev-5986/lib/python3.9/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: 3.47, per 1000 atoms: 0.20 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: 1.52 Conformation dependent library (CDL) restraints added in 553.6 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: 2.93 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: 5.16 Time building geometry restraints manager: 2.04 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=" CB ASP A 123 " pdb=" CG ASP A 123 " ideal model delta sigma weight residual 1.516 1.450 0.066 2.50e-02 1.60e+03 7.04e+00 bond pdb=" CG LEU C 83 " pdb=" CD1 LEU C 83 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.19e+00 bond pdb=" CB ILE C 78 " pdb=" CG2 ILE C 78 " ideal model delta sigma weight residual 1.521 1.439 0.082 3.30e-02 9.18e+02 6.15e+00 bond pdb=" C3' DA J 23 " pdb=" O3' DA J 23 " ideal model delta sigma weight residual 1.422 1.491 -0.069 3.00e-02 1.11e+03 5.28e+00 bond pdb=" C2' DC J 58 " pdb=" C1' DC J 58 " ideal model delta sigma weight residual 1.525 1.480 0.045 2.00e-02 2.50e+03 5.07e+00 ... (remaining 17974 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 24333 2.38 - 4.75: 1044 4.75 - 7.13: 106 7.13 - 9.51: 17 9.51 - 11.88: 7 Bond angle restraints: 25507 Sorted by residual: 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=" C ASN O1049 " pdb=" N ASN O1050 " pdb=" CA ASN O1050 " ideal model delta sigma weight residual 121.54 130.88 -9.34 1.91e+00 2.74e-01 2.39e+01 angle pdb=" C ASN O 930 " pdb=" N LEU O 931 " pdb=" CA LEU O 931 " ideal model delta sigma weight residual 121.80 133.56 -11.76 2.44e+00 1.68e-01 2.32e+01 angle pdb=" C GLU O 933 " pdb=" N LEU O 934 " pdb=" CA LEU O 934 " ideal model delta sigma weight residual 121.19 128.57 -7.38 1.59e+00 3.96e-01 2.15e+01 angle pdb=" C PHE O1065 " pdb=" N GLU O1066 " pdb=" CA GLU O1066 " ideal model delta sigma weight residual 121.54 130.23 -8.69 1.91e+00 2.74e-01 2.07e+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: 2027 0.058 - 0.117: 713 0.117 - 0.175: 133 0.175 - 0.234: 14 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: 0.630 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: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.660 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 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 : 0.010 0.110 17979 Z= 0.447 Angle : 1.094 11.882 25507 Z= 0.614 Chirality : 0.060 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 covalent geometry : bond 0.01040 (17979) covalent geometry : angle 1.09393 (25507) hydrogen bonds : bond 0.12484 ( 872) hydrogen bonds : angle 5.93182 ( 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 : 0.507 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: 0.8476 (tttm) REVERT: C 95 LYS cc_start: 0.8990 (tttp) cc_final: 0.8753 (ttpt) REVERT: D 30 ARG cc_start: 0.7230 (ttm-80) cc_final: 0.6722 (tpm170) REVERT: D 68 ASP cc_start: 0.8085 (t0) cc_final: 0.7776 (t0) REVERT: E 79 LYS cc_start: 0.8353 (tptt) cc_final: 0.8053 (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: 0.8724 (p) REVERT: O 800 ILE cc_start: 0.7524 (mt) cc_final: 0.7221 (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: 0.1685 time to fit residues: 65.1281 Evaluate side-chains 160 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 156 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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: 4.9990 chunk 107 optimal weight: 0.0030 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 20.0000 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 10.0000 chunk 149 optimal weight: 10.0000 overall best weight: 4.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 31 HIS C 73 ASN C 104 GLN D 82 HIS D 109 HIS E 113 HIS F 25 ASN F 64 ASN F 93 GLN G 68 ASN O 687 ASN O 749 HIS O 776 GLN ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 911 ASN O 928 GLN 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: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.131092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.093816 restraints weight = 36445.566| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.72 r_work: 0.2988 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.049 17979 Z= 0.335 Angle : 0.776 11.431 25507 Z= 0.431 Chirality : 0.044 0.164 2892 Planarity : 0.006 0.054 2206 Dihedral : 30.632 177.760 4739 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.55 % Favored : 92.37 % Rotamer: Outliers : 3.48 % Allowed : 7.72 % Favored : 88.79 % 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: -2.29 (0.21), residues: 1337 helix: -0.48 (0.17), residues: 812 sheet: -3.44 (0.53), residues: 66 loop : -3.05 (0.26), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 72 TYR 0.023 0.002 TYR B 51 PHE 0.022 0.003 PHE B 100 TRP 0.018 0.002 TRP O1083 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00764 (17979) covalent geometry : angle 0.77628 (25507) hydrogen bonds : bond 0.06615 ( 872) hydrogen bonds : angle 4.59899 ( 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 204 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.473 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8381 (mm-30) cc_final: 0.8176 (mm-30) REVERT: B 59 LYS cc_start: 0.9110 (tttt) cc_final: 0.8776 (tttm) REVERT: C 95 LYS cc_start: 0.9089 (tttp) cc_final: 0.8758 (ttpt) REVERT: D 30 ARG cc_start: 0.7413 (ttm-80) cc_final: 0.6515 (tpm170) REVERT: D 68 ASP cc_start: 0.8751 (t0) cc_final: 0.8542 (t0) REVERT: E 79 LYS cc_start: 0.8558 (tptt) cc_final: 0.8157 (tttp) REVERT: E 81 ASP cc_start: 0.8074 (t70) cc_final: 0.7813 (t70) REVERT: G 92 GLU cc_start: 0.7974 (pm20) cc_final: 0.7536 (pm20) REVERT: G 93 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9223 (mm) REVERT: H 59 MET cc_start: 0.8781 (tpp) cc_final: 0.8421 (tpp) REVERT: O 794 MET cc_start: 0.6842 (tmm) cc_final: 0.6594 (tpp) REVERT: O 949 VAL cc_start: 0.0311 (OUTLIER) cc_final: 0.0003 (t) REVERT: O 1261 GLU cc_start: 0.7031 (OUTLIER) cc_final: 0.6600 (tm-30) REVERT: O 1268 ARG cc_start: 0.3759 (ttt180) cc_final: 0.3086 (ptp-170) REVERT: O 1293 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6560 (mm-30) REVERT: O 1309 GLU cc_start: 0.7332 (tp30) cc_final: 0.6168 (pm20) outliers start: 41 outliers final: 27 residues processed: 193 average time/residue: 0.1297 time to fit residues: 37.7339 Evaluate side-chains 175 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 145 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 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 O residue 746 ASN Chi-restraints excluded: chain O residue 807 THR Chi-restraints excluded: chain O residue 815 ILE 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 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 Chi-restraints excluded: chain O residue 1261 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 87 optimal weight: 7.9990 chunk 142 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 137 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 104 optimal weight: 20.0000 chunk 24 optimal weight: 3.9990 chunk 159 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 140 optimal weight: 9.9990 chunk 126 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 776 GLN ** O 801 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 = 0.4061 r_free = 0.4061 target = 0.135531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.098034 restraints weight = 36704.194| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.67 r_work: 0.3078 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17979 Z= 0.161 Angle : 0.615 8.312 25507 Z= 0.349 Chirality : 0.037 0.161 2892 Planarity : 0.004 0.045 2206 Dihedral : 29.979 176.860 4737 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 2.80 % Allowed : 9.93 % Favored : 87.27 % 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: -0.85 (0.23), residues: 1337 helix: 0.84 (0.18), residues: 798 sheet: -3.28 (0.51), residues: 78 loop : -2.62 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 42 TYR 0.014 0.001 TYR B 51 PHE 0.020 0.002 PHE O1063 TRP 0.011 0.002 TRP O1083 HIS 0.007 0.001 HIS O 984 Details of bonding type rmsd covalent geometry : bond 0.00349 (17979) covalent geometry : angle 0.61548 (25507) hydrogen bonds : bond 0.04911 ( 872) hydrogen bonds : angle 3.98040 ( 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 195 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 162 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: A 118 THR cc_start: 0.9263 (m) cc_final: 0.9035 (p) REVERT: B 59 LYS cc_start: 0.9092 (tttt) cc_final: 0.8771 (tttm) REVERT: C 95 LYS cc_start: 0.9164 (tttp) cc_final: 0.8824 (ttpt) REVERT: D 30 ARG cc_start: 0.7293 (ttm-80) cc_final: 0.6473 (tpm170) REVERT: E 79 LYS cc_start: 0.8442 (tptt) cc_final: 0.8034 (tttp) REVERT: G 50 TYR cc_start: 0.9156 (t80) cc_final: 0.8801 (t80) REVERT: H 34 LYS cc_start: 0.8333 (ptpp) cc_final: 0.7895 (mmtt) REVERT: H 59 MET cc_start: 0.8471 (tpp) cc_final: 0.8063 (tpp) REVERT: H 122 THR cc_start: 0.9048 (m) cc_final: 0.8699 (p) REVERT: O 675 LYS cc_start: 0.6756 (mttt) cc_final: 0.6438 (mmtt) REVERT: O 949 VAL cc_start: 0.0220 (OUTLIER) cc_final: -0.0161 (t) REVERT: O 990 PHE cc_start: 0.7268 (m-10) cc_final: 0.6928 (m-80) REVERT: O 1268 ARG cc_start: 0.3739 (ttt180) cc_final: 0.3181 (ptp-170) REVERT: O 1293 GLU cc_start: 0.6952 (mt-10) cc_final: 0.6477 (mm-30) REVERT: O 1337 ARG cc_start: 0.7210 (mmt-90) cc_final: 0.6166 (mmm160) outliers start: 33 outliers final: 21 residues processed: 185 average time/residue: 0.1264 time to fit residues: 35.3169 Evaluate side-chains 172 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 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 F residue 95 ARG 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 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 1148 LEU Chi-restraints excluded: chain O residue 1157 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: 6.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 161 optimal weight: 9.9990 chunk 140 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 142 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 39 HIS O 749 HIS O 776 GLN ** O 890 HIS ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.132540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.095037 restraints weight = 36556.002| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.82 r_work: 0.3003 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 17979 Z= 0.271 Angle : 0.679 9.387 25507 Z= 0.380 Chirality : 0.041 0.171 2892 Planarity : 0.005 0.045 2206 Dihedral : 30.073 177.227 4737 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.85 % Favored : 92.07 % Rotamer: Outliers : 3.99 % Allowed : 11.12 % Favored : 84.89 % 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: -0.69 (0.23), residues: 1337 helix: 0.89 (0.18), residues: 805 sheet: -2.58 (0.61), residues: 66 loop : -2.61 (0.27), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 854 TYR 0.015 0.002 TYR C 57 PHE 0.022 0.002 PHE O1063 TRP 0.015 0.002 TRP O 838 HIS 0.005 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00623 (17979) covalent geometry : angle 0.67865 (25507) hydrogen bonds : bond 0.05785 ( 872) hydrogen bonds : angle 4.19376 ( 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 201 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 154 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.4179 (OUTLIER) cc_final: 0.3874 (pt) REVERT: B 59 LYS cc_start: 0.9097 (tttt) cc_final: 0.8811 (tttm) REVERT: C 35 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.8078 (ttp80) REVERT: C 64 GLU cc_start: 0.8316 (tt0) cc_final: 0.8084 (tp30) REVERT: C 95 LYS cc_start: 0.9161 (tttp) cc_final: 0.8819 (ttpt) REVERT: D 30 ARG cc_start: 0.7441 (ttm-80) cc_final: 0.6434 (tpm170) REVERT: E 41 TYR cc_start: 0.8710 (m-10) cc_final: 0.8430 (m-10) REVERT: E 79 LYS cc_start: 0.8651 (tptt) cc_final: 0.8264 (tttp) REVERT: G 50 TYR cc_start: 0.9270 (t80) cc_final: 0.8905 (t80) REVERT: G 92 GLU cc_start: 0.8310 (pm20) cc_final: 0.7697 (pm20) REVERT: H 59 MET cc_start: 0.8738 (tpp) cc_final: 0.8357 (tpp) REVERT: O 949 VAL cc_start: -0.0053 (OUTLIER) cc_final: -0.0434 (t) REVERT: O 1261 GLU cc_start: 0.6757 (OUTLIER) cc_final: 0.6392 (tm-30) REVERT: O 1268 ARG cc_start: 0.3785 (ttt180) cc_final: 0.3174 (ptp-170) REVERT: O 1293 GLU cc_start: 0.6902 (mt-10) cc_final: 0.6397 (mm-30) REVERT: O 1337 ARG cc_start: 0.7309 (mmt-90) cc_final: 0.6186 (mmm160) outliers start: 47 outliers final: 33 residues processed: 187 average time/residue: 0.1301 time to fit residues: 36.6921 Evaluate side-chains 182 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 145 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 A residue 87 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 35 ARG 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 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 815 ILE Chi-restraints excluded: chain O residue 858 GLN 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 1231 ILE Chi-restraints excluded: chain O residue 1261 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 20 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 145 optimal weight: 2.9990 chunk 151 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 155 optimal weight: 30.0000 chunk 100 optimal weight: 8.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 24 GLN C 84 GLN O 749 HIS O 783 ASN ** O 801 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 = 0.4074 r_free = 0.4074 target = 0.136285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.097222 restraints weight = 36384.591| |-----------------------------------------------------------------------------| r_work (start): 0.3416 rms_B_bonded: 2.37 r_work: 0.3105 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17979 Z= 0.154 Angle : 0.593 7.642 25507 Z= 0.335 Chirality : 0.036 0.155 2892 Planarity : 0.004 0.043 2206 Dihedral : 29.697 176.550 4737 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.90 % Allowed : 11.04 % Favored : 85.06 % 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: -0.10 (0.24), residues: 1337 helix: 1.39 (0.19), residues: 811 sheet: -2.79 (0.59), residues: 71 loop : -2.36 (0.27), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 72 TYR 0.010 0.001 TYR B 51 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 covalent geometry : bond 0.00335 (17979) covalent geometry : angle 0.59267 (25507) hydrogen bonds : bond 0.04674 ( 872) hydrogen bonds : angle 3.80987 ( 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 203 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 157 time to evaluate : 0.497 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.3835 (OUTLIER) cc_final: 0.3580 (pt) REVERT: B 59 LYS cc_start: 0.9040 (tttt) cc_final: 0.8755 (tttm) REVERT: C 95 LYS cc_start: 0.9230 (tttp) cc_final: 0.8929 (ttpt) REVERT: D 30 ARG cc_start: 0.7223 (ttm-80) cc_final: 0.6458 (tpm170) REVERT: D 93 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7707 (mp0) REVERT: E 79 LYS cc_start: 0.8398 (tptt) cc_final: 0.7980 (tttp) REVERT: G 50 TYR cc_start: 0.9122 (t80) cc_final: 0.8768 (t80) REVERT: G 92 GLU cc_start: 0.8340 (pm20) cc_final: 0.7871 (pm20) REVERT: H 34 LYS cc_start: 0.8334 (ptpp) cc_final: 0.7916 (mmtt) REVERT: H 59 MET cc_start: 0.8497 (tpp) cc_final: 0.8126 (tpp) REVERT: H 83 TYR cc_start: 0.8519 (m-10) cc_final: 0.8193 (m-10) REVERT: H 122 THR cc_start: 0.9032 (m) cc_final: 0.8658 (p) REVERT: O 675 LYS cc_start: 0.6644 (mttt) cc_final: 0.6353 (mmtt) REVERT: O 769 ASP cc_start: 0.7835 (m-30) cc_final: 0.7464 (p0) REVERT: O 949 VAL cc_start: -0.0280 (OUTLIER) cc_final: -0.0652 (t) REVERT: O 990 PHE cc_start: 0.7533 (m-10) cc_final: 0.7192 (m-80) REVERT: O 1190 ASP cc_start: 0.8371 (t0) cc_final: 0.7829 (t0) REVERT: O 1268 ARG cc_start: 0.3938 (ttt180) cc_final: 0.3292 (ptp-170) REVERT: O 1293 GLU cc_start: 0.6868 (mt-10) cc_final: 0.6387 (mm-30) REVERT: O 1337 ARG cc_start: 0.7373 (mmt-90) cc_final: 0.6076 (mmm160) outliers start: 46 outliers final: 28 residues processed: 191 average time/residue: 0.1242 time to fit residues: 36.7696 Evaluate side-chains 181 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 150 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 B residue 22 LEU 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 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER 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 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 1148 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1181 PHE Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1261 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 76 optimal weight: 10.0000 chunk 121 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 137 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 114 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 84 ASN O 749 HIS O 776 GLN O 890 HIS ** 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 = 0.4066 r_free = 0.4066 target = 0.135633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.096831 restraints weight = 36294.739| |-----------------------------------------------------------------------------| r_work (start): 0.3420 rms_B_bonded: 2.50 r_work: 0.3086 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.3311 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= 0.177 Angle : 0.613 9.877 25507 Z= 0.342 Chirality : 0.037 0.154 2892 Planarity : 0.004 0.044 2206 Dihedral : 29.705 176.537 4737 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 4.16 % Allowed : 12.14 % Favored : 83.70 % 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: 0.00 (0.24), residues: 1337 helix: 1.42 (0.18), residues: 814 sheet: -2.60 (0.59), residues: 71 loop : -2.28 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.013 0.001 TYR D 83 PHE 0.021 0.002 PHE O1063 TRP 0.025 0.002 TRP O 831 HIS 0.005 0.001 HIS O 984 Details of bonding type rmsd covalent geometry : bond 0.00395 (17979) covalent geometry : angle 0.61289 (25507) hydrogen bonds : bond 0.04880 ( 872) hydrogen bonds : angle 3.84859 ( 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 200 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 151 time to evaluate : 0.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.3852 (OUTLIER) cc_final: 0.3642 (pt) REVERT: B 59 LYS cc_start: 0.9067 (tttt) cc_final: 0.8796 (tttm) REVERT: C 35 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.8034 (ttp80) REVERT: C 95 LYS cc_start: 0.9217 (tttp) cc_final: 0.8909 (ttpt) REVERT: D 30 ARG cc_start: 0.7243 (ttm-80) cc_final: 0.6471 (tpm170) REVERT: D 93 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: E 79 LYS cc_start: 0.8481 (tptt) cc_final: 0.8053 (tttp) REVERT: G 50 TYR cc_start: 0.9174 (t80) cc_final: 0.8899 (t80) REVERT: G 92 GLU cc_start: 0.8370 (pm20) cc_final: 0.8104 (pm20) REVERT: H 59 MET cc_start: 0.8572 (tpp) cc_final: 0.8141 (tpp) REVERT: H 83 TYR cc_start: 0.8596 (m-10) cc_final: 0.8146 (m-10) REVERT: H 122 THR cc_start: 0.9036 (m) cc_final: 0.8663 (p) REVERT: O 675 LYS cc_start: 0.6693 (mttt) cc_final: 0.6377 (mmtt) REVERT: O 769 ASP cc_start: 0.7821 (m-30) cc_final: 0.7499 (p0) REVERT: O 949 VAL cc_start: -0.0332 (OUTLIER) cc_final: -0.0697 (t) REVERT: O 990 PHE cc_start: 0.7554 (m-10) cc_final: 0.7193 (m-80) REVERT: O 1119 MET cc_start: 0.8462 (tpp) cc_final: 0.8247 (tpp) REVERT: O 1190 ASP cc_start: 0.8339 (t0) cc_final: 0.7803 (t0) REVERT: O 1268 ARG cc_start: 0.3922 (ttt180) cc_final: 0.3289 (ptp-170) REVERT: O 1293 GLU cc_start: 0.6882 (mt-10) cc_final: 0.6226 (mm-30) REVERT: O 1337 ARG cc_start: 0.7341 (mmt-90) cc_final: 0.6064 (mmm160) outliers start: 49 outliers final: 34 residues processed: 188 average time/residue: 0.1231 time to fit residues: 34.9765 Evaluate side-chains 186 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 148 time to evaluate : 0.493 ------------------------------------------------------------------------------- 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 B residue 22 LEU Chi-restraints excluded: chain C residue 35 ARG 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 87 SER 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 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 913 HIS 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 1148 LEU Chi-restraints excluded: chain O residue 1157 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1181 PHE Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1231 ILE Chi-restraints excluded: chain O residue 1261 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 76 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 161 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 143 optimal weight: 10.0000 chunk 27 optimal weight: 0.0040 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 749 HIS ** 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 = 0.4069 r_free = 0.4069 target = 0.135822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.097799 restraints weight = 36441.593| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.71 r_work: 0.3073 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3408 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= 0.170 Angle : 0.607 11.816 25507 Z= 0.338 Chirality : 0.037 0.254 2892 Planarity : 0.004 0.045 2206 Dihedral : 29.667 176.602 4737 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.36 % Favored : 93.64 % Rotamer: Outliers : 3.90 % Allowed : 12.39 % Favored : 83.70 % 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: 0.13 (0.24), residues: 1337 helix: 1.48 (0.18), residues: 822 sheet: -2.44 (0.61), residues: 71 loop : -2.22 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 854 TYR 0.016 0.001 TYR G 57 PHE 0.020 0.002 PHE O1063 TRP 0.032 0.002 TRP O 831 HIS 0.005 0.001 HIS O 984 Details of bonding type rmsd covalent geometry : bond 0.00377 (17979) covalent geometry : angle 0.60691 (25507) hydrogen bonds : bond 0.04796 ( 872) hydrogen bonds : angle 3.81052 ( 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 199 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 153 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.3876 (OUTLIER) cc_final: 0.3601 (pt) REVERT: B 59 LYS cc_start: 0.9081 (tttt) cc_final: 0.8798 (tttm) REVERT: C 35 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.8027 (ttp80) REVERT: C 95 LYS cc_start: 0.9243 (tttp) cc_final: 0.8928 (ttpt) REVERT: D 30 ARG cc_start: 0.7228 (ttm-80) cc_final: 0.6471 (tpm170) REVERT: D 93 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.7772 (mp0) REVERT: E 79 LYS cc_start: 0.8457 (tptt) cc_final: 0.8036 (tttp) REVERT: G 50 TYR cc_start: 0.9176 (t80) cc_final: 0.8893 (t80) REVERT: G 85 LEU cc_start: 0.8721 (OUTLIER) cc_final: 0.8293 (mp) REVERT: G 92 GLU cc_start: 0.8418 (pm20) cc_final: 0.8178 (pm20) REVERT: H 47 GLN cc_start: 0.8577 (mt0) cc_final: 0.8265 (tt0) REVERT: H 59 MET cc_start: 0.8591 (tpp) cc_final: 0.8189 (tpp) REVERT: H 83 TYR cc_start: 0.8590 (m-10) cc_final: 0.8184 (m-10) REVERT: H 122 THR cc_start: 0.9019 (m) cc_final: 0.8645 (p) REVERT: O 675 LYS cc_start: 0.6635 (mttt) cc_final: 0.6318 (mmtt) REVERT: O 769 ASP cc_start: 0.7894 (m-30) cc_final: 0.7526 (p0) REVERT: O 949 VAL cc_start: -0.1191 (OUTLIER) cc_final: -0.1574 (t) REVERT: O 990 PHE cc_start: 0.7583 (m-10) cc_final: 0.7214 (m-80) REVERT: O 1190 ASP cc_start: 0.8339 (t0) cc_final: 0.7844 (t0) REVERT: O 1268 ARG cc_start: 0.3598 (ttt180) cc_final: 0.2995 (ptp-170) REVERT: O 1337 ARG cc_start: 0.7326 (mmt-90) cc_final: 0.6113 (mmm160) outliers start: 46 outliers final: 35 residues processed: 188 average time/residue: 0.1293 time to fit residues: 36.9131 Evaluate side-chains 188 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 148 time to evaluate : 0.342 ------------------------------------------------------------------------------- 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 B residue 22 LEU Chi-restraints excluded: chain C residue 35 ARG 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 87 SER 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 85 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 858 GLN Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 877 ILE 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 913 HIS 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 1148 LEU Chi-restraints excluded: chain O residue 1157 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1181 PHE Chi-restraints excluded: chain O residue 1188 HIS Chi-restraints excluded: chain O residue 1231 ILE Chi-restraints excluded: chain O residue 1261 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 74 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 158 optimal weight: 7.9990 chunk 26 optimal weight: 0.9990 chunk 136 optimal weight: 0.0670 chunk 91 optimal weight: 10.0000 chunk 145 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 49 HIS 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.137315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.098042 restraints weight = 36611.302| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.39 r_work: 0.3124 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17979 Z= 0.151 Angle : 0.598 12.382 25507 Z= 0.332 Chirality : 0.037 0.301 2892 Planarity : 0.004 0.046 2206 Dihedral : 29.456 176.404 4737 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.74 % Allowed : 12.90 % Favored : 83.36 % 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: 1.62 (0.19), residues: 822 sheet: -2.25 (0.61), residues: 71 loop : -2.12 (0.29), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O1289 TYR 0.034 0.001 TYR D 83 PHE 0.020 0.002 PHE O1063 TRP 0.027 0.002 TRP O 831 HIS 0.005 0.001 HIS O 984 Details of bonding type rmsd covalent geometry : bond 0.00328 (17979) covalent geometry : angle 0.59832 (25507) hydrogen bonds : bond 0.04491 ( 872) hydrogen bonds : angle 3.72594 ( 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 199 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 155 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9056 (tttt) cc_final: 0.8787 (tttm) REVERT: C 35 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.8038 (ttp80) REVERT: C 95 LYS cc_start: 0.9202 (tttp) cc_final: 0.8904 (ttpt) REVERT: D 30 ARG cc_start: 0.7146 (ttm-80) cc_final: 0.6507 (tpm170) REVERT: D 83 TYR cc_start: 0.8034 (m-80) cc_final: 0.7394 (m-80) REVERT: D 93 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7688 (mp0) REVERT: E 79 LYS cc_start: 0.8350 (tptt) cc_final: 0.7936 (tttp) REVERT: G 50 TYR cc_start: 0.9160 (t80) cc_final: 0.8851 (t80) REVERT: G 85 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8265 (mp) REVERT: G 92 GLU cc_start: 0.8355 (pm20) cc_final: 0.8071 (pm20) REVERT: H 34 LYS cc_start: 0.8285 (ptpp) cc_final: 0.7840 (mmtt) REVERT: H 47 GLN cc_start: 0.8581 (mt0) cc_final: 0.8291 (tt0) REVERT: H 59 MET cc_start: 0.8424 (tpp) cc_final: 0.8072 (tpp) REVERT: H 83 TYR cc_start: 0.8476 (m-10) cc_final: 0.8242 (m-10) REVERT: H 122 THR cc_start: 0.8962 (m) cc_final: 0.8679 (p) REVERT: O 675 LYS cc_start: 0.6618 (mttt) cc_final: 0.6312 (mmtt) REVERT: O 749 HIS cc_start: 0.6923 (OUTLIER) cc_final: 0.6420 (m90) REVERT: O 769 ASP cc_start: 0.7825 (m-30) cc_final: 0.7584 (p0) REVERT: O 949 VAL cc_start: -0.1675 (OUTLIER) cc_final: -0.2000 (t) REVERT: O 990 PHE cc_start: 0.7588 (m-10) cc_final: 0.7222 (m-80) REVERT: O 1058 ILE cc_start: 0.7406 (OUTLIER) cc_final: 0.7097 (pt) REVERT: O 1185 TRP cc_start: 0.7092 (m100) cc_final: 0.6202 (m100) REVERT: O 1190 ASP cc_start: 0.8460 (t0) cc_final: 0.7783 (t0) REVERT: O 1268 ARG cc_start: 0.3661 (ttt180) cc_final: 0.3125 (ptp-170) outliers start: 44 outliers final: 32 residues processed: 188 average time/residue: 0.1286 time to fit residues: 36.4521 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 : 0.473 ------------------------------------------------------------------------------- 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 35 ARG 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 87 SER 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 32 THR Chi-restraints excluded: chain O residue 746 ASN Chi-restraints excluded: chain O residue 749 HIS 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 877 ILE 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 913 HIS Chi-restraints excluded: chain O residue 944 LYS Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1058 ILE Chi-restraints excluded: chain O residue 1068 VAL 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 1181 PHE Chi-restraints excluded: chain O residue 1261 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 142 optimal weight: 8.9990 chunk 85 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 105 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 chunk 70 optimal weight: 3.9990 chunk 47 optimal weight: 0.7980 chunk 10 optimal weight: 0.1980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4076 r_free = 0.4076 target = 0.136286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.096973 restraints weight = 36704.147| |-----------------------------------------------------------------------------| r_work (start): 0.3415 rms_B_bonded: 2.37 r_work: 0.3103 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3716 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= 0.172 Angle : 0.618 14.476 25507 Z= 0.340 Chirality : 0.037 0.339 2892 Planarity : 0.004 0.048 2206 Dihedral : 29.497 176.390 4737 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.65 % Allowed : 13.41 % Favored : 82.94 % 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: 1.61 (0.19), residues: 819 sheet: -2.26 (0.61), residues: 71 loop : -2.15 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 854 TYR 0.034 0.002 TYR D 83 PHE 0.021 0.002 PHE O1063 TRP 0.032 0.002 TRP O 831 HIS 0.010 0.001 HIS O 749 Details of bonding type rmsd covalent geometry : bond 0.00382 (17979) covalent geometry : angle 0.61823 (25507) hydrogen bonds : bond 0.04728 ( 872) hydrogen bonds : angle 3.78076 ( 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 189 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 146 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9070 (tttt) cc_final: 0.8795 (tttm) REVERT: C 35 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8095 (ttp80) REVERT: C 95 LYS cc_start: 0.9169 (tttp) cc_final: 0.8860 (ttpt) REVERT: D 30 ARG cc_start: 0.7149 (ttm-80) cc_final: 0.6457 (tpm170) REVERT: D 93 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7727 (mp0) REVERT: E 79 LYS cc_start: 0.8410 (tptt) cc_final: 0.7989 (tttp) REVERT: G 50 TYR cc_start: 0.9175 (t80) cc_final: 0.8861 (t80) REVERT: G 85 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8313 (mp) REVERT: G 92 GLU cc_start: 0.8391 (pm20) cc_final: 0.8134 (pm20) REVERT: H 47 GLN cc_start: 0.8574 (mt0) cc_final: 0.8277 (tt0) REVERT: H 59 MET cc_start: 0.8496 (tpp) cc_final: 0.8111 (tpp) REVERT: H 83 TYR cc_start: 0.8525 (m-10) cc_final: 0.8219 (m-10) REVERT: H 122 THR cc_start: 0.9052 (m) cc_final: 0.8719 (p) REVERT: O 675 LYS cc_start: 0.6492 (mttt) cc_final: 0.6208 (mmtt) REVERT: O 769 ASP cc_start: 0.7765 (m-30) cc_final: 0.7545 (p0) REVERT: O 794 MET cc_start: 0.6606 (tmm) cc_final: 0.5925 (tmm) REVERT: O 949 VAL cc_start: -0.1707 (OUTLIER) cc_final: -0.2032 (t) REVERT: O 990 PHE cc_start: 0.7603 (m-10) cc_final: 0.7225 (m-80) REVERT: O 1058 ILE cc_start: 0.7416 (OUTLIER) cc_final: 0.7183 (pt) REVERT: O 1119 MET cc_start: 0.8363 (tpp) cc_final: 0.8061 (tpp) REVERT: O 1190 ASP cc_start: 0.8351 (t0) cc_final: 0.7999 (t0) REVERT: O 1337 ARG cc_start: 0.7267 (mmt-90) cc_final: 0.6211 (mmm160) outliers start: 43 outliers final: 34 residues processed: 176 average time/residue: 0.1253 time to fit residues: 33.5887 Evaluate side-chains 184 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 145 time to evaluate : 0.492 ------------------------------------------------------------------------------- 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 35 ARG 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 87 SER 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 85 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 858 GLN Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 877 ILE 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 913 HIS Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 944 LYS Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1058 ILE 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 1157 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1181 PHE Chi-restraints excluded: chain O residue 1261 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 50 optimal weight: 0.2980 chunk 100 optimal weight: 10.0000 chunk 127 optimal weight: 4.9990 chunk 75 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 145 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 chunk 130 optimal weight: 9.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4075 r_free = 0.4075 target = 0.136256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.096711 restraints weight = 36259.622| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 2.34 r_work: 0.3106 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3741 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= 0.174 Angle : 0.623 14.802 25507 Z= 0.342 Chirality : 0.037 0.355 2892 Planarity : 0.004 0.048 2206 Dihedral : 29.503 176.432 4737 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 3.48 % Allowed : 13.58 % Favored : 82.94 % 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: 0.32 (0.24), residues: 1337 helix: 1.64 (0.19), residues: 817 sheet: -2.27 (0.61), residues: 71 loop : -2.14 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 854 TYR 0.040 0.002 TYR D 83 PHE 0.021 0.002 PHE O1063 TRP 0.034 0.002 TRP O 831 HIS 0.005 0.001 HIS O 749 Details of bonding type rmsd covalent geometry : bond 0.00387 (17979) covalent geometry : angle 0.62301 (25507) hydrogen bonds : bond 0.04747 ( 872) hydrogen bonds : angle 3.79564 ( 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 185 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 144 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9067 (tttt) cc_final: 0.8793 (tttm) REVERT: C 35 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.8152 (ttp80) REVERT: C 95 LYS cc_start: 0.9174 (tttp) cc_final: 0.8863 (ttpt) REVERT: D 30 ARG cc_start: 0.7140 (ttm-80) cc_final: 0.6459 (tpm170) REVERT: D 93 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7723 (mp0) REVERT: E 79 LYS cc_start: 0.8413 (tptt) cc_final: 0.7994 (tttp) REVERT: G 50 TYR cc_start: 0.9141 (t80) cc_final: 0.8840 (t80) REVERT: G 85 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8272 (mp) REVERT: G 92 GLU cc_start: 0.8386 (pm20) cc_final: 0.8116 (pm20) REVERT: H 47 GLN cc_start: 0.8595 (mt0) cc_final: 0.8296 (tt0) REVERT: H 59 MET cc_start: 0.8489 (tpp) cc_final: 0.8137 (tpp) REVERT: H 83 TYR cc_start: 0.8520 (m-10) cc_final: 0.8237 (m-10) REVERT: H 122 THR cc_start: 0.9007 (m) cc_final: 0.8643 (p) REVERT: O 675 LYS cc_start: 0.6508 (mttt) cc_final: 0.6212 (mmtt) REVERT: O 769 ASP cc_start: 0.7773 (m-30) cc_final: 0.7522 (p0) REVERT: O 949 VAL cc_start: -0.1742 (OUTLIER) cc_final: -0.2062 (t) REVERT: O 990 PHE cc_start: 0.7618 (m-10) cc_final: 0.7242 (m-80) REVERT: O 1058 ILE cc_start: 0.7434 (OUTLIER) cc_final: 0.7196 (pt) REVERT: O 1190 ASP cc_start: 0.8329 (t0) cc_final: 0.8020 (t0) REVERT: O 1337 ARG cc_start: 0.7375 (mmt-90) cc_final: 0.6219 (mmm160) outliers start: 41 outliers final: 34 residues processed: 175 average time/residue: 0.1226 time to fit residues: 33.0619 Evaluate side-chains 183 residues out of total 1183 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 144 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 35 ARG 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 87 SER 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 85 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 858 GLN Chi-restraints excluded: chain O residue 871 THR Chi-restraints excluded: chain O residue 877 ILE 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 913 HIS Chi-restraints excluded: chain O residue 929 ASN Chi-restraints excluded: chain O residue 944 LYS Chi-restraints excluded: chain O residue 949 VAL Chi-restraints excluded: chain O residue 999 VAL Chi-restraints excluded: chain O residue 1058 ILE 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 1157 LEU Chi-restraints excluded: chain O residue 1161 LEU Chi-restraints excluded: chain O residue 1181 PHE Chi-restraints excluded: chain O residue 1261 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 162 random chunks: chunk 6 optimal weight: 0.8980 chunk 137 optimal weight: 6.9990 chunk 17 optimal weight: 0.9980 chunk 54 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 132 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 85 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 928 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O1198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.137335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.097329 restraints weight = 36562.603| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 2.19 r_work: 0.3154 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17979 Z= 0.143 Angle : 0.599 14.641 25507 Z= 0.329 Chirality : 0.036 0.360 2892 Planarity : 0.004 0.051 2206 Dihedral : 29.349 176.169 4737 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.97 % Allowed : 14.01 % Favored : 83.02 % 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: 0.57 (0.24), residues: 1337 helix: 1.80 (0.19), residues: 821 sheet: -2.11 (0.61), residues: 71 loop : -2.00 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 131 TYR 0.034 0.001 TYR D 83 PHE 0.019 0.001 PHE O1063 TRP 0.029 0.002 TRP O 831 HIS 0.005 0.001 HIS O 984 Details of bonding type rmsd covalent geometry : bond 0.00306 (17979) covalent geometry : angle 0.59946 (25507) hydrogen bonds : bond 0.04309 ( 872) hydrogen bonds : angle 3.63371 ( 2302) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3689.11 seconds wall clock time: 63 minutes 49.20 seconds (3829.20 seconds total)