Starting phenix.real_space_refine on Wed Sep 17 10:29:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y8k_39050/09_2025/8y8k_39050.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y8k_39050/09_2025/8y8k_39050.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y8k_39050/09_2025/8y8k_39050.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y8k_39050/09_2025/8y8k_39050.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y8k_39050/09_2025/8y8k_39050.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y8k_39050/09_2025/8y8k_39050.map" } resolution = 2.89 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= 0.150 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: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 5352 2.51 5 N 1330 2.21 5 O 1336 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8052 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4026 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 33, 'TRANS': 480} Chain breaks: 1 Chain: "B" Number of atoms: 4026 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4026 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 33, 'TRANS': 480} Chain breaks: 1 Time building chain proxies: 2.29, per 1000 atoms: 0.28 Number of scatterers: 8052 At special positions: 0 Unit cell: (108.9, 106.7, 83.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1336 8.00 N 1330 7.00 C 5352 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: 0.68 Conformation dependent library (CDL) restraints added in 446.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 4 sheets defined 74.3% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 682 through 693 Processing helix chain 'A' and resid 695 through 702 Processing helix chain 'A' and resid 706 through 734 removed outlier: 3.702A pdb=" N ALA A 710 " --> pdb=" O SER A 706 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE A 717 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N SER A 721 " --> pdb=" O PHE A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix Processing helix chain 'A' and resid 739 through 758 removed outlier: 3.677A pdb=" N LEU A 743 " --> pdb=" O GLY A 739 " (cutoff:3.500A) Processing helix chain 'A' and resid 768 through 785 Processing helix chain 'A' and resid 788 through 810 Processing helix chain 'A' and resid 811 through 819 removed outlier: 3.823A pdb=" N PHE A 814 " --> pdb=" O GLU A 811 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU A 815 " --> pdb=" O GLY A 812 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL A 816 " --> pdb=" O SER A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 850 removed outlier: 3.575A pdb=" N GLN A 824 " --> pdb=" O SER A 820 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N VAL A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE A 847 " --> pdb=" O LEU A 843 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR A 848 " --> pdb=" O TYR A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 913 Processing helix chain 'A' and resid 914 through 916 No H-bonds generated for 'chain 'A' and resid 914 through 916' Processing helix chain 'A' and resid 920 through 930 Processing helix chain 'A' and resid 930 through 946 removed outlier: 3.520A pdb=" N ILE A 946 " --> pdb=" O VAL A 942 " (cutoff:3.500A) Processing helix chain 'A' and resid 982 through 989 removed outlier: 3.544A pdb=" N MET A 986 " --> pdb=" O PRO A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 989 through 1012 removed outlier: 3.613A pdb=" N ALA A 993 " --> pdb=" O ALA A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1013 through 1017 removed outlier: 3.534A pdb=" N ARG A1017 " --> pdb=" O LYS A1014 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1039 removed outlier: 3.692A pdb=" N GLY A1039 " --> pdb=" O GLY A1035 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1042 No H-bonds generated for 'chain 'A' and resid 1040 through 1042' Processing helix chain 'A' and resid 1050 through 1060 removed outlier: 3.600A pdb=" N LEU A1060 " --> pdb=" O HIS A1056 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1095 removed outlier: 3.575A pdb=" N VAL A1086 " --> pdb=" O ARG A1082 " (cutoff:3.500A) Processing helix chain 'A' and resid 1098 through 1103 Processing helix chain 'A' and resid 1106 through 1122 removed outlier: 4.228A pdb=" N LEU A1110 " --> pdb=" O PRO A1106 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A1122 " --> pdb=" O GLY A1118 " (cutoff:3.500A) Processing helix chain 'A' and resid 1125 through 1136 removed outlier: 3.697A pdb=" N GLN A1129 " --> pdb=" O ILE A1125 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ILE A1134 " --> pdb=" O ARG A1130 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU A1135 " --> pdb=" O LEU A1131 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N MET A1136 " --> pdb=" O LEU A1132 " (cutoff:3.500A) Processing helix chain 'A' and resid 1144 through 1149 removed outlier: 3.708A pdb=" N LYS A1149 " --> pdb=" O PRO A1145 " (cutoff:3.500A) Processing helix chain 'A' and resid 1151 through 1175 removed outlier: 3.731A pdb=" N LEU A1157 " --> pdb=" O TRP A1153 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N PHE A1158 " --> pdb=" O ARG A1154 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N THR A1159 " --> pdb=" O MET A1155 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1179 No H-bonds generated for 'chain 'A' and resid 1177 through 1179' Processing helix chain 'A' and resid 1180 through 1187 removed outlier: 3.520A pdb=" N LEU A1186 " --> pdb=" O PRO A1182 " (cutoff:3.500A) Processing helix chain 'A' and resid 1187 through 1195 removed outlier: 3.911A pdb=" N LEU A1191 " --> pdb=" O LEU A1187 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A1192 " --> pdb=" O THR A1188 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS A1193 " --> pdb=" O VAL A1189 " (cutoff:3.500A) Processing helix chain 'A' and resid 1195 through 1200 removed outlier: 3.579A pdb=" N LEU A1199 " --> pdb=" O LEU A1195 " (cutoff:3.500A) Processing helix chain 'A' and resid 1201 through 1209 removed outlier: 3.508A pdb=" N ALA A1207 " --> pdb=" O ARG A1203 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 693 Processing helix chain 'B' and resid 695 through 702 Processing helix chain 'B' and resid 706 through 734 removed outlier: 3.693A pdb=" N ALA B 710 " --> pdb=" O SER B 706 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N PHE B 717 " --> pdb=" O LEU B 713 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N SER B 721 " --> pdb=" O PHE B 717 " (cutoff:3.500A) Proline residue: B 722 - end of helix Processing helix chain 'B' and resid 739 through 758 removed outlier: 3.815A pdb=" N LEU B 743 " --> pdb=" O GLY B 739 " (cutoff:3.500A) Processing helix chain 'B' and resid 768 through 785 Processing helix chain 'B' and resid 788 through 810 Processing helix chain 'B' and resid 811 through 819 removed outlier: 3.718A pdb=" N PHE B 814 " --> pdb=" O GLU B 811 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU B 815 " --> pdb=" O GLY B 812 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N VAL B 816 " --> pdb=" O SER B 813 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 850 Processing helix chain 'B' and resid 892 through 913 Processing helix chain 'B' and resid 914 through 916 No H-bonds generated for 'chain 'B' and resid 914 through 916' Processing helix chain 'B' and resid 920 through 930 Processing helix chain 'B' and resid 930 through 946 removed outlier: 3.550A pdb=" N ILE B 946 " --> pdb=" O VAL B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 982 through 989 removed outlier: 3.519A pdb=" N MET B 986 " --> pdb=" O PRO B 982 " (cutoff:3.500A) Processing helix chain 'B' and resid 989 through 1012 removed outlier: 3.583A pdb=" N ALA B 993 " --> pdb=" O ALA B 989 " (cutoff:3.500A) Processing helix chain 'B' and resid 1013 through 1017 Processing helix chain 'B' and resid 1025 through 1039 removed outlier: 3.712A pdb=" N GLY B1039 " --> pdb=" O GLY B1035 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1042 No H-bonds generated for 'chain 'B' and resid 1040 through 1042' Processing helix chain 'B' and resid 1049 through 1060 removed outlier: 3.597A pdb=" N LEU B1060 " --> pdb=" O HIS B1056 " (cutoff:3.500A) Processing helix chain 'B' and resid 1082 through 1095 removed outlier: 3.541A pdb=" N VAL B1086 " --> pdb=" O ARG B1082 " (cutoff:3.500A) Processing helix chain 'B' and resid 1098 through 1103 Processing helix chain 'B' and resid 1106 through 1122 removed outlier: 4.186A pdb=" N LEU B1110 " --> pdb=" O PRO B1106 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LEU B1122 " --> pdb=" O GLY B1118 " (cutoff:3.500A) Processing helix chain 'B' and resid 1125 through 1133 removed outlier: 3.680A pdb=" N GLN B1129 " --> pdb=" O ILE B1125 " (cutoff:3.500A) Processing helix chain 'B' and resid 1144 through 1149 removed outlier: 3.678A pdb=" N LYS B1149 " --> pdb=" O PRO B1145 " (cutoff:3.500A) Processing helix chain 'B' and resid 1151 through 1175 removed outlier: 3.902A pdb=" N LEU B1157 " --> pdb=" O TRP B1153 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N PHE B1158 " --> pdb=" O ARG B1154 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR B1159 " --> pdb=" O MET B1155 " (cutoff:3.500A) Processing helix chain 'B' and resid 1177 through 1179 No H-bonds generated for 'chain 'B' and resid 1177 through 1179' Processing helix chain 'B' and resid 1180 through 1187 removed outlier: 3.546A pdb=" N LEU B1186 " --> pdb=" O PRO B1182 " (cutoff:3.500A) Processing helix chain 'B' and resid 1187 through 1195 removed outlier: 3.862A pdb=" N LEU B1191 " --> pdb=" O LEU B1187 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG B1192 " --> pdb=" O THR B1188 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS B1193 " --> pdb=" O VAL B1189 " (cutoff:3.500A) Processing helix chain 'B' and resid 1196 through 1199 Processing helix chain 'B' and resid 1201 through 1209 Processing sheet with id=AA1, first strand: chain 'A' and resid 764 through 766 removed outlier: 4.874A pdb=" N VAL A 764 " --> pdb=" O ALA A1049 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 1061 through 1063 Processing sheet with id=AA3, first strand: chain 'B' and resid 765 through 766 Processing sheet with id=AA4, first strand: chain 'B' and resid 1061 through 1063 488 hydrogen bonds defined for protein. 1428 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2466 1.34 - 1.46: 1559 1.46 - 1.58: 4179 1.58 - 1.69: 0 1.69 - 1.81: 56 Bond restraints: 8260 Sorted by residual: bond pdb=" CA ASP A1209 " pdb=" CB ASP A1209 " ideal model delta sigma weight residual 1.526 1.553 -0.027 1.53e-02 4.27e+03 3.06e+00 bond pdb=" CG ARG B 817 " pdb=" CD ARG B 817 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 1.01e+00 bond pdb=" CA ASP B1209 " pdb=" CB ASP B1209 " ideal model delta sigma weight residual 1.528 1.553 -0.025 2.61e-02 1.47e+03 9.30e-01 bond pdb=" N GLU A 811 " pdb=" CA GLU A 811 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.47e-01 bond pdb=" C THR B 839 " pdb=" O THR B 839 " ideal model delta sigma weight residual 1.236 1.247 -0.010 1.15e-02 7.56e+03 8.17e-01 ... (remaining 8255 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 10923 1.35 - 2.71: 254 2.71 - 4.06: 52 4.06 - 5.42: 15 5.42 - 6.77: 4 Bond angle restraints: 11248 Sorted by residual: angle pdb=" CB ARG B 817 " pdb=" CG ARG B 817 " pdb=" CD ARG B 817 " ideal model delta sigma weight residual 111.30 118.07 -6.77 2.30e+00 1.89e-01 8.68e+00 angle pdb=" CG ARG B 817 " pdb=" CD ARG B 817 " pdb=" NE ARG B 817 " ideal model delta sigma weight residual 112.00 117.77 -5.77 2.20e+00 2.07e-01 6.88e+00 angle pdb=" CB ARG B 917 " pdb=" CG ARG B 917 " pdb=" CD ARG B 917 " ideal model delta sigma weight residual 111.30 116.76 -5.46 2.30e+00 1.89e-01 5.63e+00 angle pdb=" CA GLU A 811 " pdb=" CB GLU A 811 " pdb=" CG GLU A 811 " ideal model delta sigma weight residual 114.10 118.36 -4.26 2.00e+00 2.50e-01 4.53e+00 angle pdb=" CG ARG B 917 " pdb=" CD ARG B 917 " pdb=" NE ARG B 917 " ideal model delta sigma weight residual 112.00 116.45 -4.45 2.20e+00 2.07e-01 4.10e+00 ... (remaining 11243 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 4193 16.46 - 32.92: 508 32.92 - 49.39: 141 49.39 - 65.85: 26 65.85 - 82.31: 12 Dihedral angle restraints: 4880 sinusoidal: 1922 harmonic: 2958 Sorted by residual: dihedral pdb=" CA THR A 947 " pdb=" C THR A 947 " pdb=" N ASP A 948 " pdb=" CA ASP A 948 " ideal model delta harmonic sigma weight residual 180.00 162.65 17.35 0 5.00e+00 4.00e-02 1.20e+01 dihedral pdb=" CA THR B 947 " pdb=" C THR B 947 " pdb=" N ASP B 948 " pdb=" CA ASP B 948 " ideal model delta harmonic sigma weight residual 180.00 163.33 16.67 0 5.00e+00 4.00e-02 1.11e+01 dihedral pdb=" CA ASP A1071 " pdb=" CB ASP A1071 " pdb=" CG ASP A1071 " pdb=" OD1 ASP A1071 " ideal model delta sinusoidal sigma weight residual -30.00 -84.16 54.16 1 2.00e+01 2.50e-03 9.95e+00 ... (remaining 4877 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 727 0.026 - 0.051: 357 0.051 - 0.077: 175 0.077 - 0.102: 52 0.102 - 0.128: 35 Chirality restraints: 1346 Sorted by residual: chirality pdb=" CA ILE A 972 " pdb=" N ILE A 972 " pdb=" C ILE A 972 " pdb=" CB ILE A 972 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA SER A 721 " pdb=" N SER A 721 " pdb=" C SER A 721 " pdb=" CB SER A 721 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA ILE B 972 " pdb=" N ILE B 972 " pdb=" C ILE B 972 " pdb=" CB ILE B 972 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.85e-01 ... (remaining 1343 not shown) Planarity restraints: 1380 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A1196 " -0.050 5.00e-02 4.00e+02 7.51e-02 9.04e+00 pdb=" N PRO A1197 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO A1197 " -0.038 5.00e-02 4.00e+02 pdb=" CD PRO A1197 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A1181 " -0.033 5.00e-02 4.00e+02 5.00e-02 4.00e+00 pdb=" N PRO A1182 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO A1182 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A1182 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER B 820 " -0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO B 821 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 821 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 821 " -0.026 5.00e-02 4.00e+02 ... (remaining 1377 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1653 2.78 - 3.31: 7331 3.31 - 3.84: 12723 3.84 - 4.37: 14174 4.37 - 4.90: 26001 Nonbonded interactions: 61882 Sorted by model distance: nonbonded pdb=" O ALA A1049 " pdb=" OG SER A1053 " model vdw 2.248 3.040 nonbonded pdb=" O ALA B1049 " pdb=" OG SER B1053 " model vdw 2.258 3.040 nonbonded pdb=" NH2 ARG A1130 " pdb=" OE1 GLN A1162 " model vdw 2.276 3.120 nonbonded pdb=" NH2 ARG B1130 " pdb=" OE1 GLN B1162 " model vdw 2.281 3.120 nonbonded pdb=" NH2 ARG A 793 " pdb=" O LEU A1043 " model vdw 2.286 3.120 ... (remaining 61877 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.210 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.310 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 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 : 0.003 0.031 8260 Z= 0.144 Angle : 0.540 6.775 11248 Z= 0.287 Chirality : 0.040 0.128 1346 Planarity : 0.006 0.075 1380 Dihedral : 16.016 82.309 2972 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.28 % Allowed : 19.36 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.26), residues: 1020 helix: 1.80 (0.20), residues: 688 sheet: None (None), residues: 0 loop : -0.30 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 817 TYR 0.010 0.001 TYR B 856 PHE 0.023 0.001 PHE B 847 TRP 0.012 0.001 TRP A 795 HIS 0.002 0.001 HIS A1140 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8260) covalent geometry : angle 0.53986 (11248) hydrogen bonds : bond 0.14188 ( 488) hydrogen bonds : angle 4.70945 ( 1428) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.266 Fit side-chains REVERT: B 817 ARG cc_start: 0.7940 (ttp-110) cc_final: 0.7329 (ptm-80) REVERT: B 917 ARG cc_start: 0.6917 (mtp-110) cc_final: 0.6549 (tpp-160) outliers start: 20 outliers final: 15 residues processed: 117 average time/residue: 0.6608 time to fit residues: 81.3407 Evaluate side-chains 113 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 98 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 808 VAL Chi-restraints excluded: chain A residue 823 THR Chi-restraints excluded: chain A residue 961 SER Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1022 SER Chi-restraints excluded: chain A residue 1076 GLN Chi-restraints excluded: chain A residue 1150 VAL Chi-restraints excluded: chain A residue 1172 VAL Chi-restraints excluded: chain A residue 1178 SER Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 1022 SER Chi-restraints excluded: chain B residue 1150 VAL Chi-restraints excluded: chain B residue 1172 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.7980 chunk 97 optimal weight: 0.5980 chunk 53 optimal weight: 0.0270 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1074 GLN B1076 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.179781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.143282 restraints weight = 8423.763| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.84 r_work: 0.3486 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.0810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8260 Z= 0.110 Angle : 0.467 5.353 11248 Z= 0.239 Chirality : 0.039 0.124 1346 Planarity : 0.005 0.058 1380 Dihedral : 4.256 37.171 1129 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.08 % Allowed : 17.77 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.16 (0.27), residues: 1020 helix: 2.24 (0.20), residues: 684 sheet: None (None), residues: 0 loop : -0.27 (0.34), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 817 TYR 0.006 0.001 TYR A1146 PHE 0.015 0.001 PHE B 847 TRP 0.012 0.001 TRP A 795 HIS 0.003 0.001 HIS A1025 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8260) covalent geometry : angle 0.46682 (11248) hydrogen bonds : bond 0.05119 ( 488) hydrogen bonds : angle 3.77707 ( 1428) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.308 Fit side-chains REVERT: A 1063 MET cc_start: 0.8066 (OUTLIER) cc_final: 0.7742 (mtm) REVERT: A 1067 ILE cc_start: 0.3798 (OUTLIER) cc_final: 0.3379 (mt) REVERT: B 688 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6826 (m-30) REVERT: B 917 ARG cc_start: 0.7194 (mtp180) cc_final: 0.6706 (tpp-160) outliers start: 27 outliers final: 11 residues processed: 117 average time/residue: 0.6332 time to fit residues: 78.2512 Evaluate side-chains 114 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain B residue 688 ASP Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 1.9990 chunk 26 optimal weight: 0.0470 chunk 35 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 83 optimal weight: 0.0020 chunk 67 optimal weight: 0.6980 chunk 56 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 99 optimal weight: 1.9990 overall best weight: 0.4286 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1074 GLN B1076 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.180352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.143932 restraints weight = 8385.519| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.86 r_work: 0.3486 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8260 Z= 0.105 Angle : 0.452 5.443 11248 Z= 0.229 Chirality : 0.038 0.122 1346 Planarity : 0.005 0.052 1380 Dihedral : 3.326 16.402 1110 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.99 % Allowed : 17.88 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.28 (0.27), residues: 1020 helix: 2.29 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.27 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 817 TYR 0.006 0.001 TYR A1146 PHE 0.014 0.001 PHE B 822 TRP 0.009 0.001 TRP A 795 HIS 0.002 0.000 HIS A1025 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8260) covalent geometry : angle 0.45229 (11248) hydrogen bonds : bond 0.04894 ( 488) hydrogen bonds : angle 3.62278 ( 1428) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 99 time to evaluate : 0.309 Fit side-chains REVERT: A 1063 MET cc_start: 0.8022 (OUTLIER) cc_final: 0.7695 (mtm) REVERT: A 1067 ILE cc_start: 0.3764 (OUTLIER) cc_final: 0.3340 (mt) REVERT: A 1206 GLN cc_start: 0.7959 (OUTLIER) cc_final: 0.7644 (tt0) REVERT: B 688 ASP cc_start: 0.7023 (OUTLIER) cc_final: 0.6751 (m-30) REVERT: B 917 ARG cc_start: 0.7370 (mtp180) cc_final: 0.6835 (tpp-160) REVERT: B 1063 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.6855 (mtm) REVERT: B 1203 ARG cc_start: 0.5809 (ttp-110) cc_final: 0.5202 (ptt-90) outliers start: 35 outliers final: 16 residues processed: 120 average time/residue: 0.5414 time to fit residues: 69.0393 Evaluate side-chains 118 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1199 LEU Chi-restraints excluded: chain A residue 1206 GLN Chi-restraints excluded: chain B residue 688 ASP Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 845 LYS Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 1063 MET Chi-restraints excluded: chain B residue 1096 ILE Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1074 GLN B1076 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.176918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.141686 restraints weight = 8530.664| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.83 r_work: 0.3359 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.1055 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8260 Z= 0.126 Angle : 0.474 5.497 11248 Z= 0.240 Chirality : 0.040 0.125 1346 Planarity : 0.005 0.050 1380 Dihedral : 3.402 16.447 1110 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.10 % Allowed : 18.56 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.11 (0.27), residues: 1020 helix: 2.16 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.33 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 817 TYR 0.007 0.001 TYR B 856 PHE 0.017 0.001 PHE B 822 TRP 0.010 0.001 TRP A 795 HIS 0.002 0.001 HIS A1025 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8260) covalent geometry : angle 0.47402 (11248) hydrogen bonds : bond 0.05892 ( 488) hydrogen bonds : angle 3.68505 ( 1428) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 101 time to evaluate : 0.257 Fit side-chains REVERT: A 817 ARG cc_start: 0.7984 (ttm110) cc_final: 0.7712 (ttp-110) REVERT: A 943 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7326 (t70) REVERT: A 1063 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.7704 (mtm) REVERT: A 1067 ILE cc_start: 0.3854 (OUTLIER) cc_final: 0.3421 (mt) REVERT: A 1206 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7611 (tt0) REVERT: B 688 ASP cc_start: 0.7109 (OUTLIER) cc_final: 0.6673 (m-30) REVERT: B 732 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6788 (tt0) REVERT: B 917 ARG cc_start: 0.7457 (mtp180) cc_final: 0.6875 (tpp-160) REVERT: B 943 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7372 (t70) REVERT: B 1063 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.6797 (mtm) REVERT: B 1203 ARG cc_start: 0.5821 (ttp-110) cc_final: 0.5204 (ptt-90) outliers start: 36 outliers final: 18 residues processed: 120 average time/residue: 0.6001 time to fit residues: 76.2012 Evaluate side-chains 119 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1206 GLN Chi-restraints excluded: chain B residue 688 ASP Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 845 LYS Chi-restraints excluded: chain B residue 846 VAL Chi-restraints excluded: chain B residue 943 ASP Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1063 MET Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1195 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 37 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 95 optimal weight: 0.0370 chunk 62 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 20 optimal weight: 1.9990 chunk 44 optimal weight: 0.0370 chunk 94 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.0980 overall best weight: 0.2336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1076 GLN 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 = 0.183001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.147100 restraints weight = 8483.268| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.86 r_work: 0.3525 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8260 Z= 0.094 Angle : 0.428 5.315 11248 Z= 0.216 Chirality : 0.038 0.122 1346 Planarity : 0.005 0.046 1380 Dihedral : 3.194 16.292 1110 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.08 % Allowed : 19.59 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.46 (0.27), residues: 1020 helix: 2.44 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.24 (0.35), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 817 TYR 0.006 0.001 TYR A 789 PHE 0.011 0.001 PHE A 822 TRP 0.011 0.001 TRP B 795 HIS 0.002 0.000 HIS B1025 Details of bonding type rmsd covalent geometry : bond 0.00194 ( 8260) covalent geometry : angle 0.42759 (11248) hydrogen bonds : bond 0.03946 ( 488) hydrogen bonds : angle 3.48112 ( 1428) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.328 Fit side-chains REVERT: A 817 ARG cc_start: 0.7998 (ttm110) cc_final: 0.7784 (ttp-110) REVERT: A 825 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7901 (mt-10) REVERT: A 1063 MET cc_start: 0.8041 (OUTLIER) cc_final: 0.7681 (mtm) REVERT: A 1206 GLN cc_start: 0.7940 (OUTLIER) cc_final: 0.7659 (tt0) REVERT: B 917 ARG cc_start: 0.7399 (mtp180) cc_final: 0.6976 (tpp-160) REVERT: B 1063 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.6919 (mtm) REVERT: B 1203 ARG cc_start: 0.5859 (ttp-110) cc_final: 0.5230 (ptt-90) outliers start: 27 outliers final: 11 residues processed: 107 average time/residue: 0.5769 time to fit residues: 65.5958 Evaluate side-chains 111 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 97 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1186 LEU Chi-restraints excluded: chain A residue 1206 GLN Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 845 LYS Chi-restraints excluded: chain B residue 1063 MET Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 0.0770 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 78 optimal weight: 0.0870 chunk 43 optimal weight: 0.9990 chunk 41 optimal weight: 2.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1076 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.179263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142749 restraints weight = 8383.640| |-----------------------------------------------------------------------------| r_work (start): 0.3629 rms_B_bonded: 1.85 r_work: 0.3477 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8260 Z= 0.110 Angle : 0.456 5.497 11248 Z= 0.229 Chirality : 0.039 0.124 1346 Planarity : 0.005 0.046 1380 Dihedral : 3.231 15.422 1110 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.62 % Allowed : 20.05 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.38 (0.27), residues: 1020 helix: 2.33 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.17 (0.35), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 817 TYR 0.006 0.001 TYR A1146 PHE 0.015 0.001 PHE B 822 TRP 0.009 0.001 TRP B 795 HIS 0.002 0.001 HIS B1025 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 8260) covalent geometry : angle 0.45642 (11248) hydrogen bonds : bond 0.05146 ( 488) hydrogen bonds : angle 3.53142 ( 1428) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.323 Fit side-chains REVERT: A 1063 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7712 (mtm) REVERT: A 1206 GLN cc_start: 0.7930 (OUTLIER) cc_final: 0.7657 (tt0) REVERT: B 732 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6825 (tt0) REVERT: B 917 ARG cc_start: 0.7569 (mtp180) cc_final: 0.7107 (tpp-160) REVERT: B 1063 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.6885 (mtm) outliers start: 23 outliers final: 13 residues processed: 113 average time/residue: 0.7073 time to fit residues: 84.1341 Evaluate side-chains 110 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1206 GLN Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 845 LYS Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1063 MET Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1186 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1081 GLN B1076 GLN ** B1140 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 = 0.3791 r_free = 0.3791 target = 0.158420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.121199 restraints weight = 8867.665| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.96 r_work: 0.3124 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 8260 Z= 0.229 Angle : 0.609 6.313 11248 Z= 0.310 Chirality : 0.045 0.145 1346 Planarity : 0.006 0.054 1380 Dihedral : 3.833 16.410 1110 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.64 % Allowed : 19.36 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.26), residues: 1020 helix: 1.58 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.50 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B1203 TYR 0.013 0.002 TYR A 856 PHE 0.019 0.002 PHE B 822 TRP 0.010 0.002 TRP A 795 HIS 0.003 0.001 HIS B1141 Details of bonding type rmsd covalent geometry : bond 0.00578 ( 8260) covalent geometry : angle 0.60948 (11248) hydrogen bonds : bond 0.08755 ( 488) hydrogen bonds : angle 4.02412 ( 1428) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 102 time to evaluate : 0.318 Fit side-chains REVERT: A 705 HIS cc_start: 0.7809 (t-90) cc_final: 0.7528 (t-90) REVERT: A 818 TYR cc_start: 0.7685 (m-10) cc_final: 0.7444 (m-10) REVERT: A 917 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7523 (tpp-160) REVERT: A 943 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7655 (t70) REVERT: A 1063 MET cc_start: 0.7996 (OUTLIER) cc_final: 0.7742 (mtm) REVERT: A 1067 ILE cc_start: 0.3848 (OUTLIER) cc_final: 0.3338 (mt) REVERT: A 1206 GLN cc_start: 0.7808 (OUTLIER) cc_final: 0.7553 (tt0) REVERT: B 732 GLU cc_start: 0.7028 (mt-10) cc_final: 0.6795 (tt0) REVERT: B 917 ARG cc_start: 0.7762 (mtp180) cc_final: 0.6967 (tpp-160) REVERT: B 1203 ARG cc_start: 0.5944 (ttp-110) cc_final: 0.4982 (ptt-90) outliers start: 32 outliers final: 19 residues processed: 120 average time/residue: 0.6326 time to fit residues: 80.0139 Evaluate side-chains 126 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 102 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 732 GLU Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 917 ARG Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain A residue 1152 THR Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1206 GLN Chi-restraints excluded: chain B residue 706 SER Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 961 SER Chi-restraints excluded: chain B residue 999 LEU Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1186 LEU Chi-restraints excluded: chain B residue 1195 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 0.7980 chunk 58 optimal weight: 0.8980 chunk 22 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 97 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1076 GLN B1076 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.176435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.142570 restraints weight = 8450.024| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.75 r_work: 0.3440 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8260 Z= 0.119 Angle : 0.484 5.435 11248 Z= 0.245 Chirality : 0.039 0.125 1346 Planarity : 0.005 0.048 1380 Dihedral : 3.523 18.307 1110 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.96 % Allowed : 20.39 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.27), residues: 1020 helix: 1.95 (0.20), residues: 704 sheet: None (None), residues: 0 loop : -0.59 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B1203 TYR 0.006 0.001 TYR A1146 PHE 0.015 0.001 PHE A 855 TRP 0.015 0.001 TRP A 795 HIS 0.002 0.001 HIS B1025 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8260) covalent geometry : angle 0.48388 (11248) hydrogen bonds : bond 0.05683 ( 488) hydrogen bonds : angle 3.72510 ( 1428) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.304 Fit side-chains REVERT: A 1063 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7855 (mtm) REVERT: A 1067 ILE cc_start: 0.3766 (OUTLIER) cc_final: 0.3310 (mt) REVERT: A 1206 GLN cc_start: 0.7923 (OUTLIER) cc_final: 0.7709 (tt0) REVERT: B 917 ARG cc_start: 0.7548 (mtp180) cc_final: 0.7170 (tpp-160) REVERT: B 1063 MET cc_start: 0.8093 (mmm) cc_final: 0.7401 (mtm) REVERT: B 1203 ARG cc_start: 0.6134 (ttp-110) cc_final: 0.5226 (ptt-90) outliers start: 26 outliers final: 15 residues processed: 116 average time/residue: 0.6679 time to fit residues: 81.8327 Evaluate side-chains 113 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 804 VAL Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1206 GLN Chi-restraints excluded: chain B residue 738 MET Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 961 SER Chi-restraints excluded: chain B residue 1178 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 59 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 82 optimal weight: 0.1980 chunk 36 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 86 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 48 optimal weight: 0.2980 chunk 60 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1076 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.178249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.142015 restraints weight = 8424.388| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 1.85 r_work: 0.3466 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3331 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8260 Z= 0.110 Angle : 0.469 5.897 11248 Z= 0.237 Chirality : 0.039 0.138 1346 Planarity : 0.005 0.046 1380 Dihedral : 3.367 16.717 1110 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.28 % Allowed : 21.07 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.04 (0.27), residues: 1020 helix: 2.12 (0.20), residues: 708 sheet: None (None), residues: 0 loop : -0.45 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 817 TYR 0.006 0.001 TYR A 844 PHE 0.014 0.001 PHE B 822 TRP 0.012 0.001 TRP A 795 HIS 0.002 0.000 HIS A1025 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 8260) covalent geometry : angle 0.46936 (11248) hydrogen bonds : bond 0.05033 ( 488) hydrogen bonds : angle 3.62444 ( 1428) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 95 time to evaluate : 0.309 Fit side-chains REVERT: A 817 ARG cc_start: 0.8157 (ttp-110) cc_final: 0.7811 (ttp80) REVERT: A 1063 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7843 (mtm) REVERT: A 1067 ILE cc_start: 0.3793 (OUTLIER) cc_final: 0.3350 (mt) REVERT: A 1206 GLN cc_start: 0.7918 (OUTLIER) cc_final: 0.7704 (tt0) REVERT: B 917 ARG cc_start: 0.7552 (mtp180) cc_final: 0.7167 (tpp-160) REVERT: B 1203 ARG cc_start: 0.6138 (ttp-110) cc_final: 0.5206 (ptt-90) outliers start: 20 outliers final: 15 residues processed: 105 average time/residue: 0.6540 time to fit residues: 72.5661 Evaluate side-chains 115 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1206 GLN Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 961 SER Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 96 optimal weight: 0.8980 chunk 54 optimal weight: 3.9990 chunk 28 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 95 optimal weight: 0.0050 chunk 20 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 43 optimal weight: 0.0770 chunk 89 optimal weight: 3.9990 overall best weight: 0.9956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1076 GLN B1140 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.163809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.125701 restraints weight = 8667.589| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.92 r_work: 0.3193 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8260 Z= 0.142 Angle : 0.509 6.561 11248 Z= 0.258 Chirality : 0.040 0.155 1346 Planarity : 0.006 0.048 1380 Dihedral : 3.491 16.283 1110 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.51 % Allowed : 21.07 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.27), residues: 1020 helix: 1.98 (0.20), residues: 706 sheet: None (None), residues: 0 loop : -0.52 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 817 TYR 0.007 0.001 TYR B 856 PHE 0.017 0.001 PHE B 822 TRP 0.010 0.001 TRP B 795 HIS 0.002 0.001 HIS B 695 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 8260) covalent geometry : angle 0.50855 (11248) hydrogen bonds : bond 0.06392 ( 488) hydrogen bonds : angle 3.74284 ( 1428) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.301 Fit side-chains REVERT: A 817 ARG cc_start: 0.8089 (ttp-110) cc_final: 0.7668 (ttp80) REVERT: A 1063 MET cc_start: 0.7982 (OUTLIER) cc_final: 0.7662 (mtm) REVERT: A 1067 ILE cc_start: 0.3771 (OUTLIER) cc_final: 0.3338 (mt) REVERT: A 1206 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7560 (tt0) REVERT: B 917 ARG cc_start: 0.7615 (mtp180) cc_final: 0.6987 (tpp-160) REVERT: B 1198 ARG cc_start: 0.7047 (mtt90) cc_final: 0.6842 (mtt180) REVERT: B 1203 ARG cc_start: 0.5931 (ttp-110) cc_final: 0.4990 (ptt-90) outliers start: 22 outliers final: 15 residues processed: 114 average time/residue: 0.7211 time to fit residues: 86.4141 Evaluate side-chains 121 residues out of total 878 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 738 MET Chi-restraints excluded: chain A residue 750 LEU Chi-restraints excluded: chain A residue 755 SER Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 943 ASP Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1063 MET Chi-restraints excluded: chain A residue 1067 ILE Chi-restraints excluded: chain A residue 1195 LEU Chi-restraints excluded: chain A residue 1206 GLN Chi-restraints excluded: chain B residue 755 SER Chi-restraints excluded: chain B residue 804 VAL Chi-restraints excluded: chain B residue 805 LEU Chi-restraints excluded: chain B residue 939 MET Chi-restraints excluded: chain B residue 961 SER Chi-restraints excluded: chain B residue 1168 LEU Chi-restraints excluded: chain B residue 1178 SER Chi-restraints excluded: chain B residue 1195 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 0.0000 chunk 95 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 26 optimal weight: 0.0040 chunk 5 optimal weight: 0.5980 chunk 74 optimal weight: 0.8980 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B1076 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.173573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.135039 restraints weight = 8379.648| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.03 r_work: 0.3389 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8260 Z= 0.107 Angle : 0.470 7.736 11248 Z= 0.237 Chirality : 0.039 0.164 1346 Planarity : 0.005 0.047 1380 Dihedral : 3.331 16.831 1110 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.05 % Allowed : 21.30 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.27), residues: 1020 helix: 2.25 (0.20), residues: 702 sheet: None (None), residues: 0 loop : -0.50 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 817 TYR 0.006 0.001 TYR B 818 PHE 0.013 0.001 PHE A 822 TRP 0.012 0.001 TRP B 795 HIS 0.002 0.001 HIS B1025 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8260) covalent geometry : angle 0.46974 (11248) hydrogen bonds : bond 0.04848 ( 488) hydrogen bonds : angle 3.60023 ( 1428) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3231.75 seconds wall clock time: 55 minutes 35.69 seconds (3335.69 seconds total)