Starting phenix.real_space_refine on Fri Oct 23 00:15:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v4p_64782/10_2026/9v4p_64782.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v4p_64782/10_2026/9v4p_64782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9v4p_64782/10_2026/9v4p_64782.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v4p_64782/10_2026/9v4p_64782.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9v4p_64782/10_2026/9v4p_64782.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v4p_64782/10_2026/9v4p_64782.map" } resolution = 2.34 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= 0.028 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 32 5.49 5 S 35 5.16 5 C 4242 2.51 5 N 1197 2.21 5 O 1343 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6851 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 343 Classifications: {'DNA': 17} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "C" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 351 Unusual residues: {'C49': 1} Classifications: {'DNA': 16, 'DNA_mixed': 1} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 16} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 6 Chain: "A" Number of atoms: 6137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 775, 6137 Classifications: {'peptide': 775} Link IDs: {'PTRANS': 42, 'TRANS': 732} Chain breaks: 4 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 19 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'SAH:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4202 SG CYS A1198 39.043 36.083 46.052 1.00 52.81 S ATOM 1587 SG CYS A 800 34.102 47.572 87.400 1.00 57.30 S ATOM 2238 SG CYS A 880 37.341 47.523 89.447 1.00 65.28 S ATOM 2257 SG CYS A 883 35.009 50.727 89.383 1.00 66.95 S Time building chain proxies: 1.49, per 1000 atoms: 0.22 Number of scatterers: 6851 At special positions: 0 Unit cell: (76.095, 94.905, 119.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 35 16.00 P 32 15.00 F 1 9.00 O 1343 8.00 N 1197 7.00 C 4242 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 286.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1602 " pdb="ZN ZN A1602 " - pdb=" NE2 HIS A 773 " pdb="ZN ZN A1602 " - pdb=" SG CYS A 800 " pdb="ZN ZN A1602 " - pdb=" SG CYS A 883 " pdb="ZN ZN A1602 " - pdb=" SG CYS A 880 " Number of angles added : 3 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1428 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 9 sheets defined 31.0% alpha, 27.1% beta 9 base pairs and 26 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 781 through 783 No H-bonds generated for 'chain 'A' and resid 781 through 783' Processing helix chain 'A' and resid 785 through 789 removed outlier: 3.980A pdb=" N ALA A 789 " --> pdb=" O GLY A 786 " (cutoff:3.500A) Processing helix chain 'A' and resid 825 through 846 removed outlier: 3.586A pdb=" N THR A 831 " --> pdb=" O LYS A 827 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 892 Processing helix chain 'A' and resid 976 through 980 Processing helix chain 'A' and resid 981 through 987 removed outlier: 3.563A pdb=" N ALA A 987 " --> pdb=" O GLU A 983 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1005 No H-bonds generated for 'chain 'A' and resid 1003 through 1005' Processing helix chain 'A' and resid 1103 through 1112 Processing helix chain 'A' and resid 1124 through 1135 Processing helix chain 'A' and resid 1144 through 1157 Processing helix chain 'A' and resid 1158 through 1160 No H-bonds generated for 'chain 'A' and resid 1158 through 1160' Processing helix chain 'A' and resid 1165 through 1173 Processing helix chain 'A' and resid 1176 through 1182 Processing helix chain 'A' and resid 1210 through 1231 removed outlier: 3.594A pdb=" N VAL A1215 " --> pdb=" O SER A1211 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N ILE A1220 " --> pdb=" O GLN A1216 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N LEU A1221 " --> pdb=" O CYS A1217 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA A1222 " --> pdb=" O GLU A1218 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA A1227 " --> pdb=" O PHE A1223 " (cutoff:3.500A) Processing helix chain 'A' and resid 1242 through 1246 removed outlier: 3.966A pdb=" N PHE A1246 " --> pdb=" O PHE A1243 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1263 removed outlier: 3.569A pdb=" N MET A1262 " --> pdb=" O SER A1258 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY A1263 " --> pdb=" O LEU A1259 " (cutoff:3.500A) Processing helix chain 'A' and resid 1274 through 1277 removed outlier: 3.785A pdb=" N GLY A1277 " --> pdb=" O GLY A1274 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1274 through 1277' Processing helix chain 'A' and resid 1337 through 1343 Processing helix chain 'A' and resid 1365 through 1373 removed outlier: 3.580A pdb=" N GLY A1373 " --> pdb=" O LYS A1369 " (cutoff:3.500A) Processing helix chain 'A' and resid 1387 through 1395 Processing helix chain 'A' and resid 1404 through 1408 Processing helix chain 'A' and resid 1426 through 1431 removed outlier: 3.553A pdb=" N ASN A1430 " --> pdb=" O PHE A1426 " (cutoff:3.500A) Processing helix chain 'A' and resid 1477 through 1485 Processing helix chain 'A' and resid 1496 through 1506 Processing helix chain 'A' and resid 1509 through 1525 Processing sheet with id=AA1, first strand: chain 'A' and resid 629 through 630 Processing sheet with id=AA2, first strand: chain 'A' and resid 710 through 713 removed outlier: 4.310A pdb=" N GLN A 729 " --> pdb=" O ASP A 713 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 726 through 727 removed outlier: 4.093A pdb=" N MET A 762 " --> pdb=" O TYR A 727 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ALA A 742 " --> pdb=" O ALA A 812 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLY A 810 " --> pdb=" O THR A 744 " (cutoff:3.500A) removed outlier: 9.637A pdb=" N TYR A 852 " --> pdb=" O VAL A 811 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N SER A 813 " --> pdb=" O TYR A 852 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N CYS A 854 " --> pdb=" O SER A 813 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU A 815 " --> pdb=" O CYS A 854 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N SER A 856 " --> pdb=" O GLU A 815 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A1192 " --> pdb=" O LEU A1236 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N GLU A1238 " --> pdb=" O ILE A1192 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY A1194 " --> pdb=" O GLU A1238 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N VAL A1240 " --> pdb=" O GLY A1194 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ASP A1097 " --> pdb=" O LYS A1118 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA A1120 " --> pdb=" O ASP A1097 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR A1139 " --> pdb=" O ASP A1116 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS A1118 " --> pdb=" O THR A1139 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N PHE A1141 " --> pdb=" O LYS A1118 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA A1120 " --> pdb=" O PHE A1141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 726 through 727 removed outlier: 4.093A pdb=" N MET A 762 " --> pdb=" O TYR A 727 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ILE A 756 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS A 773 " --> pdb=" O GLU A 760 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N MET A 762 " --> pdb=" O MET A 771 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N MET A 771 " --> pdb=" O MET A 762 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N GLU A 799 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N GLN A 778 " --> pdb=" O THR A 797 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N THR A 797 " --> pdb=" O GLN A 778 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU A 794 " --> pdb=" O SER A 856 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N TYR A 858 " --> pdb=" O LEU A 794 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU A 796 " --> pdb=" O TYR A 858 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A1192 " --> pdb=" O LEU A1236 " (cutoff:3.500A) removed outlier: 8.255A pdb=" N GLU A1238 " --> pdb=" O ILE A1192 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N GLY A1194 " --> pdb=" O GLU A1238 " (cutoff:3.500A) removed outlier: 9.239A pdb=" N VAL A1240 " --> pdb=" O GLY A1194 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ASP A1097 " --> pdb=" O LYS A1118 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ALA A1120 " --> pdb=" O ASP A1097 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR A1139 " --> pdb=" O ASP A1116 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N LYS A1118 " --> pdb=" O THR A1139 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N PHE A1141 " --> pdb=" O LYS A1118 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ALA A1120 " --> pdb=" O PHE A1141 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 896 through 897 Processing sheet with id=AA6, first strand: chain 'A' and resid 992 through 995 removed outlier: 7.089A pdb=" N LEU A 993 " --> pdb=" O CYS A1034 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N LEU A1036 " --> pdb=" O LEU A 993 " (cutoff:3.500A) removed outlier: 6.076A pdb=" N TYR A 918 " --> pdb=" O GLU A1008 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N LYS A1010 " --> pdb=" O PHE A 916 " (cutoff:3.500A) removed outlier: 7.421A pdb=" N PHE A 916 " --> pdb=" O LYS A1010 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N LEU A 951 " --> pdb=" O ARG A 972 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ARG A 972 " --> pdb=" O LEU A 951 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A 953 " --> pdb=" O LYS A 970 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1312 through 1315 Processing sheet with id=AA8, first strand: chain 'A' and resid 1356 through 1357 Processing sheet with id=AA9, first strand: chain 'A' and resid 1412 through 1414 240 hydrogen bonds defined for protein. 657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 44 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 26 stacking parallelities Total time for adding SS restraints: 1.33 Time building geometry restraints manager: 0.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1082 1.31 - 1.44: 2085 1.44 - 1.57: 3791 1.57 - 1.70: 67 1.70 - 1.83: 53 Bond restraints: 7078 Sorted by residual: bond pdb=" C3' 5CM B 11 " pdb=" C2' 5CM B 11 " ideal model delta sigma weight residual 1.520 1.326 0.194 2.00e-02 2.50e+03 9.41e+01 bond pdb=" C5' 5CM B 11 " pdb=" C4' 5CM B 11 " ideal model delta sigma weight residual 1.517 1.339 0.178 2.00e-02 2.50e+03 7.90e+01 bond pdb=" C4' 5CM B 11 " pdb=" O4' 5CM B 11 " ideal model delta sigma weight residual 1.432 1.594 -0.162 2.00e-02 2.50e+03 6.59e+01 bond pdb=" C2' 5CM B 11 " pdb=" C1' 5CM B 11 " ideal model delta sigma weight residual 1.530 1.686 -0.156 2.00e-02 2.50e+03 6.10e+01 bond pdb=" C5' C49 C 9 " pdb=" C4' C49 C 9 " ideal model delta sigma weight residual 1.511 1.356 0.155 2.00e-02 2.50e+03 5.98e+01 ... (remaining 7073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 9469 2.38 - 4.76: 208 4.76 - 7.13: 24 7.13 - 9.51: 7 9.51 - 11.89: 3 Bond angle restraints: 9711 Sorted by residual: angle pdb=" O5' DG C 10 " pdb=" C5' DG C 10 " pdb=" C4' DG C 10 " ideal model delta sigma weight residual 109.40 114.32 -4.92 8.00e-01 1.56e+00 3.78e+01 angle pdb=" C ALA A1432 " pdb=" N GLU A1433 " pdb=" CA GLU A1433 " ideal model delta sigma weight residual 121.54 130.65 -9.11 1.91e+00 2.74e-01 2.28e+01 angle pdb=" CA GLU A1293 " pdb=" C GLU A1293 " pdb=" O GLU A1293 " ideal model delta sigma weight residual 119.78 114.62 5.16 1.19e+00 7.06e-01 1.88e+01 angle pdb=" N3 DT B 4 " pdb=" C4 DT B 4 " pdb=" O4 DT B 4 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" N3 DT B 19 " pdb=" C4 DT B 19 " pdb=" O4 DT B 19 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 ... (remaining 9706 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.67: 3859 27.67 - 55.33: 293 55.33 - 83.00: 28 83.00 - 110.66: 0 110.66 - 138.33: 1 Dihedral angle restraints: 4181 sinusoidal: 1959 harmonic: 2222 Sorted by residual: dihedral pdb=" CA SER A1115 " pdb=" C SER A1115 " pdb=" N ASP A1116 " pdb=" CA ASP A1116 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA TYR A1264 " pdb=" C TYR A1264 " pdb=" N GLN A1265 " pdb=" CA GLN A1265 " ideal model delta harmonic sigma weight residual 180.00 160.93 19.07 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA SER A 937 " pdb=" C SER A 937 " pdb=" N GLY A 938 " pdb=" CA GLY A 938 " ideal model delta harmonic sigma weight residual 180.00 161.36 18.64 0 5.00e+00 4.00e-02 1.39e+01 ... (remaining 4178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 1030 0.145 - 0.290: 9 0.290 - 0.436: 0 0.436 - 0.581: 0 0.581 - 0.726: 1 Chirality restraints: 1040 Sorted by residual: chirality pdb=" C5 C49 C 9 " pdb=" C4 C49 C 9 " pdb=" C6 C49 C 9 " pdb=" CM5 C49 C 9 " both_signs ideal model delta sigma weight residual False -2.62 -1.89 -0.73 2.00e-01 2.50e+01 1.32e+01 chirality pdb=" CA LEU A1311 " pdb=" N LEU A1311 " pdb=" C LEU A1311 " pdb=" CB LEU A1311 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" C4' C49 C 9 " pdb=" C5' C49 C 9 " pdb=" O4' C49 C 9 " pdb=" C3' C49 C 9 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.19 2.00e-01 2.50e+01 9.12e-01 ... (remaining 1037 not shown) Planarity restraints: 1144 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C49 C 9 " 0.034 2.00e-02 2.50e+03 1.01e-01 2.31e+02 pdb=" N1 C49 C 9 " -0.054 2.00e-02 2.50e+03 pdb=" C2 C49 C 9 " -0.023 2.00e-02 2.50e+03 pdb=" O2 C49 C 9 " 0.124 2.00e-02 2.50e+03 pdb=" N3 C49 C 9 " -0.162 2.00e-02 2.50e+03 pdb=" C4 C49 C 9 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C49 C 9 " 0.021 2.00e-02 2.50e+03 pdb=" C5 C49 C 9 " 0.179 2.00e-02 2.50e+03 pdb=" C6 C49 C 9 " -0.117 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A1292 " 0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C PRO A1292 " -0.065 2.00e-02 2.50e+03 pdb=" O PRO A1292 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU A1293 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A1121 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.42e+00 pdb=" C ILE A1121 " -0.053 2.00e-02 2.50e+03 pdb=" O ILE A1121 " 0.021 2.00e-02 2.50e+03 pdb=" N GLU A1122 " 0.018 2.00e-02 2.50e+03 ... (remaining 1141 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1313 2.78 - 3.31: 5523 3.31 - 3.84: 11020 3.84 - 4.37: 13873 4.37 - 4.90: 22533 Nonbonded interactions: 54262 Sorted by model distance: nonbonded pdb=" OD2 ASP A1097 " pdb=" OG SER A1106 " model vdw 2.246 3.040 nonbonded pdb=" NH2 ARG A 792 " pdb=" OD2 ASP A 836 " model vdw 2.271 3.120 nonbonded pdb=" OH TYR A1025 " pdb=" O GLY A1277 " model vdw 2.282 3.040 nonbonded pdb=" F C49 C 9 " pdb=" CB CYS A1198 " model vdw 2.285 3.390 nonbonded pdb=" O2 C49 C 9 " pdb=" NH2 ARG A1282 " model vdw 2.297 3.120 ... (remaining 54257 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.530 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.220 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:7.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 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 : 0.008 0.194 7083 Z= 0.470 Angle : 0.853 11.889 9714 Z= 0.536 Chirality : 0.054 0.726 1040 Planarity : 0.007 0.101 1144 Dihedral : 17.675 138.326 2753 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 0.61 % Allowed : 0.61 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.27), residues: 765 helix: -0.73 (0.34), residues: 210 sheet: 0.14 (0.44), residues: 124 loop : -1.42 (0.26), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 886 TYR 0.013 0.002 TYR A 761 PHE 0.019 0.002 PHE A1033 TRP 0.015 0.002 TRP A 837 HIS 0.005 0.001 HIS A1381 Details of bonding type rmsd/Z covalent geometry : bond 0.00808 / 0.47 ( 7078) covalent geometry : angle 0.85208 / 0.54 ( 9711) hydrogen bonds : bond 0.19332 / 21.49 ( 234) hydrogen bonds : angle 6.85656 / 8.15 ( 701) metal coordination : bond 0.01851 / 1.39 ( 4) metal coordination : angle 2.55760 / 1.89 ( 3) Misc. bond : bond 0.01549 / 0.62 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 148 time to evaluate : 0.218 Fit side-chains REVERT: A 1023 ARG cc_start: 0.8049 (mmm-85) cc_final: 0.7849 (mmt90) outliers start: 4 outliers final: 0 residues processed: 149 average time/residue: 0.6616 time to fit residues: 102.6322 Evaluate side-chains 108 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [49, 53, 5, 33, 65, 62, 51, 38, 61, 45, 74] chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.0970 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.0050 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 0.5980 overall best weight: 0.4792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.110828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.094991 restraints weight = 9613.631| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.62 r_work: 0.3299 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 7083 Z= 0.167 Angle : 0.683 6.717 9714 Z= 0.361 Chirality : 0.048 0.184 1040 Planarity : 0.005 0.044 1144 Dihedral : 19.444 145.674 1250 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.27 % Allowed : 11.35 % Favored : 86.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.28), residues: 765 helix: 0.46 (0.35), residues: 215 sheet: -0.06 (0.44), residues: 124 loop : -1.12 (0.26), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1354 TYR 0.032 0.002 TYR A1025 PHE 0.014 0.002 PHE A1235 TRP 0.015 0.002 TRP A 837 HIS 0.005 0.001 HIS A1525 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 7078) covalent geometry : angle 0.68041 / 0.36 ( 9711) hydrogen bonds : bond 0.05856 / 6.36 ( 234) hydrogen bonds : angle 4.89200 / 5.51 ( 701) metal coordination : bond 0.01149 / 0.65 ( 4) metal coordination : angle 3.73306 / 3.09 ( 3) Misc. bond : bond 0.00111 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.265 Fit side-chains REVERT: A 719 LYS cc_start: 0.8377 (mttt) cc_final: 0.8171 (mtpt) REVERT: A 1038 PHE cc_start: 0.7706 (t80) cc_final: 0.7489 (t80) REVERT: A 1310 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8417 (ttpp) REVERT: A 1370 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7375 (tm-30) outliers start: 15 outliers final: 4 residues processed: 126 average time/residue: 0.6384 time to fit residues: 83.8278 Evaluate side-chains 113 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 107 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1370 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [0, 55, 45, 38, 6, 4, 5, 31, 54, 11, 48] chunk 0 optimal weight: 4.9990 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 54 optimal weight: 0.4980 chunk 11 optimal weight: 0.0970 chunk 48 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 790 ASN A1485 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.108067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.092206 restraints weight = 9583.721| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.61 r_work: 0.3255 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8825 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.125 7083 Z= 0.177 Angle : 0.643 11.341 9714 Z= 0.339 Chirality : 0.045 0.202 1040 Planarity : 0.005 0.056 1144 Dihedral : 19.115 136.278 1250 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.48 % Allowed : 13.46 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.29), residues: 765 helix: 1.27 (0.37), residues: 215 sheet: -0.16 (0.42), residues: 126 loop : -0.79 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1354 TYR 0.019 0.002 TYR A1025 PHE 0.013 0.002 PHE A1252 TRP 0.011 0.001 TRP A1288 HIS 0.002 0.001 HIS A 823 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 ( 7078) covalent geometry : angle 0.64113 / 0.34 ( 9711) hydrogen bonds : bond 0.06193 / 6.83 ( 234) hydrogen bonds : angle 4.49255 / 5.05 ( 701) metal coordination : bond 0.00632 / 0.44 ( 4) metal coordination : angle 2.71204 / 1.70 ( 3) Misc. bond : bond 0.00134 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.247 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 719 LYS cc_start: 0.8514 (mttt) cc_final: 0.8312 (mtpt) REVERT: A 1021 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8400 (mp) REVERT: A 1209 GLN cc_start: 0.8636 (OUTLIER) cc_final: 0.8094 (mp10) REVERT: A 1370 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7546 (tm-30) outliers start: 23 outliers final: 6 residues processed: 127 average time/residue: 0.6923 time to fit residues: 91.3030 Evaluate side-chains 112 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 103 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 870 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1370 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [15, 55, 9, 61, 19, 50, 22, 6, 67, 29, 64] chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 0.0670 chunk 50 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 790 ASN A 898 ASN A1485 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.106142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.090302 restraints weight = 9748.747| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.65 r_work: 0.3223 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 7083 Z= 0.171 Angle : 0.627 5.976 9714 Z= 0.331 Chirality : 0.045 0.158 1040 Planarity : 0.005 0.044 1144 Dihedral : 19.100 136.851 1250 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.33 % Allowed : 14.22 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.29), residues: 765 helix: 1.41 (0.37), residues: 214 sheet: -0.08 (0.43), residues: 123 loop : -0.78 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A1354 TYR 0.017 0.002 TYR A1025 PHE 0.013 0.002 PHE A 758 TRP 0.012 0.002 TRP A1288 HIS 0.003 0.001 HIS A 768 Details of bonding type rmsd/Z covalent geometry : bond 0.00414 / 0.17 ( 7078) covalent geometry : angle 0.62250 / 0.33 ( 9711) hydrogen bonds : bond 0.05172 / 5.57 ( 234) hydrogen bonds : angle 4.42446 / 4.95 ( 701) metal coordination : bond 0.01204 / 0.72 ( 4) metal coordination : angle 4.20274 / 3.12 ( 3) Misc. bond : bond 0.00125 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.244 Fit side-chains REVERT: A 719 LYS cc_start: 0.8660 (mttt) cc_final: 0.8425 (mtpt) REVERT: A 897 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8578 (tt) REVERT: A 1310 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8531 (ttpp) REVERT: A 1370 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7587 (tm-30) outliers start: 22 outliers final: 7 residues processed: 119 average time/residue: 0.7025 time to fit residues: 86.9202 Evaluate side-chains 112 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 739 VAL Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 897 LEU Chi-restraints excluded: chain A residue 1310 LYS Chi-restraints excluded: chain A residue 1316 SER Chi-restraints excluded: chain A residue 1370 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [46, 64, 33, 14, 47, 1, 58, 70, 9, 36, 15] chunk 46 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 47 optimal weight: 0.0970 chunk 1 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 70 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 728 GLN A 898 ASN A1317 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.105980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.090032 restraints weight = 9719.687| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.65 r_work: 0.3215 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8926 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7083 Z= 0.144 Angle : 0.585 8.396 9714 Z= 0.310 Chirality : 0.042 0.148 1040 Planarity : 0.004 0.041 1144 Dihedral : 19.004 133.758 1250 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.48 % Allowed : 14.52 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.29), residues: 765 helix: 1.68 (0.37), residues: 214 sheet: -0.07 (0.43), residues: 123 loop : -0.66 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1354 TYR 0.010 0.001 TYR A1025 PHE 0.013 0.001 PHE A 758 TRP 0.012 0.001 TRP A1288 HIS 0.002 0.001 HIS A 773 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.14 ( 7078) covalent geometry : angle 0.58316 / 0.31 ( 9711) hydrogen bonds : bond 0.05010 / 5.52 ( 234) hydrogen bonds : angle 4.31169 / 4.81 ( 701) metal coordination : bond 0.01021 / 0.49 ( 4) metal coordination : angle 2.48514 / 1.76 ( 3) Misc. bond : bond 0.00189 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.243 Fit side-chains REVERT: A 719 LYS cc_start: 0.8656 (mttt) cc_final: 0.8402 (mtpt) REVERT: A 1209 GLN cc_start: 0.8765 (OUTLIER) cc_final: 0.8260 (mp10) REVERT: A 1370 GLU cc_start: 0.7967 (OUTLIER) cc_final: 0.7552 (tm-30) outliers start: 23 outliers final: 7 residues processed: 116 average time/residue: 0.7104 time to fit residues: 85.7757 Evaluate side-chains 110 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1209 GLN Chi-restraints excluded: chain A residue 1370 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [55, 35, 62, 47, 23, 3, 71, 42, 45, 37, 33] chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 47 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 0.0570 chunk 33 optimal weight: 0.6980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 729 GLN A1317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.105420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.089343 restraints weight = 9792.964| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.66 r_work: 0.3199 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8951 moved from start: 0.5164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7083 Z= 0.157 Angle : 0.595 7.501 9714 Z= 0.315 Chirality : 0.043 0.156 1040 Planarity : 0.005 0.041 1144 Dihedral : 19.002 133.984 1250 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.18 % Allowed : 14.22 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.17 (0.30), residues: 765 helix: 1.73 (0.37), residues: 214 sheet: -0.15 (0.43), residues: 123 loop : -0.64 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1354 TYR 0.013 0.001 TYR A1025 PHE 0.014 0.002 PHE A 758 TRP 0.013 0.001 TRP A1288 HIS 0.003 0.001 HIS A 773 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 ( 7078) covalent geometry : angle 0.59273 / 0.31 ( 9711) hydrogen bonds : bond 0.04967 / 5.46 ( 234) hydrogen bonds : angle 4.35174 / 4.90 ( 701) metal coordination : bond 0.01110 / 0.55 ( 4) metal coordination : angle 2.87211 / 1.99 ( 3) Misc. bond : bond 0.00229 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.245 Fit side-chains REVERT: A 719 LYS cc_start: 0.8650 (mttt) cc_final: 0.8399 (mtpt) REVERT: A 897 LEU cc_start: 0.8789 (tp) cc_final: 0.8574 (tt) REVERT: A 1370 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7604 (tm-30) outliers start: 21 outliers final: 9 residues processed: 118 average time/residue: 0.7391 time to fit residues: 90.4943 Evaluate side-chains 116 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 1145 CYS Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1250 GLN Chi-restraints excluded: chain A residue 1370 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [9, 63, 54, 15, 76, 69, 64, 74, 53, 73, 17] chunk 9 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 15 optimal weight: 0.0770 chunk 76 optimal weight: 0.6980 chunk 69 optimal weight: 0.0060 chunk 64 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 73 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 overall best weight: 0.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 729 GLN A1159 GLN A1317 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.106253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.090310 restraints weight = 9660.001| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.65 r_work: 0.3215 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 7083 Z= 0.125 Angle : 0.570 8.333 9714 Z= 0.302 Chirality : 0.042 0.153 1040 Planarity : 0.004 0.039 1144 Dihedral : 18.913 132.940 1250 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.87 % Allowed : 14.67 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.30), residues: 765 helix: 1.88 (0.37), residues: 214 sheet: 0.02 (0.45), residues: 113 loop : -0.61 (0.28), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1354 TYR 0.009 0.001 TYR A1025 PHE 0.013 0.001 PHE A 758 TRP 0.012 0.001 TRP A1288 HIS 0.002 0.001 HIS A 773 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.12 ( 7078) covalent geometry : angle 0.56760 / 0.30 ( 9711) hydrogen bonds : bond 0.04497 / 4.95 ( 234) hydrogen bonds : angle 4.25910 / 4.77 ( 701) metal coordination : bond 0.01121 / 0.52 ( 4) metal coordination : angle 2.73496 / 1.85 ( 3) Misc. bond : bond 0.00218 / 0.09 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.270 Fit side-chains REVERT: A 719 LYS cc_start: 0.8630 (mttt) cc_final: 0.8391 (mtpt) outliers start: 19 outliers final: 13 residues processed: 117 average time/residue: 0.7396 time to fit residues: 89.9344 Evaluate side-chains 118 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 813 SER Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 1145 CYS Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1220 ILE Chi-restraints excluded: chain A residue 1250 GLN Chi-restraints excluded: chain A residue 1360 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [17, 49, 58, 66, 20, 61, 0, 35, 5, 70, 39] chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 66 optimal weight: 0.8980 chunk 20 optimal weight: 0.0020 chunk 61 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1159 GLN A1317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.105390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.089174 restraints weight = 9777.262| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.69 r_work: 0.3191 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8962 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 7083 Z= 0.152 Angle : 0.597 7.271 9714 Z= 0.314 Chirality : 0.043 0.151 1040 Planarity : 0.005 0.041 1144 Dihedral : 18.927 133.227 1250 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.12 % Allowed : 16.04 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.30), residues: 765 helix: 1.86 (0.37), residues: 214 sheet: -0.17 (0.43), residues: 123 loop : -0.54 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1411 TYR 0.014 0.001 TYR A1025 PHE 0.014 0.002 PHE A 758 TRP 0.012 0.001 TRP A1288 HIS 0.003 0.001 HIS A 773 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.15 ( 7078) covalent geometry : angle 0.59533 / 0.31 ( 9711) hydrogen bonds : bond 0.04788 / 5.25 ( 234) hydrogen bonds : angle 4.26134 / 4.76 ( 701) metal coordination : bond 0.01036 / 0.52 ( 4) metal coordination : angle 2.75579 / 1.81 ( 3) Misc. bond : bond 0.00252 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.239 Fit side-chains REVERT: A 719 LYS cc_start: 0.8656 (mttt) cc_final: 0.8400 (mtpt) REVERT: A 897 LEU cc_start: 0.8847 (tp) cc_final: 0.8626 (tt) REVERT: A 1411 ARG cc_start: 0.8821 (ttm-80) cc_final: 0.8610 (ttp-110) outliers start: 14 outliers final: 9 residues processed: 117 average time/residue: 0.7431 time to fit residues: 90.2476 Evaluate side-chains 114 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1250 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [66, 2, 73, 15, 56, 63, 68, 75, 5, 40, 38] chunk 66 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 63 optimal weight: 0.8980 chunk 68 optimal weight: 0.7980 chunk 75 optimal weight: 0.0980 chunk 5 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1159 GLN A1317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.104997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.088963 restraints weight = 9684.712| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.62 r_work: 0.3194 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8966 moved from start: 0.5553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 7083 Z= 0.160 Angle : 0.605 9.593 9714 Z= 0.318 Chirality : 0.043 0.166 1040 Planarity : 0.004 0.041 1144 Dihedral : 18.934 133.124 1250 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.97 % Allowed : 16.19 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.30), residues: 765 helix: 1.84 (0.37), residues: 214 sheet: -0.20 (0.43), residues: 123 loop : -0.54 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1411 TYR 0.011 0.001 TYR A1025 PHE 0.014 0.002 PHE A 758 TRP 0.013 0.001 TRP A1288 HIS 0.003 0.001 HIS A 773 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 ( 7078) covalent geometry : angle 0.60334 / 0.32 ( 9711) hydrogen bonds : bond 0.04871 / 5.37 ( 234) hydrogen bonds : angle 4.28041 / 4.77 ( 701) metal coordination : bond 0.00919 / 0.53 ( 4) metal coordination : angle 2.60998 / 1.76 ( 3) Misc. bond : bond 0.00277 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.171 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 110 average time/residue: 0.7085 time to fit residues: 80.9229 Evaluate side-chains 112 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1250 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [50, 22, 13, 45, 28, 58, 67, 33, 17, 6, 29] chunk 50 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1159 GLN A1317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.104927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.088922 restraints weight = 9613.985| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.61 r_work: 0.3193 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 7083 Z= 0.159 Angle : 0.616 9.365 9714 Z= 0.323 Chirality : 0.044 0.167 1040 Planarity : 0.004 0.040 1144 Dihedral : 18.922 133.530 1250 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.97 % Allowed : 16.19 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.30), residues: 765 helix: 1.84 (0.37), residues: 214 sheet: -0.22 (0.43), residues: 126 loop : -0.54 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1411 TYR 0.015 0.001 TYR A1025 PHE 0.015 0.002 PHE A 758 TRP 0.013 0.001 TRP A1288 HIS 0.003 0.001 HIS A 773 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 7078) covalent geometry : angle 0.61431 / 0.32 ( 9711) hydrogen bonds : bond 0.04843 / 5.36 ( 234) hydrogen bonds : angle 4.28380 / 4.78 ( 701) metal coordination : bond 0.01023 / 0.47 ( 4) metal coordination : angle 2.47192 / 1.93 ( 3) Misc. bond : bond 0.00272 / 0.11 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1530 Ramachandran restraints generated. 765 Oldfield, 0 Emsley, 765 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.242 Fit side-chains REVERT: A 871 SER cc_start: 0.8551 (m) cc_final: 0.8291 (p) outliers start: 13 outliers final: 11 residues processed: 106 average time/residue: 0.7553 time to fit residues: 83.0898 Evaluate side-chains 111 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 100 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 GLU Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 811 VAL Chi-restraints excluded: chain A residue 856 SER Chi-restraints excluded: chain A residue 884 LYS Chi-restraints excluded: chain A residue 894 THR Chi-restraints excluded: chain A residue 906 ILE Chi-restraints excluded: chain A residue 951 LEU Chi-restraints excluded: chain A residue 1145 CYS Chi-restraints excluded: chain A residue 1165 THR Chi-restraints excluded: chain A residue 1250 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: [47, 54, 59, 57, 38, 74, 15, 16, 42, 0, 45] chunk 47 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 38 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1159 GLN A1317 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.104104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.088181 restraints weight = 9511.791| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 1.59 r_work: 0.3181 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3036 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 7083 Z= 0.187 Angle : 0.645 9.436 9714 Z= 0.335 Chirality : 0.045 0.171 1040 Planarity : 0.005 0.041 1144 Dihedral : 18.972 133.768 1250 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.97 % Allowed : 16.79 % Favored : 81.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.30), residues: 765 helix: 1.79 (0.37), residues: 214 sheet: -0.20 (0.43), residues: 126 loop : -0.54 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1411 TYR 0.014 0.002 TYR A1025 PHE 0.016 0.002 PHE A 758 TRP 0.013 0.001 TRP A1288 HIS 0.003 0.001 HIS A 773 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 ( 7078) covalent geometry : angle 0.64362 / 0.33 ( 9711) hydrogen bonds : bond 0.05227 / 5.78 ( 234) hydrogen bonds : angle 4.32609 / 4.85 ( 701) metal coordination : bond 0.00996 / 0.48 ( 4) metal coordination : angle 2.49371 / 2.11 ( 3) Misc. bond : bond 0.00312 / 0.12 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3138.67 seconds wall clock time: 54 minutes 4.44 seconds (3244.44 seconds total)