Starting phenix.real_space_refine on Fri Mar 14 04:42:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t78_41087/03_2025/8t78_41087.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t78_41087/03_2025/8t78_41087.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8t78_41087/03_2025/8t78_41087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t78_41087/03_2025/8t78_41087.map" model { file = "/net/cci-nas-00/data/ceres_data/8t78_41087/03_2025/8t78_41087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t78_41087/03_2025/8t78_41087.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 116 5.49 5 S 14 5.16 5 C 5661 2.51 5 N 1696 2.21 5 O 2074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 9561 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 863, 7101 Classifications: {'peptide': 863} Link IDs: {'PTRANS': 25, 'TRANS': 837} Chain breaks: 7 Chain: "B" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 1908 Classifications: {'RNA': 89} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 47, 'rna3p_pyr': 31} Link IDs: {'rna2p': 10, 'rna3p': 78} Chain: "C" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Time building chain proxies: 7.20, per 1000 atoms: 0.75 Number of scatterers: 9561 At special positions: 0 Unit cell: (87.486, 119.981, 122.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 116 15.00 O 2074 8.00 N 1696 7.00 C 5661 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: 2.44 Conformation dependent library (CDL) restraints added in 825.8 milliseconds 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1648 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 4 sheets defined 56.2% alpha, 10.2% beta 38 base pairs and 64 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.697A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.826A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.566A pdb=" N PHE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.534A pdb=" N ASP A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.032A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.157A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.776A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.523A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.508A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 602 removed outlier: 4.338A pdb=" N LEU A 598 " --> pdb=" O TYR A 594 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS A 599 " --> pdb=" O HIS A 595 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE A 600 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.832A pdb=" N LEU A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 643 removed outlier: 5.259A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 643 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 removed outlier: 3.807A pdb=" N MET A 648 " --> pdb=" O ASP A 644 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 removed outlier: 3.698A pdb=" N ASN A 726 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 750 Processing helix chain 'A' and resid 922 through 933 removed outlier: 3.594A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.075A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS A 968 " --> pdb=" O SER A 964 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A 970 " --> pdb=" O PHE A 966 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1000 removed outlier: 4.442A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1088 removed outlier: 4.602A pdb=" N ARG A1084 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N LYS A1085 " --> pdb=" O ALA A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 4.340A pdb=" N SER A1172 " --> pdb=" O ILE A1168 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N SER A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1239 Processing helix chain 'A' and resid 1241 through 1246 removed outlier: 4.763A pdb=" N LYS A1246 " --> pdb=" O TYR A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1252 through 1258 removed outlier: 3.927A pdb=" N GLN A1256 " --> pdb=" O ASN A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1259 through 1262 Processing helix chain 'A' and resid 1263 through 1280 removed outlier: 4.026A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1298 Processing helix chain 'A' and resid 1301 through 1312 Processing helix chain 'A' and resid 1313 through 1316 Processing helix chain 'A' and resid 1339 through 1343 removed outlier: 3.505A pdb=" N VAL A1342 " --> pdb=" O THR A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 3.624A pdb=" N ILE A 759 " --> pdb=" O LYS A 954 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 9.911A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1106 through 1111 removed outlier: 6.772A pdb=" N LYS A1107 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N SER A1109 " --> pdb=" O LEU A1135 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N LEU A1135 " --> pdb=" O SER A1109 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 5.970A pdb=" N LYS A1156 " --> pdb=" O GLU A1150 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU A1150 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LYS A1158 " --> pdb=" O LYS A1148 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N LYS A1148 " --> pdb=" O LYS A1158 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N VAL A1160 " --> pdb=" O VAL A1146 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N VAL A1146 " --> pdb=" O VAL A1160 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N GLU A1162 " --> pdb=" O LEU A1144 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N LEU A1144 " --> pdb=" O GLU A1162 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A1164 " --> pdb=" O SER A1142 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N SER A1142 " --> pdb=" O LEU A1164 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ILE A1166 " --> pdb=" O ALA A1140 " (cutoff:3.500A) 322 hydrogen bonds defined for protein. 927 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 94 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 64 stacking parallelities Total time for adding SS restraints: 4.39 Time building geometry restraints manager: 2.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1752 1.33 - 1.45: 2963 1.45 - 1.57: 5014 1.57 - 1.69: 231 1.69 - 1.82: 27 Bond restraints: 9987 Sorted by residual: bond pdb=" CG MET A 648 " pdb=" SD MET A 648 " ideal model delta sigma weight residual 1.803 1.746 0.057 2.50e-02 1.60e+03 5.22e+00 bond pdb=" CG LEU A 419 " pdb=" CD2 LEU A 419 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.08e+00 bond pdb=" CB LYS A 954 " pdb=" CG LYS A 954 " ideal model delta sigma weight residual 1.520 1.576 -0.056 3.00e-02 1.11e+03 3.44e+00 bond pdb=" CB PHE A1235 " pdb=" CG PHE A1235 " ideal model delta sigma weight residual 1.502 1.545 -0.043 2.30e-02 1.89e+03 3.43e+00 bond pdb=" CB ARG A 78 " pdb=" CG ARG A 78 " ideal model delta sigma weight residual 1.520 1.466 0.054 3.00e-02 1.11e+03 3.20e+00 ... (remaining 9982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 13861 4.20 - 8.40: 104 8.40 - 12.61: 20 12.61 - 16.81: 1 16.81 - 21.01: 2 Bond angle restraints: 13988 Sorted by residual: angle pdb=" CA PRO A 475 " pdb=" N PRO A 475 " pdb=" CD PRO A 475 " ideal model delta sigma weight residual 112.00 102.32 9.68 1.40e+00 5.10e-01 4.78e+01 angle pdb=" O3' DC C 26 " pdb=" P DA C 27 " pdb=" OP1 DA C 27 " ideal model delta sigma weight residual 108.00 127.52 -19.52 3.00e+00 1.11e-01 4.24e+01 angle pdb=" CA LEU A1282 " pdb=" CB LEU A1282 " pdb=" CG LEU A1282 " ideal model delta sigma weight residual 116.30 137.31 -21.01 3.50e+00 8.16e-02 3.60e+01 angle pdb=" N MET A 648 " pdb=" CA MET A 648 " pdb=" CB MET A 648 " ideal model delta sigma weight residual 110.30 118.05 -7.75 1.54e+00 4.22e-01 2.53e+01 angle pdb=" CA MET A 648 " pdb=" CB MET A 648 " pdb=" CG MET A 648 " ideal model delta sigma weight residual 114.10 123.94 -9.84 2.00e+00 2.50e-01 2.42e+01 ... (remaining 13983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.36: 5535 30.36 - 60.71: 462 60.71 - 91.07: 80 91.07 - 121.42: 1 121.42 - 151.78: 1 Dihedral angle restraints: 6079 sinusoidal: 3542 harmonic: 2537 Sorted by residual: dihedral pdb=" CA ASP A 644 " pdb=" C ASP A 644 " pdb=" N ASP A 645 " pdb=" CA ASP A 645 " ideal model delta harmonic sigma weight residual 180.00 -157.82 -22.18 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA PRO A1301 " pdb=" C PRO A1301 " pdb=" N ILE A1302 " pdb=" CA ILE A1302 " ideal model delta harmonic sigma weight residual -180.00 -158.91 -21.09 0 5.00e+00 4.00e-02 1.78e+01 dihedral pdb=" CA SER A1248 " pdb=" C SER A1248 " pdb=" N PRO A1249 " pdb=" CA PRO A1249 " ideal model delta harmonic sigma weight residual -180.00 -160.13 -19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 6076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1441 0.083 - 0.166: 159 0.166 - 0.248: 20 0.248 - 0.331: 1 0.331 - 0.414: 3 Chirality restraints: 1624 Sorted by residual: chirality pdb=" P DT C 23 " pdb=" OP1 DT C 23 " pdb=" OP2 DT C 23 " pdb=" O5' DT C 23 " both_signs ideal model delta sigma weight residual True 2.35 -2.76 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CB ILE A 927 " pdb=" CA ILE A 927 " pdb=" CG1 ILE A 927 " pdb=" CG2 ILE A 927 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" P DA C 27 " pdb=" OP1 DA C 27 " pdb=" OP2 DA C 27 " pdb=" O5' DA C 27 " both_signs ideal model delta sigma weight residual True 2.35 -2.68 -0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 1621 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 12 " 0.050 2.00e-02 2.50e+03 4.07e-02 4.96e+01 pdb=" N9 G B 12 " -0.117 2.00e-02 2.50e+03 pdb=" C8 G B 12 " 0.002 2.00e-02 2.50e+03 pdb=" N7 G B 12 " 0.011 2.00e-02 2.50e+03 pdb=" C5 G B 12 " 0.023 2.00e-02 2.50e+03 pdb=" C6 G B 12 " 0.004 2.00e-02 2.50e+03 pdb=" O6 G B 12 " -0.015 2.00e-02 2.50e+03 pdb=" N1 G B 12 " 0.012 2.00e-02 2.50e+03 pdb=" C2 G B 12 " -0.006 2.00e-02 2.50e+03 pdb=" N2 G B 12 " -0.008 2.00e-02 2.50e+03 pdb=" N3 G B 12 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G B 12 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 474 " 0.098 5.00e-02 4.00e+02 1.42e-01 3.22e+01 pdb=" N PRO A 475 " -0.245 5.00e-02 4.00e+02 pdb=" CA PRO A 475 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO A 475 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DC C 26 " 0.037 2.00e-02 2.50e+03 2.17e-02 1.06e+01 pdb=" N1 DC C 26 " -0.051 2.00e-02 2.50e+03 pdb=" C2 DC C 26 " 0.006 2.00e-02 2.50e+03 pdb=" O2 DC C 26 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC C 26 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DC C 26 " -0.001 2.00e-02 2.50e+03 pdb=" N4 DC C 26 " 0.008 2.00e-02 2.50e+03 pdb=" C5 DC C 26 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DC C 26 " 0.000 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 679 2.72 - 3.27: 9035 3.27 - 3.81: 16941 3.81 - 4.36: 20865 4.36 - 4.90: 31889 Nonbonded interactions: 79409 Sorted by model distance: nonbonded pdb=" O GLY A 736 " pdb=" OG1 THR A 740 " model vdw 2.181 3.040 nonbonded pdb=" OH TYR A 450 " pdb=" OP1 DA C 27 " model vdw 2.182 3.040 nonbonded pdb=" OD2 ASP A 618 " pdb=" OH TYR A 639 " model vdw 2.222 3.040 nonbonded pdb=" OH TYR A 5 " pdb=" O HIS A 754 " model vdw 2.273 3.040 nonbonded pdb=" O PHE A1080 " pdb=" NH1 ARG A1084 " model vdw 2.288 3.120 ... (remaining 79404 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=0.00 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: 3.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 29.110 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 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 : 0.007 0.082 9987 Z= 0.417 Angle : 1.071 21.009 13988 Z= 0.547 Chirality : 0.056 0.414 1624 Planarity : 0.008 0.142 1346 Dihedral : 19.852 151.777 4431 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.51 % Allowed : 20.08 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.26), residues: 848 helix: -0.65 (0.24), residues: 395 sheet: 0.14 (0.53), residues: 86 loop : -0.68 (0.30), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP A1136 HIS 0.015 0.002 HIS A 328 PHE 0.048 0.004 PHE A1327 TYR 0.037 0.004 TYR A 988 ARG 0.019 0.002 ARG A 967 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 79 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 450 TYR cc_start: 0.8121 (p90) cc_final: 0.7300 (p90) REVERT: A 1082 THR cc_start: 0.8102 (m) cc_final: 0.7724 (p) REVERT: A 1297 HIS cc_start: 0.8724 (m170) cc_final: 0.8414 (m-70) outliers start: 4 outliers final: 1 residues processed: 82 average time/residue: 0.2234 time to fit residues: 26.0401 Evaluate side-chains 68 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 462 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.0980 chunk 48 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 74 optimal weight: 0.0970 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.125155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.083472 restraints weight = 19595.646| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 2.82 r_work: 0.3038 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9987 Z= 0.248 Angle : 0.583 11.744 13988 Z= 0.307 Chirality : 0.039 0.183 1624 Planarity : 0.004 0.077 1346 Dihedral : 19.697 155.222 2583 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.73 % Allowed : 16.22 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.28), residues: 848 helix: 0.30 (0.25), residues: 401 sheet: 0.30 (0.56), residues: 78 loop : -0.47 (0.31), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A1136 HIS 0.005 0.001 HIS A 328 PHE 0.018 0.002 PHE A1105 TYR 0.014 0.002 TYR A 362 ARG 0.006 0.000 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8186 (mm) REVERT: A 23 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8122 (p0) REVERT: A 174 LEU cc_start: 0.6500 (OUTLIER) cc_final: 0.6023 (tt) REVERT: A 631 MET cc_start: 0.6791 (OUTLIER) cc_final: 0.6206 (tmm) REVERT: A 926 GLN cc_start: 0.8319 (mm-40) cc_final: 0.8093 (mm-40) REVERT: A 1082 THR cc_start: 0.8204 (m) cc_final: 0.7891 (p) REVERT: A 1115 ASN cc_start: 0.9262 (OUTLIER) cc_final: 0.8935 (t0) REVERT: A 1271 GLU cc_start: 0.8493 (mt-10) cc_final: 0.8284 (tm-30) REVERT: A 1297 HIS cc_start: 0.8785 (m170) cc_final: 0.8458 (m170) outliers start: 29 outliers final: 11 residues processed: 90 average time/residue: 0.2435 time to fit residues: 31.6389 Evaluate side-chains 72 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1291 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 44 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.119466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.079414 restraints weight = 19468.318| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.64 r_work: 0.2933 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9987 Z= 0.333 Angle : 0.620 11.014 13988 Z= 0.324 Chirality : 0.040 0.187 1624 Planarity : 0.004 0.061 1346 Dihedral : 19.705 155.723 2581 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.73 % Allowed : 17.89 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.28), residues: 848 helix: 0.45 (0.25), residues: 411 sheet: -0.09 (0.51), residues: 98 loop : -0.39 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1136 HIS 0.007 0.001 HIS A 328 PHE 0.028 0.002 PHE A 86 TYR 0.034 0.002 TYR A 136 ARG 0.005 0.001 ARG A 165 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 65 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.8968 (m) cc_final: 0.8764 (m) REVERT: A 11 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8471 (mm) REVERT: A 174 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6836 (tt) REVERT: A 465 MET cc_start: 0.8982 (ttp) cc_final: 0.8693 (ttp) REVERT: A 489 GLN cc_start: 0.8804 (pt0) cc_final: 0.8469 (pp30) REVERT: A 631 MET cc_start: 0.6327 (tmm) cc_final: 0.6070 (tmm) REVERT: A 1236 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8404 (mp) REVERT: A 1254 GLN cc_start: 0.8828 (pm20) cc_final: 0.8531 (pm20) outliers start: 29 outliers final: 18 residues processed: 86 average time/residue: 0.2248 time to fit residues: 27.5880 Evaluate side-chains 79 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 58 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1094 ILE Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1327 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.120289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.080788 restraints weight = 19290.283| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 2.65 r_work: 0.2962 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9987 Z= 0.194 Angle : 0.515 9.806 13988 Z= 0.272 Chirality : 0.036 0.182 1624 Planarity : 0.003 0.055 1346 Dihedral : 19.583 155.130 2581 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 3.47 % Allowed : 18.53 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.28), residues: 848 helix: 0.93 (0.26), residues: 408 sheet: 0.19 (0.57), residues: 81 loop : -0.20 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 464 HIS 0.005 0.001 HIS A 328 PHE 0.014 0.001 PHE A1327 TYR 0.016 0.001 TYR A 136 ARG 0.004 0.000 ARG A 967 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 62 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.8915 (m) cc_final: 0.8711 (m) REVERT: A 11 ILE cc_start: 0.8610 (OUTLIER) cc_final: 0.8263 (mm) REVERT: A 174 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6585 (tt) REVERT: A 465 MET cc_start: 0.8974 (ttp) cc_final: 0.8692 (ttp) REVERT: A 489 GLN cc_start: 0.8725 (pt0) cc_final: 0.8286 (pp30) REVERT: A 631 MET cc_start: 0.6324 (tmm) cc_final: 0.6030 (tmm) REVERT: A 648 MET cc_start: 0.7734 (pmm) cc_final: 0.7270 (pmm) REVERT: A 1291 LEU cc_start: 0.8860 (OUTLIER) cc_final: 0.8639 (mm) outliers start: 27 outliers final: 16 residues processed: 82 average time/residue: 0.2167 time to fit residues: 25.9219 Evaluate side-chains 77 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 58 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1327 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 11 optimal weight: 0.1980 chunk 29 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 45 optimal weight: 8.9990 chunk 80 optimal weight: 3.9990 chunk 77 optimal weight: 0.0980 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 20 optimal weight: 0.0370 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.120672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.078989 restraints weight = 19472.723| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.83 r_work: 0.2959 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9987 Z= 0.186 Angle : 0.504 9.390 13988 Z= 0.265 Chirality : 0.036 0.182 1624 Planarity : 0.003 0.053 1346 Dihedral : 19.458 154.536 2581 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.35 % Allowed : 18.92 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.29), residues: 848 helix: 1.15 (0.26), residues: 405 sheet: 0.12 (0.56), residues: 81 loop : -0.08 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 464 HIS 0.005 0.001 HIS A 328 PHE 0.011 0.001 PHE A1105 TYR 0.020 0.001 TYR A 5 ARG 0.004 0.000 ARG A 967 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 6 SER cc_start: 0.8915 (m) cc_final: 0.8708 (m) REVERT: A 11 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8143 (mm) REVERT: A 174 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.6576 (tt) REVERT: A 465 MET cc_start: 0.8974 (ttp) cc_final: 0.8687 (ttp) REVERT: A 489 GLN cc_start: 0.8710 (pt0) cc_final: 0.8354 (pp30) REVERT: A 631 MET cc_start: 0.6319 (OUTLIER) cc_final: 0.6017 (tmm) REVERT: A 1297 HIS cc_start: 0.8709 (m170) cc_final: 0.8507 (m90) REVERT: A 1304 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7666 (mt-10) outliers start: 26 outliers final: 17 residues processed: 75 average time/residue: 0.2448 time to fit residues: 27.1707 Evaluate side-chains 77 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 631 MET Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1327 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 72 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 926 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.118178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.076225 restraints weight = 19400.510| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.81 r_work: 0.2904 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9987 Z= 0.275 Angle : 0.547 9.221 13988 Z= 0.285 Chirality : 0.038 0.183 1624 Planarity : 0.004 0.050 1346 Dihedral : 19.553 155.459 2581 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.73 % Allowed : 18.92 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.29), residues: 848 helix: 1.12 (0.26), residues: 406 sheet: -0.04 (0.57), residues: 80 loop : -0.11 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.006 0.001 HIS A 328 PHE 0.014 0.002 PHE A1258 TYR 0.018 0.002 TYR A 988 ARG 0.003 0.000 ARG A 967 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 54 time to evaluate : 1.846 Fit side-chains revert: symmetry clash REVERT: A 6 SER cc_start: 0.8880 (m) cc_final: 0.8665 (m) REVERT: A 11 ILE cc_start: 0.8681 (OUTLIER) cc_final: 0.8372 (mm) REVERT: A 23 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8155 (p0) REVERT: A 174 LEU cc_start: 0.7270 (OUTLIER) cc_final: 0.6956 (tt) REVERT: A 465 MET cc_start: 0.9010 (ttp) cc_final: 0.8715 (ttp) REVERT: A 489 GLN cc_start: 0.8763 (pt0) cc_final: 0.8267 (tm-30) REVERT: A 1080 PHE cc_start: 0.2960 (m-80) cc_final: 0.2273 (m-10) REVERT: A 1236 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8331 (mp) REVERT: A 1297 HIS cc_start: 0.8804 (m170) cc_final: 0.8596 (m170) REVERT: A 1304 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7681 (mt-10) outliers start: 29 outliers final: 20 residues processed: 74 average time/residue: 0.3318 time to fit residues: 37.3574 Evaluate side-chains 77 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1327 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 971 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.115287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.074009 restraints weight = 19896.950| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 2.79 r_work: 0.2858 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.4430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 9987 Z= 0.385 Angle : 0.598 8.775 13988 Z= 0.312 Chirality : 0.040 0.195 1624 Planarity : 0.004 0.061 1346 Dihedral : 19.762 156.359 2581 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.38 % Allowed : 18.40 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.29), residues: 848 helix: 0.90 (0.26), residues: 412 sheet: -0.34 (0.57), residues: 85 loop : -0.31 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 476 HIS 0.007 0.001 HIS A 328 PHE 0.013 0.002 PHE A1258 TYR 0.017 0.002 TYR A 155 ARG 0.017 0.001 ARG A1084 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 51 time to evaluate : 1.016 Fit side-chains REVERT: A 11 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8581 (mm) REVERT: A 23 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8213 (p0) REVERT: A 174 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.7068 (tt) REVERT: A 465 MET cc_start: 0.9041 (ttp) cc_final: 0.8727 (ttp) REVERT: A 489 GLN cc_start: 0.8851 (pt0) cc_final: 0.8384 (tm-30) REVERT: A 648 MET cc_start: 0.7719 (pmm) cc_final: 0.7163 (pmm) REVERT: A 939 MET cc_start: 0.4215 (mmm) cc_final: 0.3483 (ptt) REVERT: A 1205 GLU cc_start: 0.9033 (OUTLIER) cc_final: 0.7985 (tp30) REVERT: A 1297 HIS cc_start: 0.8833 (m170) cc_final: 0.8620 (m170) REVERT: A 1304 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7727 (mt-10) outliers start: 34 outliers final: 22 residues processed: 75 average time/residue: 0.2486 time to fit residues: 28.2844 Evaluate side-chains 74 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 1.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1205 GLU Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1327 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 67 optimal weight: 0.9990 chunk 17 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1262 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.117697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.077938 restraints weight = 19579.213| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.71 r_work: 0.2924 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9987 Z= 0.180 Angle : 0.511 12.020 13988 Z= 0.267 Chirality : 0.037 0.181 1624 Planarity : 0.003 0.050 1346 Dihedral : 19.630 155.353 2581 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.60 % Allowed : 19.43 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.29), residues: 848 helix: 1.09 (0.26), residues: 405 sheet: -0.02 (0.58), residues: 81 loop : -0.10 (0.33), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 464 HIS 0.005 0.001 HIS A 328 PHE 0.010 0.001 PHE A1313 TYR 0.024 0.001 TYR A 5 ARG 0.003 0.000 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 52 time to evaluate : 1.044 Fit side-chains REVERT: A 11 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8301 (mm) REVERT: A 23 ASP cc_start: 0.8447 (OUTLIER) cc_final: 0.8135 (p0) REVERT: A 174 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6996 (tt) REVERT: A 465 MET cc_start: 0.8987 (ttp) cc_final: 0.8728 (ttp) REVERT: A 489 GLN cc_start: 0.8803 (pt0) cc_final: 0.8345 (tm-30) REVERT: A 648 MET cc_start: 0.7786 (pmm) cc_final: 0.7300 (pmm) REVERT: A 939 MET cc_start: 0.4040 (mmm) cc_final: 0.3546 (ppp) REVERT: A 1297 HIS cc_start: 0.8850 (m170) cc_final: 0.8585 (m170) REVERT: A 1304 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7728 (mt-10) outliers start: 28 outliers final: 22 residues processed: 73 average time/residue: 0.1947 time to fit residues: 21.8690 Evaluate side-chains 74 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 397 ASP Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1327 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 6 optimal weight: 2.9990 chunk 79 optimal weight: 0.0570 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.117771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.078880 restraints weight = 19430.143| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.63 r_work: 0.2928 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9987 Z= 0.207 Angle : 0.509 11.604 13988 Z= 0.266 Chirality : 0.037 0.182 1624 Planarity : 0.003 0.051 1346 Dihedral : 19.558 154.964 2581 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.60 % Allowed : 19.56 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.29), residues: 848 helix: 1.13 (0.26), residues: 408 sheet: -0.02 (0.58), residues: 81 loop : -0.04 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 464 HIS 0.005 0.001 HIS A 328 PHE 0.027 0.001 PHE A 966 TYR 0.022 0.001 TYR A 5 ARG 0.004 0.000 ARG A 976 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 50 time to evaluate : 0.840 Fit side-chains revert: symmetry clash REVERT: A 11 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8265 (mm) REVERT: A 23 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.8098 (p0) REVERT: A 174 LEU cc_start: 0.7397 (OUTLIER) cc_final: 0.7074 (tt) REVERT: A 465 MET cc_start: 0.8977 (ttp) cc_final: 0.8721 (ttp) REVERT: A 489 GLN cc_start: 0.8817 (pt0) cc_final: 0.8359 (tm-30) REVERT: A 648 MET cc_start: 0.7859 (pmm) cc_final: 0.7400 (pmm) REVERT: A 1297 HIS cc_start: 0.8848 (m170) cc_final: 0.8577 (m170) REVERT: A 1304 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7723 (mt-10) outliers start: 28 outliers final: 22 residues processed: 70 average time/residue: 0.1885 time to fit residues: 20.1235 Evaluate side-chains 74 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 49 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 357 ASN Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1327 PHE Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 15 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 74 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 chunk 64 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1286 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.117463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.076701 restraints weight = 19779.674| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.79 r_work: 0.2898 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9987 Z= 0.251 Angle : 0.526 11.535 13988 Z= 0.275 Chirality : 0.038 0.201 1624 Planarity : 0.003 0.050 1346 Dihedral : 19.581 155.358 2581 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.60 % Allowed : 19.43 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.29), residues: 848 helix: 1.09 (0.26), residues: 409 sheet: -0.22 (0.57), residues: 86 loop : -0.07 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 464 HIS 0.006 0.001 HIS A 328 PHE 0.026 0.001 PHE A 966 TYR 0.022 0.001 TYR A 5 ARG 0.005 0.000 ARG A 976 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1696 Ramachandran restraints generated. 848 Oldfield, 0 Emsley, 848 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 48 time to evaluate : 0.852 Fit side-chains REVERT: A 11 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8329 (mm) REVERT: A 23 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8106 (p0) REVERT: A 174 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.6922 (tt) REVERT: A 390 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8581 (mm) REVERT: A 465 MET cc_start: 0.9005 (ttp) cc_final: 0.8724 (ttp) REVERT: A 489 GLN cc_start: 0.8815 (pt0) cc_final: 0.8365 (tm-30) REVERT: A 648 MET cc_start: 0.7874 (pmm) cc_final: 0.7435 (pmm) REVERT: A 1297 HIS cc_start: 0.8841 (m170) cc_final: 0.8590 (m170) REVERT: A 1304 GLU cc_start: 0.8180 (mm-30) cc_final: 0.7730 (mt-10) outliers start: 28 outliers final: 21 residues processed: 70 average time/residue: 0.1623 time to fit residues: 18.1481 Evaluate side-chains 72 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 47 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 109 GLU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 651 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1275 GLU Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1291 LEU Chi-restraints excluded: chain A residue 1310 ILE Chi-restraints excluded: chain A residue 1327 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.117612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.078957 restraints weight = 19469.003| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.62 r_work: 0.2930 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9987 Z= 0.206 Angle : 0.506 11.551 13988 Z= 0.265 Chirality : 0.037 0.192 1624 Planarity : 0.003 0.051 1346 Dihedral : 19.507 155.031 2581 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 3.60 % Allowed : 19.43 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.29), residues: 848 helix: 1.19 (0.26), residues: 409 sheet: -0.15 (0.58), residues: 86 loop : 0.01 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 464 HIS 0.005 0.001 HIS A 328 PHE 0.025 0.001 PHE A 966 TYR 0.022 0.001 TYR A 5 ARG 0.003 0.000 ARG A 976 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5373.41 seconds wall clock time: 95 minutes 17.92 seconds (5717.92 seconds total)