Starting phenix.real_space_refine on Tue May 13 01:40:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t78_41087/05_2025/8t78_41087.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t78_41087/05_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_41087/05_2025/8t78_41087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t78_41087/05_2025/8t78_41087.map" model { file = "/net/cci-nas-00/data/ceres_data/8t78_41087/05_2025/8t78_41087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t78_41087/05_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-5687/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: 6.99, per 1000 atoms: 0.73 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: 2.13 Conformation dependent library (CDL) restraints added in 814.1 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: 3.65 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: 4.13 Time building geometry restraints manager: 2.54 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: 3.570 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.930 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: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.930 ------------------------------------------------------------------------------- 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= 0.287 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 Details of bonding type rmsd hydrogen bonds : bond 0.15248 ( 416) hydrogen bonds : angle 6.29289 ( 1111) covalent geometry : bond 0.00654 ( 9987) covalent geometry : angle 1.07055 (13988) *********************** 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 : 0.865 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: 0.2264 time to fit residues: 26.2286 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 : 0.876 ------------------------------------------------------------------------------- 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 = 19595.649| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.82 r_work: 0.3044 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 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= 0.175 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 Details of bonding type rmsd hydrogen bonds : bond 0.04143 ( 416) hydrogen bonds : angle 4.78012 ( 1111) covalent geometry : bond 0.00386 ( 9987) covalent geometry : angle 0.58322 (13988) *********************** 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 : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8191 (mm) REVERT: A 23 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8117 (p0) REVERT: A 174 LEU cc_start: 0.6508 (OUTLIER) cc_final: 0.6030 (tt) REVERT: A 631 MET cc_start: 0.6810 (OUTLIER) cc_final: 0.6221 (tmm) REVERT: A 926 GLN cc_start: 0.8318 (mm-40) cc_final: 0.8087 (mm-40) REVERT: A 1082 THR cc_start: 0.8202 (m) cc_final: 0.7889 (p) REVERT: A 1115 ASN cc_start: 0.9258 (OUTLIER) cc_final: 0.8931 (t0) REVERT: A 1297 HIS cc_start: 0.8776 (m170) cc_final: 0.8452 (m170) outliers start: 29 outliers final: 11 residues processed: 90 average time/residue: 0.2198 time to fit residues: 28.2812 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 : 0.943 ------------------------------------------------------------------------------- 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: 3.9990 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: 0.9980 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: 1.9986 ------------------------------------------------------------------------------- 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** A1241 HIS A1261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.118135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.078049 restraints weight = 19465.013| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.65 r_work: 0.2904 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 9987 Z= 0.292 Angle : 0.672 11.112 13988 Z= 0.350 Chirality : 0.042 0.194 1624 Planarity : 0.005 0.060 1346 Dihedral : 19.857 156.073 2581 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.86 % Allowed : 18.02 % Favored : 78.12 % 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: -0.18 (0.28), residues: 848 helix: 0.32 (0.25), residues: 410 sheet: -0.15 (0.52), residues: 98 loop : -0.48 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A1136 HIS 0.008 0.001 HIS A 328 PHE 0.029 0.002 PHE A 86 TYR 0.038 0.002 TYR A 136 ARG 0.006 0.001 ARG A 165 Details of bonding type rmsd hydrogen bonds : bond 0.05040 ( 416) hydrogen bonds : angle 4.76632 ( 1111) covalent geometry : bond 0.00657 ( 9987) covalent geometry : angle 0.67166 (13988) *********************** 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 90 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.8912 (OUTLIER) cc_final: 0.8593 (mm) REVERT: A 174 LEU cc_start: 0.7277 (OUTLIER) cc_final: 0.7035 (tt) REVERT: A 465 MET cc_start: 0.9023 (ttp) cc_final: 0.8739 (ttp) REVERT: A 489 GLN cc_start: 0.8849 (pt0) cc_final: 0.8514 (pp30) REVERT: A 631 MET cc_start: 0.6504 (tmm) cc_final: 0.6241 (tmm) REVERT: A 939 MET cc_start: 0.4013 (mmm) cc_final: 0.3635 (mtt) REVERT: A 1236 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8433 (mp) REVERT: A 1266 LEU cc_start: 0.8821 (tt) cc_final: 0.8601 (mt) outliers start: 30 outliers final: 18 residues processed: 83 average time/residue: 0.2275 time to fit residues: 26.3315 Evaluate side-chains 72 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 51 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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: 2.9990 chunk 61 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 980 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.120212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.080666 restraints weight = 19216.018| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.63 r_work: 0.2963 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3422 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= 0.126 Angle : 0.508 9.547 13988 Z= 0.268 Chirality : 0.036 0.181 1624 Planarity : 0.004 0.054 1346 Dihedral : 19.630 155.126 2581 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.60 % Allowed : 18.02 % 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: 0.48 (0.28), residues: 848 helix: 0.95 (0.26), residues: 404 sheet: -0.07 (0.56), residues: 86 loop : -0.18 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 464 HIS 0.005 0.001 HIS A 328 PHE 0.014 0.001 PHE A1105 TYR 0.018 0.001 TYR A 5 ARG 0.007 0.000 ARG A1337 Details of bonding type rmsd hydrogen bonds : bond 0.03589 ( 416) hydrogen bonds : angle 4.42616 ( 1111) covalent geometry : bond 0.00273 ( 9987) covalent geometry : angle 0.50784 (13988) *********************** 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 90 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 62 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8241 (mm) REVERT: A 174 LEU cc_start: 0.7049 (OUTLIER) cc_final: 0.6625 (tt) REVERT: A 465 MET cc_start: 0.8971 (ttp) cc_final: 0.8677 (ttp) REVERT: A 489 GLN cc_start: 0.8734 (pt0) cc_final: 0.8370 (pp30) REVERT: A 631 MET cc_start: 0.6405 (OUTLIER) cc_final: 0.6090 (tmm) REVERT: A 738 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8121 (mm) REVERT: A 1225 GLU cc_start: 0.8150 (mt-10) cc_final: 0.7546 (mt-10) outliers start: 28 outliers final: 15 residues processed: 82 average time/residue: 0.2144 time to fit residues: 25.5755 Evaluate side-chains 76 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 57 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 404 THR Chi-restraints excluded: chain A residue 432 PHE 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 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 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: 3.9990 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 0.0970 chunk 46 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 45 optimal weight: 0.4980 chunk 80 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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** ** A1297 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 = 0.3810 r_free = 0.3810 target = 0.119350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.079540 restraints weight = 19221.814| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.68 r_work: 0.2958 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.3703 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= 0.130 Angle : 0.504 9.154 13988 Z= 0.264 Chirality : 0.036 0.182 1624 Planarity : 0.003 0.053 1346 Dihedral : 19.469 154.338 2581 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.35 % Allowed : 19.31 % 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: 0.74 (0.29), residues: 848 helix: 1.14 (0.26), residues: 409 sheet: 0.04 (0.57), residues: 81 loop : -0.05 (0.32), residues: 358 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 A1258 TYR 0.014 0.001 TYR A 988 ARG 0.004 0.000 ARG A1337 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 416) hydrogen bonds : angle 4.27735 ( 1111) covalent geometry : bond 0.00285 ( 9987) covalent geometry : angle 0.50404 (13988) *********************** 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 81 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 55 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 11 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8113 (mm) REVERT: A 174 LEU cc_start: 0.7027 (OUTLIER) cc_final: 0.6600 (tt) REVERT: A 465 MET cc_start: 0.8962 (ttp) cc_final: 0.8676 (ttp) REVERT: A 489 GLN cc_start: 0.8729 (pt0) cc_final: 0.8195 (tm-30) REVERT: A 631 MET cc_start: 0.6304 (tmm) cc_final: 0.5999 (tmm) REVERT: A 648 MET cc_start: 0.7757 (pmm) cc_final: 0.7218 (pmm) REVERT: A 1304 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7739 (pt0) outliers start: 26 outliers final: 19 residues processed: 74 average time/residue: 0.2079 time to fit residues: 22.5562 Evaluate side-chains 76 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 55 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE 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 623 LEU Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 738 LEU 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 1087 LEU 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 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: 2.9990 chunk 90 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 68 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 73 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.118417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.076445 restraints weight = 19441.050| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.82 r_work: 0.2906 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9987 Z= 0.175 Angle : 0.529 8.952 13988 Z= 0.277 Chirality : 0.037 0.182 1624 Planarity : 0.004 0.052 1346 Dihedral : 19.522 155.267 2581 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.25 % Allowed : 19.05 % Favored : 76.71 % 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: 0.68 (0.29), residues: 848 helix: 1.16 (0.26), residues: 408 sheet: -0.25 (0.56), residues: 86 loop : -0.08 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 PHE 0.012 0.001 PHE A 643 TYR 0.015 0.001 TYR A 155 ARG 0.011 0.001 ARG A1084 Details of bonding type rmsd hydrogen bonds : bond 0.03815 ( 416) hydrogen bonds : angle 4.31116 ( 1111) covalent geometry : bond 0.00388 ( 9987) covalent geometry : angle 0.52941 (13988) *********************** 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 89 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 56 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 11 ILE cc_start: 0.8616 (OUTLIER) cc_final: 0.8303 (mm) REVERT: A 23 ASP cc_start: 0.8504 (OUTLIER) cc_final: 0.8169 (p0) REVERT: A 174 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.6903 (tt) REVERT: A 465 MET cc_start: 0.9005 (ttp) cc_final: 0.8727 (ttp) REVERT: A 489 GLN cc_start: 0.8739 (pt0) cc_final: 0.8244 (tm-30) REVERT: A 1304 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7670 (mt-10) outliers start: 33 outliers final: 23 residues processed: 78 average time/residue: 0.2276 time to fit residues: 27.0004 Evaluate side-chains 79 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 53 time to evaluate : 0.904 ------------------------------------------------------------------------------- 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 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 639 TYR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 LEU 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 1087 LEU 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 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: 3.9990 chunk 7 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 39 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 overall best weight: 1.3742 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.116437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.077272 restraints weight = 19592.352| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.64 r_work: 0.2897 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9987 Z= 0.200 Angle : 0.552 12.902 13988 Z= 0.287 Chirality : 0.038 0.183 1624 Planarity : 0.004 0.050 1346 Dihedral : 19.623 155.764 2581 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 4.25 % Allowed : 19.31 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.12 (0.26), residues: 406 sheet: -0.23 (0.57), residues: 86 loop : -0.10 (0.33), residues: 356 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 0.027 0.002 PHE A 966 TYR 0.017 0.001 TYR A 988 ARG 0.005 0.000 ARG A 976 Details of bonding type rmsd hydrogen bonds : bond 0.04008 ( 416) hydrogen bonds : angle 4.36472 ( 1111) covalent geometry : bond 0.00446 ( 9987) covalent geometry : angle 0.55171 (13988) *********************** 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: 33 poor density : 52 time to evaluate : 0.862 Fit side-chains REVERT: A 11 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8480 (mm) REVERT: A 23 ASP cc_start: 0.8461 (OUTLIER) cc_final: 0.8150 (p0) REVERT: A 161 MET cc_start: 0.9230 (mtt) cc_final: 0.8955 (mtt) REVERT: A 174 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6936 (tt) REVERT: A 489 GLN cc_start: 0.8841 (pt0) cc_final: 0.8367 (tm-30) REVERT: A 648 MET cc_start: 0.7803 (pmm) cc_final: 0.7332 (pmm) REVERT: A 1205 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.7910 (tp30) REVERT: A 1304 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7746 (mt-10) outliers start: 33 outliers final: 23 residues processed: 76 average time/residue: 0.1984 time to fit residues: 22.4788 Evaluate side-chains 77 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 50 time to evaluate : 0.956 ------------------------------------------------------------------------------- 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 376 ILE 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 639 TYR Chi-restraints excluded: chain A residue 730 SER Chi-restraints excluded: chain A residue 738 LEU 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 1205 GLU 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 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: 0.2980 chunk 17 optimal weight: 10.0000 chunk 61 optimal weight: 3.9990 chunk 80 optimal weight: 0.6980 chunk 28 optimal weight: 0.1980 chunk 51 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** ** A1297 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 = 0.3800 r_free = 0.3800 target = 0.119311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.078481 restraints weight = 19737.389| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.80 r_work: 0.2940 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9987 Z= 0.114 Angle : 0.496 11.595 13988 Z= 0.258 Chirality : 0.036 0.179 1624 Planarity : 0.003 0.051 1346 Dihedral : 19.510 154.799 2581 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.22 % Allowed : 20.33 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.83 (0.29), residues: 848 helix: 1.26 (0.26), residues: 407 sheet: -0.18 (0.57), residues: 86 loop : 0.05 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 464 HIS 0.004 0.001 HIS A 328 PHE 0.023 0.001 PHE A 966 TYR 0.012 0.001 TYR A 155 ARG 0.004 0.000 ARG A1084 Details of bonding type rmsd hydrogen bonds : bond 0.03446 ( 416) hydrogen bonds : angle 4.21024 ( 1111) covalent geometry : bond 0.00244 ( 9987) covalent geometry : angle 0.49616 (13988) *********************** 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 76 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 51 time to evaluate : 0.903 Fit side-chains REVERT: A 11 ILE cc_start: 0.8547 (OUTLIER) cc_final: 0.8184 (mm) REVERT: A 23 ASP cc_start: 0.8426 (OUTLIER) cc_final: 0.8129 (p0) REVERT: A 174 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6939 (tt) REVERT: A 465 MET cc_start: 0.8951 (ttp) cc_final: 0.8692 (ttp) REVERT: A 489 GLN cc_start: 0.8777 (pt0) cc_final: 0.8323 (tm-30) REVERT: A 648 MET cc_start: 0.7824 (pmm) cc_final: 0.7362 (pmm) REVERT: A 939 MET cc_start: 0.4482 (mmm) cc_final: 0.3390 (ppp) REVERT: A 1304 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7719 (mt-10) REVERT: A 1327 PHE cc_start: 0.8034 (OUTLIER) cc_final: 0.7623 (m-80) outliers start: 25 outliers final: 17 residues processed: 68 average time/residue: 0.1856 time to fit residues: 19.2295 Evaluate side-chains 69 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 48 time to evaluate : 0.834 ------------------------------------------------------------------------------- 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 23 ASP Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 174 LEU 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 469 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1145 VAL 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 Chi-restraints excluded: chain A residue 1327 PHE Chi-restraints excluded: chain A residue 1329 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 6 optimal weight: 1.9990 chunk 79 optimal weight: 0.0670 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 43 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 overall best weight: 0.8722 ------------------------------------------------------------------------------- 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** ** A1297 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 = 0.3787 r_free = 0.3787 target = 0.118457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.077572 restraints weight = 19612.512| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.80 r_work: 0.2920 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4571 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= 0.144 Angle : 0.504 11.765 13988 Z= 0.262 Chirality : 0.036 0.180 1624 Planarity : 0.003 0.051 1346 Dihedral : 19.474 154.776 2581 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.35 % Allowed : 20.21 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.88 (0.29), residues: 848 helix: 1.36 (0.26), residues: 405 sheet: -0.20 (0.57), residues: 86 loop : 0.02 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 PHE 0.022 0.001 PHE A 966 TYR 0.013 0.001 TYR A 155 ARG 0.004 0.000 ARG A 976 Details of bonding type rmsd hydrogen bonds : bond 0.03577 ( 416) hydrogen bonds : angle 4.18664 ( 1111) covalent geometry : bond 0.00319 ( 9987) covalent geometry : angle 0.50366 (13988) *********************** 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 74 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 48 time to evaluate : 0.853 Fit side-chains REVERT: A 11 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8220 (mm) REVERT: A 23 ASP cc_start: 0.8373 (OUTLIER) cc_final: 0.8074 (p0) REVERT: A 174 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7006 (tt) REVERT: A 465 MET cc_start: 0.8976 (ttp) cc_final: 0.8718 (ttp) REVERT: A 489 GLN cc_start: 0.8795 (pt0) cc_final: 0.8342 (tm-30) REVERT: A 648 MET cc_start: 0.7896 (pmm) cc_final: 0.7485 (pmm) REVERT: A 939 MET cc_start: 0.4624 (mmm) cc_final: 0.3544 (ppp) REVERT: A 1205 GLU cc_start: 0.8973 (OUTLIER) cc_final: 0.7896 (tp30) REVERT: A 1304 GLU cc_start: 0.8171 (mm-30) cc_final: 0.7723 (mt-10) outliers start: 26 outliers final: 21 residues processed: 68 average time/residue: 0.1869 time to fit residues: 19.3135 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 : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 21 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 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 469 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 639 TYR 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 1145 VAL Chi-restraints excluded: chain A residue 1205 GLU 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 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: 0.5980 chunk 53 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 75 optimal weight: 0.2980 chunk 77 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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** ** A1297 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 = 0.3781 r_free = 0.3781 target = 0.117704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.079038 restraints weight = 19570.852| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.63 r_work: 0.2931 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4659 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= 0.149 Angle : 0.507 11.587 13988 Z= 0.264 Chirality : 0.037 0.180 1624 Planarity : 0.003 0.050 1346 Dihedral : 19.469 154.991 2581 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.47 % Allowed : 20.33 % Favored : 76.19 % 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: 0.92 (0.29), residues: 848 helix: 1.41 (0.26), residues: 403 sheet: -0.20 (0.57), residues: 86 loop : 0.02 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 PHE 0.021 0.001 PHE A 966 TYR 0.014 0.001 TYR A 155 ARG 0.005 0.000 ARG A 976 Details of bonding type rmsd hydrogen bonds : bond 0.03606 ( 416) hydrogen bonds : angle 4.20621 ( 1111) covalent geometry : bond 0.00331 ( 9987) covalent geometry : angle 0.50694 (13988) ********************** 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: 27 poor density : 49 time to evaluate : 0.848 Fit side-chains REVERT: A 11 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8269 (mm) REVERT: A 23 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.8024 (p0) REVERT: A 174 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.6935 (tt) REVERT: A 390 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8589 (mm) REVERT: A 465 MET cc_start: 0.8980 (ttp) cc_final: 0.8713 (ttp) REVERT: A 489 GLN cc_start: 0.8805 (pt0) cc_final: 0.8353 (tm-30) REVERT: A 939 MET cc_start: 0.4667 (mmm) cc_final: 0.3771 (ppp) REVERT: A 1205 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.7907 (tp30) REVERT: A 1304 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7738 (mt-10) REVERT: A 1327 PHE cc_start: 0.8111 (OUTLIER) cc_final: 0.7686 (m-80) outliers start: 27 outliers final: 19 residues processed: 70 average time/residue: 0.1620 time to fit residues: 17.9317 Evaluate side-chains 73 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 48 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 21 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 357 ASN 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 469 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 639 TYR 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 1145 VAL Chi-restraints excluded: chain A residue 1205 GLU 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 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: 0.7980 chunk 72 optimal weight: 6.9990 chunk 30 optimal weight: 0.0470 chunk 13 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.9480 ------------------------------------------------------------------------------- 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 ** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.117611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.078951 restraints weight = 19437.191| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.62 r_work: 0.2929 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.4756 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= 0.151 Angle : 0.511 11.602 13988 Z= 0.266 Chirality : 0.037 0.186 1624 Planarity : 0.003 0.050 1346 Dihedral : 19.459 154.981 2581 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.60 % Allowed : 20.08 % Favored : 76.32 % 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: 0.93 (0.29), residues: 848 helix: 1.36 (0.26), residues: 408 sheet: -0.18 (0.58), residues: 86 loop : 0.08 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 PHE 0.021 0.002 PHE A 966 TYR 0.013 0.001 TYR A 155 ARG 0.004 0.000 ARG A 976 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 416) hydrogen bonds : angle 4.20258 ( 1111) covalent geometry : bond 0.00336 ( 9987) covalent geometry : angle 0.51087 (13988) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5274.81 seconds wall clock time: 92 minutes 5.92 seconds (5525.92 seconds total)