Starting phenix.real_space_refine on Wed Aug 5 11:05:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t78_41087/08_2026/8t78_41087.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t78_41087/08_2026/8t78_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_41087/08_2026/8t78_41087.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t78_41087/08_2026/8t78_41087.map" model { file = "/net/cci-nas-00/data/ceres_data/8t78_41087/08_2026/8t78_41087.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t78_41087/08_2026/8t78_41087.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/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: 2.07, per 1000 atoms: 0.22 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: 0.89 Conformation dependent library (CDL) restraints added in 177.6 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: 1.56 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: 2.13 Time building geometry restraints manager: 1.06 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=" C1' DC C 24 " pdb=" N1 DC C 24 " ideal model delta sigma weight residual 1.468 1.520 -0.052 1.40e-02 5.10e+03 1.38e+01 bond pdb=" N9 A B 15 " pdb=" C4 A B 15 " ideal model delta sigma weight residual 1.374 1.353 0.021 6.00e-03 2.78e+04 1.18e+01 bond pdb=" C1' DT C 25 " pdb=" N1 DT C 25 " ideal model delta sigma weight residual 1.468 1.515 -0.047 1.40e-02 5.10e+03 1.12e+01 bond pdb=" C3' DA C 27 " pdb=" C2' DA C 27 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DT C 25 " pdb=" C2' DT C 25 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.48e+00 ... (remaining 9982 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 13859 4.20 - 8.40: 106 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=" O4' DC C 26 " pdb=" C1' DC C 26 " pdb=" N1 DC C 26 " ideal model delta sigma weight residual 108.00 112.67 -4.67 7.00e-01 2.04e+00 4.46e+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=" O4' DA C 27 " pdb=" C1' DA C 27 " pdb=" N9 DA C 27 " ideal model delta sigma weight residual 108.00 103.61 4.39 7.00e-01 2.04e+00 3.94e+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 ... (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 - 0.085: 1358 0.085 - 0.170: 242 0.170 - 0.255: 20 0.255 - 0.339: 2 0.339 - 0.424: 2 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 2.34 -2.76 -0.42 2.00e-01 2.50e+01 4.50e+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 2.34 -2.68 -0.34 2.00e-01 2.50e+01 2.95e+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 ... (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: 5.430 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.500 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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= 0.406 Angle : 1.135 21.009 13988 Z= 0.726 Chirality : 0.064 0.424 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (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 ARG 0.019 0.002 ARG A 967 TYR 0.037 0.004 TYR A 988 PHE 0.048 0.004 PHE A1327 TRP 0.026 0.003 TRP A1136 HIS 0.015 0.002 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.41 ( 9987) covalent geometry : angle 1.13489 / 0.73 (13988) hydrogen bonds : bond 0.15248 / 9.88 ( 416) hydrogen bonds : angle 6.29289 / 4.43 ( 1111) *********************** 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 : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash 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: 0.0887 time to fit residues: 10.6012 Evaluate side-chains 69 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.198 ------------------------------------------------------------------------------- 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 49 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.0980 chunk 62 optimal weight: 0.1980 chunk 51 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 9.9990 chunk 74 optimal weight: 0.0570 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.129940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.088299 restraints weight = 19699.745| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.87 r_work: 0.3130 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.0937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9987 Z= 0.130 Angle : 0.603 13.317 13988 Z= 0.327 Chirality : 0.041 0.257 1624 Planarity : 0.004 0.080 1346 Dihedral : 19.932 151.955 2583 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.96 % Allowed : 16.86 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.27), residues: 848 helix: 0.05 (0.25), residues: 405 sheet: -0.04 (0.53), residues: 86 loop : -0.50 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1171 TYR 0.013 0.001 TYR A1237 PHE 0.016 0.001 PHE A1105 TRP 0.012 0.001 TRP A1136 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 ( 9987) covalent geometry : angle 0.60274 / 0.33 (13988) hydrogen bonds : bond 0.04920 / 3.30 ( 416) hydrogen bonds : angle 5.04513 / 3.66 ( 1111) *********************** 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 92 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 23 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7962 (p0) REVERT: A 631 MET cc_start: 0.7022 (OUTLIER) cc_final: 0.6717 (tmm) REVERT: A 958 LEU cc_start: 0.8135 (tp) cc_final: 0.7598 (mp) REVERT: A 1082 THR cc_start: 0.8047 (m) cc_final: 0.7709 (p) REVERT: A 1115 ASN cc_start: 0.9237 (OUTLIER) cc_final: 0.8871 (t0) REVERT: A 1268 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8160 (pt0) REVERT: A 1297 HIS cc_start: 0.8745 (m170) cc_final: 0.8352 (m-70) REVERT: A 1304 GLU cc_start: 0.7854 (mp0) cc_final: 0.7344 (pt0) outliers start: 23 outliers final: 10 residues processed: 88 average time/residue: 0.0616 time to fit residues: 8.2437 Evaluate side-chains 76 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 63 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASP Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 462 PHE Chi-restraints excluded: chain A residue 631 MET 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 1087 LEU Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1256 GLN 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 43 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 24 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 92 optimal weight: 10.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3846 r_free = 0.3846 target = 0.121991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.079525 restraints weight = 19587.802| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 2.81 r_work: 0.2969 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 9987 Z= 0.284 Angle : 0.676 10.403 13988 Z= 0.361 Chirality : 0.045 0.252 1624 Planarity : 0.005 0.069 1346 Dihedral : 19.782 153.467 2583 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.09 % Allowed : 17.12 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.25 (0.27), residues: 848 helix: 0.24 (0.25), residues: 403 sheet: 0.02 (0.52), residues: 98 loop : -0.55 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 976 TYR 0.027 0.002 TYR A 362 PHE 0.036 0.003 PHE A1105 TRP 0.011 0.002 TRP A1136 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00633 / 0.28 ( 9987) covalent geometry : angle 0.67638 / 0.36 (13988) hydrogen bonds : bond 0.05614 / 3.71 ( 416) hydrogen bonds : angle 4.88712 / 3.59 ( 1111) *********************** 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: 24 poor density : 66 time to evaluate : 0.221 Fit side-chains revert: symmetry clash REVERT: A 11 ILE cc_start: 0.8809 (OUTLIER) cc_final: 0.8375 (mm) REVERT: A 23 ASP cc_start: 0.8467 (OUTLIER) cc_final: 0.8170 (p0) REVERT: A 1082 THR cc_start: 0.8308 (m) cc_final: 0.8017 (p) REVERT: A 1115 ASN cc_start: 0.9249 (OUTLIER) cc_final: 0.8969 (t0) REVERT: A 1177 ASN cc_start: 0.8781 (t0) cc_final: 0.8279 (t0) REVERT: A 1236 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8415 (mp) REVERT: A 1256 GLN cc_start: 0.8814 (tp-100) cc_final: 0.8209 (tp40) REVERT: A 1271 GLU cc_start: 0.8545 (mt-10) cc_final: 0.8321 (tm-30) REVERT: A 1297 HIS cc_start: 0.8777 (m170) cc_final: 0.8452 (m170) REVERT: A 1303 ARG cc_start: 0.7356 (ttt180) cc_final: 0.6421 (ttm170) REVERT: A 1304 GLU cc_start: 0.8059 (mp0) cc_final: 0.7794 (pt0) REVERT: A 1325 LYS cc_start: 0.8358 (tppt) cc_final: 0.8105 (tppp) outliers start: 24 outliers final: 14 residues processed: 86 average time/residue: 0.0816 time to fit residues: 9.9994 Evaluate side-chains 79 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 109 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 340 ARG Chi-restraints excluded: chain A residue 376 ILE 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 986 ASP Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1270 ILE 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 49 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 0.0970 chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 59 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 HIS A 926 GLN A1241 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.124134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.083220 restraints weight = 19617.358| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.70 r_work: 0.3027 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9987 Z= 0.118 Angle : 0.524 9.433 13988 Z= 0.286 Chirality : 0.038 0.239 1624 Planarity : 0.004 0.059 1346 Dihedral : 19.764 152.443 2581 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.70 % Allowed : 18.40 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.28), residues: 848 helix: 0.82 (0.26), residues: 394 sheet: -0.05 (0.51), residues: 98 loop : -0.31 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 165 TYR 0.013 0.001 TYR A 155 PHE 0.014 0.001 PHE A1105 TRP 0.008 0.001 TRP A 464 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 ( 9987) covalent geometry : angle 0.52418 / 0.29 (13988) hydrogen bonds : bond 0.04157 / 2.79 ( 416) hydrogen bonds : angle 4.64110 / 3.38 ( 1111) *********************** 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 83 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.8617 (OUTLIER) cc_final: 0.8217 (mm) REVERT: A 23 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8080 (p0) REVERT: A 174 LEU cc_start: 0.6604 (OUTLIER) cc_final: 0.6204 (tt) REVERT: A 450 TYR cc_start: 0.8286 (p90) cc_final: 0.7528 (p90) REVERT: A 631 MET cc_start: 0.6835 (OUTLIER) cc_final: 0.6456 (tmm) REVERT: A 1082 THR cc_start: 0.8343 (m) cc_final: 0.8076 (p) REVERT: A 1115 ASN cc_start: 0.9205 (OUTLIER) cc_final: 0.8923 (t0) REVERT: A 1177 ASN cc_start: 0.8626 (t0) cc_final: 0.8022 (t0) REVERT: A 1188 LYS cc_start: 0.8866 (mmtm) cc_final: 0.8626 (mmtm) REVERT: A 1225 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7699 (mt-10) REVERT: A 1271 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8264 (tm-30) outliers start: 21 outliers final: 10 residues processed: 79 average time/residue: 0.0746 time to fit residues: 8.6274 Evaluate side-chains 71 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 376 ILE Chi-restraints excluded: chain A residue 432 PHE 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 953 VAL Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1115 ASN Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1291 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 0.5980 chunk 20 optimal weight: 0.0070 chunk 7 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 89 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 93 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3874 r_free = 0.3874 target = 0.123892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.081878 restraints weight = 19855.242| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.82 r_work: 0.3007 rms_B_bonded: 4.27 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9987 Z= 0.122 Angle : 0.510 8.756 13988 Z= 0.276 Chirality : 0.037 0.226 1624 Planarity : 0.003 0.054 1346 Dihedral : 19.626 152.735 2581 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.70 % Allowed : 19.05 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.28), residues: 848 helix: 1.08 (0.26), residues: 394 sheet: 0.03 (0.51), residues: 93 loop : -0.22 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 967 TYR 0.013 0.001 TYR A 155 PHE 0.019 0.001 PHE A 972 TRP 0.006 0.001 TRP A 464 HIS 0.004 0.001 HIS A1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 ( 9987) covalent geometry : angle 0.51001 / 0.28 (13988) hydrogen bonds : bond 0.03981 / 2.69 ( 416) hydrogen bonds : angle 4.54493 / 3.31 ( 1111) *********************** 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: 21 poor density : 62 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 11 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8188 (mm) REVERT: A 23 ASP cc_start: 0.8513 (OUTLIER) cc_final: 0.8123 (p0) REVERT: A 174 LEU cc_start: 0.6586 (OUTLIER) cc_final: 0.6173 (tt) REVERT: A 450 TYR cc_start: 0.8300 (p90) cc_final: 0.7530 (p90) REVERT: A 631 MET cc_start: 0.6696 (OUTLIER) cc_final: 0.6326 (tmm) REVERT: A 1082 THR cc_start: 0.8402 (m) cc_final: 0.8157 (p) REVERT: A 1084 ARG cc_start: 0.7142 (mpt180) cc_final: 0.6740 (ttm-80) REVERT: A 1115 ASN cc_start: 0.9176 (OUTLIER) cc_final: 0.8920 (t0) REVERT: A 1177 ASN cc_start: 0.8662 (t0) cc_final: 0.8091 (t0) REVERT: A 1188 LYS cc_start: 0.8928 (mmtm) cc_final: 0.8678 (mmtm) REVERT: A 1225 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7632 (mt-10) REVERT: A 1254 GLN cc_start: 0.8715 (pm20) cc_final: 0.8463 (pm20) REVERT: A 1271 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8320 (tm-30) REVERT: A 1304 GLU cc_start: 0.8186 (mp0) cc_final: 0.7779 (pt0) outliers start: 21 outliers final: 13 residues processed: 78 average time/residue: 0.0807 time to fit residues: 9.3083 Evaluate side-chains 77 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.284 ------------------------------------------------------------------------------- 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 376 ILE Chi-restraints excluded: chain A residue 432 PHE 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 953 VAL 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 1115 ASN Chi-restraints excluded: chain A residue 1145 VAL Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1291 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 19 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 980 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.119825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.077583 restraints weight = 19815.448| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.80 r_work: 0.2929 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 9987 Z= 0.215 Angle : 0.580 8.629 13988 Z= 0.309 Chirality : 0.041 0.229 1624 Planarity : 0.004 0.054 1346 Dihedral : 19.633 153.025 2581 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.28), residues: 848 helix: 0.99 (0.26), residues: 401 sheet: -0.24 (0.50), residues: 98 loop : -0.31 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 976 TYR 0.031 0.002 TYR A 136 PHE 0.021 0.002 PHE A 643 TRP 0.006 0.001 TRP A 476 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.21 ( 9987) covalent geometry : angle 0.58031 / 0.31 (13988) hydrogen bonds : bond 0.04553 / 3.01 ( 416) hydrogen bonds : angle 4.57990 / 3.34 ( 1111) *********************** 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 87 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 60 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 11 ILE cc_start: 0.8743 (OUTLIER) cc_final: 0.8395 (mm) REVERT: A 23 ASP cc_start: 0.8560 (OUTLIER) cc_final: 0.8168 (p0) REVERT: A 174 LEU cc_start: 0.6907 (OUTLIER) cc_final: 0.6568 (tt) REVERT: A 450 TYR cc_start: 0.8347 (p90) cc_final: 0.7579 (p90) REVERT: A 465 MET cc_start: 0.9106 (ttp) cc_final: 0.8809 (ttp) REVERT: A 489 GLN cc_start: 0.8742 (pt0) cc_final: 0.8364 (pp30) REVERT: A 631 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.6302 (tmm) REVERT: A 1084 ARG cc_start: 0.7173 (mpt180) cc_final: 0.6823 (ttm-80) REVERT: A 1115 ASN cc_start: 0.9212 (OUTLIER) cc_final: 0.9010 (t0) REVERT: A 1177 ASN cc_start: 0.8685 (t0) cc_final: 0.8143 (t0) REVERT: A 1236 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8186 (mp) REVERT: A 1254 GLN cc_start: 0.8751 (pm20) cc_final: 0.8484 (pm20) REVERT: A 1297 HIS cc_start: 0.8798 (m170) cc_final: 0.8464 (m170) REVERT: A 1304 GLU cc_start: 0.8264 (mp0) cc_final: 0.7948 (pt0) outliers start: 27 outliers final: 14 residues processed: 82 average time/residue: 0.0799 time to fit residues: 9.7704 Evaluate side-chains 78 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 58 time to evaluate : 0.205 ------------------------------------------------------------------------------- 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 376 ILE Chi-restraints excluded: chain A residue 432 PHE 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 953 VAL Chi-restraints excluded: chain A residue 986 ASP Chi-restraints excluded: chain A residue 1087 LEU 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 1236 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1291 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 87 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 926 GLN A1261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.120738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.078981 restraints weight = 19793.954| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.78 r_work: 0.2954 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2988 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= 0.147 Angle : 0.517 11.321 13988 Z= 0.279 Chirality : 0.038 0.225 1624 Planarity : 0.004 0.053 1346 Dihedral : 19.651 152.887 2581 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.47 % Allowed : 18.92 % Favored : 77.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.29), residues: 848 helix: 1.24 (0.26), residues: 394 sheet: -0.17 (0.51), residues: 98 loop : -0.14 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 967 TYR 0.021 0.001 TYR A 136 PHE 0.015 0.001 PHE A1327 TRP 0.007 0.001 TRP A 464 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.15 ( 9987) covalent geometry : angle 0.51677 / 0.28 (13988) hydrogen bonds : bond 0.03962 / 2.66 ( 416) hydrogen bonds : angle 4.46729 / 3.25 ( 1111) *********************** 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 84 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 11 ILE cc_start: 0.8665 (OUTLIER) cc_final: 0.8313 (mm) REVERT: A 23 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.8127 (p0) REVERT: A 174 LEU cc_start: 0.6899 (OUTLIER) cc_final: 0.6558 (tt) REVERT: A 450 TYR cc_start: 0.8298 (p90) cc_final: 0.8076 (p90) REVERT: A 465 MET cc_start: 0.9053 (ttp) cc_final: 0.8740 (ttp) REVERT: A 489 GLN cc_start: 0.8710 (pt0) cc_final: 0.8357 (pp30) REVERT: A 631 MET cc_start: 0.6672 (OUTLIER) cc_final: 0.6335 (tmm) REVERT: A 1177 ASN cc_start: 0.8639 (t0) cc_final: 0.8073 (t0) REVERT: A 1236 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8294 (mp) REVERT: A 1254 GLN cc_start: 0.8738 (pm20) cc_final: 0.8468 (pm20) REVERT: A 1297 HIS cc_start: 0.8782 (m170) cc_final: 0.8447 (m170) REVERT: A 1304 GLU cc_start: 0.8231 (mp0) cc_final: 0.7927 (pt0) outliers start: 27 outliers final: 17 residues processed: 78 average time/residue: 0.0824 time to fit residues: 9.4086 Evaluate side-chains 78 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 56 time to evaluate : 0.229 ------------------------------------------------------------------------------- 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 339 VAL Chi-restraints excluded: chain A residue 376 ILE Chi-restraints excluded: chain A residue 432 PHE Chi-restraints excluded: chain A residue 631 MET 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 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 1225 GLU Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1291 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 16 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 85 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 92 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 407 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.118715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.078054 restraints weight = 19310.562| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.64 r_work: 0.2928 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9987 Z= 0.192 Angle : 0.555 11.111 13988 Z= 0.296 Chirality : 0.040 0.222 1624 Planarity : 0.004 0.052 1346 Dihedral : 19.648 153.191 2581 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.35 % Allowed : 18.79 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.29), residues: 848 helix: 1.10 (0.26), residues: 408 sheet: -0.27 (0.50), residues: 98 loop : -0.23 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 967 TYR 0.029 0.002 TYR A 136 PHE 0.018 0.002 PHE A1327 TRP 0.005 0.001 TRP A 476 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.19 ( 9987) covalent geometry : angle 0.55544 / 0.30 (13988) hydrogen bonds : bond 0.04338 / 2.89 ( 416) hydrogen bonds : angle 4.47289 / 3.26 ( 1111) *********************** 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 84 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.330 Fit side-chains REVERT: A 11 ILE cc_start: 0.8737 (OUTLIER) cc_final: 0.8403 (mm) REVERT: A 23 ASP cc_start: 0.8588 (OUTLIER) cc_final: 0.8203 (p0) REVERT: A 174 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6748 (tt) REVERT: A 450 TYR cc_start: 0.8278 (p90) cc_final: 0.8038 (p90) REVERT: A 465 MET cc_start: 0.9047 (ttp) cc_final: 0.8739 (ttp) REVERT: A 489 GLN cc_start: 0.8790 (pt0) cc_final: 0.8281 (pp30) REVERT: A 631 MET cc_start: 0.6537 (OUTLIER) cc_final: 0.6161 (tmm) REVERT: A 939 MET cc_start: 0.1654 (mmm) cc_final: -0.0690 (ptp) REVERT: A 1080 PHE cc_start: 0.3539 (m-10) cc_final: 0.3119 (t80) REVERT: A 1236 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8377 (mp) REVERT: A 1254 GLN cc_start: 0.8732 (pm20) cc_final: 0.8458 (pm20) REVERT: A 1297 HIS cc_start: 0.8809 (m170) cc_final: 0.8511 (m170) outliers start: 26 outliers final: 20 residues processed: 77 average time/residue: 0.0892 time to fit residues: 10.1101 Evaluate side-chains 81 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 0.331 ------------------------------------------------------------------------------- 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 432 PHE Chi-restraints excluded: chain A residue 631 MET 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 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 1225 GLU Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1270 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.119080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.078416 restraints weight = 19377.791| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 2.65 r_work: 0.2935 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3467 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= 0.158 Angle : 0.533 11.372 13988 Z= 0.285 Chirality : 0.038 0.223 1624 Planarity : 0.004 0.051 1346 Dihedral : 19.675 152.985 2581 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.22 % Allowed : 19.56 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.29), residues: 848 helix: 1.23 (0.26), residues: 398 sheet: -0.16 (0.51), residues: 99 loop : -0.17 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 967 TYR 0.021 0.001 TYR A 136 PHE 0.025 0.002 PHE A 966 TRP 0.006 0.001 TRP A 464 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 9987) covalent geometry : angle 0.53317 / 0.29 (13988) hydrogen bonds : bond 0.04033 / 2.69 ( 416) hydrogen bonds : angle 4.43369 / 3.22 ( 1111) *********************** 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 81 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 0.228 Fit side-chains REVERT: A 6 SER cc_start: 0.8867 (m) cc_final: 0.8606 (m) REVERT: A 11 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8366 (mm) REVERT: A 174 LEU cc_start: 0.7094 (OUTLIER) cc_final: 0.6767 (tt) REVERT: A 450 TYR cc_start: 0.8253 (p90) cc_final: 0.8015 (p90) REVERT: A 465 MET cc_start: 0.9055 (ttp) cc_final: 0.8727 (ttp) REVERT: A 489 GLN cc_start: 0.8797 (pt0) cc_final: 0.8296 (pp30) REVERT: A 631 MET cc_start: 0.6616 (OUTLIER) cc_final: 0.6242 (tmm) REVERT: A 939 MET cc_start: 0.1691 (mmm) cc_final: -0.0696 (ptp) REVERT: A 1254 GLN cc_start: 0.8741 (pm20) cc_final: 0.8468 (pm20) REVERT: A 1297 HIS cc_start: 0.8795 (m170) cc_final: 0.8485 (m170) REVERT: A 1304 GLU cc_start: 0.8194 (mm-30) cc_final: 0.7689 (pt0) outliers start: 25 outliers final: 20 residues processed: 74 average time/residue: 0.0788 time to fit residues: 8.7555 Evaluate side-chains 77 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 54 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE 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 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 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 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 1225 GLU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1291 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 71 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 0.2980 chunk 78 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.120219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.078006 restraints weight = 19582.923| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.82 r_work: 0.2929 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 0.030 9987 Z= 0.144 Angle : 0.519 11.520 13988 Z= 0.279 Chirality : 0.038 0.220 1624 Planarity : 0.004 0.052 1346 Dihedral : 19.662 152.877 2581 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.96 % Allowed : 19.56 % Favored : 77.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.29), residues: 848 helix: 1.28 (0.26), residues: 398 sheet: -0.14 (0.56), residues: 86 loop : -0.14 (0.33), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1084 TYR 0.020 0.001 TYR A 136 PHE 0.023 0.002 PHE A 966 TRP 0.006 0.001 TRP A 464 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 9987) covalent geometry : angle 0.51877 / 0.28 (13988) hydrogen bonds : bond 0.03926 / 2.63 ( 416) hydrogen bonds : angle 4.39208 / 3.20 ( 1111) ********************** 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 78 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.255 Fit side-chains REVERT: A 6 SER cc_start: 0.8862 (m) cc_final: 0.8606 (m) REVERT: A 11 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8337 (mm) REVERT: A 174 LEU cc_start: 0.7007 (OUTLIER) cc_final: 0.6681 (tt) REVERT: A 450 TYR cc_start: 0.8213 (p90) cc_final: 0.7966 (p90) REVERT: A 465 MET cc_start: 0.9054 (ttp) cc_final: 0.8725 (ttp) REVERT: A 489 GLN cc_start: 0.8769 (pt0) cc_final: 0.8364 (pp30) REVERT: A 631 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.6172 (tmm) REVERT: A 939 MET cc_start: 0.1758 (mmm) cc_final: -0.0566 (ptp) REVERT: A 1254 GLN cc_start: 0.8747 (pm20) cc_final: 0.8468 (pm20) REVERT: A 1297 HIS cc_start: 0.8815 (m170) cc_final: 0.8487 (m170) REVERT: A 1304 GLU cc_start: 0.8185 (mm-30) cc_final: 0.7705 (pt0) outliers start: 23 outliers final: 18 residues processed: 72 average time/residue: 0.0754 time to fit residues: 8.4116 Evaluate side-chains 75 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE 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 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 730 SER 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 1145 VAL Chi-restraints excluded: chain A residue 1216 SER Chi-restraints excluded: chain A residue 1225 GLU Chi-restraints excluded: chain A residue 1270 ILE Chi-restraints excluded: chain A residue 1280 VAL Chi-restraints excluded: chain A residue 1291 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 53 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 64 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 chunk 78 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.118683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.076686 restraints weight = 19740.935| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.79 r_work: 0.2894 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9987 Z= 0.202 Angle : 0.565 10.918 13988 Z= 0.300 Chirality : 0.040 0.221 1624 Planarity : 0.004 0.051 1346 Dihedral : 19.662 153.182 2581 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 3.47 % Allowed : 19.56 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.29), residues: 848 helix: 1.14 (0.26), residues: 401 sheet: -0.21 (0.51), residues: 99 loop : -0.16 (0.34), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1084 TYR 0.026 0.002 TYR A 136 PHE 0.026 0.002 PHE A 966 TRP 0.005 0.001 TRP A 476 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.20 ( 9987) covalent geometry : angle 0.56487 / 0.30 (13988) hydrogen bonds : bond 0.04403 / 2.93 ( 416) hydrogen bonds : angle 4.47187 / 3.26 ( 1111) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2232.67 seconds wall clock time: 38 minutes 58.68 seconds (2338.68 seconds total)