Starting phenix.real_space_refine on Thu Aug 6 14:07:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6p_41074/08_2026/8t6p_41074.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6p_41074/08_2026/8t6p_41074.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t6p_41074/08_2026/8t6p_41074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6p_41074/08_2026/8t6p_41074.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t6p_41074/08_2026/8t6p_41074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6p_41074/08_2026/8t6p_41074.map" } resolution = 3.15 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= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5028 atoms to isotropic. 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 110 5.49 5 S 17 5.16 5 C 6707 2.51 5 N 1951 2.21 5 O 2391 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 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: 11176 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1108, 8838 Classifications: {'peptide': 1108} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 30, 'TRANS': 1077} Chain breaks: 4 Unresolved non-hydrogen bonds: 235 Unresolved non-hydrogen angles: 264 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 8, 'GLU:plan': 9, 'GLN:plan1': 1, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 106 Chain: "B" Number of atoms: 1887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1887 Classifications: {'RNA': 88} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 46, 'rna3p_pyr': 31} Link IDs: {'rna2p': 10, 'rna3p': 77} Chain: "C" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "D" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 205 Classifications: {'DNA': 10} Link IDs: {'rna3p': 9} Time building chain proxies: 2.14, per 1000 atoms: 0.19 Number of scatterers: 11176 At special positions: 0 Unit cell: (85.8196, 120.814, 120.814, 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 17 16.00 P 110 15.00 O 2391 8.00 N 1951 7.00 C 6707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 482.2 milliseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2114 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 6 sheets defined 57.3% alpha, 10.7% beta 34 base pairs and 63 stacking pairs defined. Time for finding SS restraints: 1.10 Creating SS restraints... Processing helix chain 'A' and resid 59 through 91 removed outlier: 4.725A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.946A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 175 through 180 Processing helix chain 'A' and resid 180 through 197 removed outlier: 3.659A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N PHE A 196 " --> pdb=" O TYR A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.558A pdb=" N ILE A 211 " --> pdb=" O ASP A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 251 through 256 removed outlier: 4.008A pdb=" N ASN A 255 " --> pdb=" O ASN A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 274 No H-bonds generated for 'chain 'A' and resid 272 through 274' Processing helix chain 'A' and resid 275 through 283 removed outlier: 4.199A pdb=" N GLN A 281 " --> pdb=" O ASN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 306 Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.938A pdb=" N THR A 310 " --> pdb=" O ARG A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 removed outlier: 3.560A pdb=" N LEU A 334 " --> pdb=" O GLN A 330 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 352 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 removed outlier: 3.667A pdb=" N VAL A 391 " --> pdb=" O GLU A 387 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS A 392 " --> pdb=" O GLU A 388 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.678A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 4.214A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.593A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 481 removed outlier: 3.508A pdb=" N GLU A 480 " --> pdb=" O ASN A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 496 Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 removed outlier: 3.527A pdb=" N LYS A 602 " --> pdb=" O LEU A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 603 through 607 Processing helix chain 'A' and resid 609 through 611 No H-bonds generated for 'chain 'A' and resid 609 through 611' Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.725A pdb=" N ILE A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 4.245A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 652 Processing helix chain 'A' and resid 664 through 668 removed outlier: 3.860A pdb=" N ASN A 668 " --> pdb=" O ARG A 664 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 664 through 668' Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 702 through 712 removed outlier: 4.317A pdb=" N GLU A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 727 Processing helix chain 'A' and resid 730 through 751 removed outlier: 4.060A pdb=" N GLY A 736 " --> pdb=" O ALA A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.805A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1000 removed outlier: 4.475A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1077 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.756A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1185 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 1240 Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.858A pdb=" N PHE A1258 " --> pdb=" O GLN A1254 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N HIS A1262 " --> pdb=" O PHE A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1263 through 1281 removed outlier: 4.204A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU A1271 " --> pdb=" O ASP A1267 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 4.314A pdb=" N ILE A1310 " --> pdb=" O ALA A1306 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.539A pdb=" N LEU A1343 " --> pdb=" O LYS A1340 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1340 through 1344' 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: 5.980A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN A 758 " --> pdb=" O TYR A 5 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 9.814A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 498 through 499 removed outlier: 5.511A pdb=" N GLU A 505 " --> pdb=" O ASP A 499 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N LYS A 506 " --> pdb=" O LEU A 662 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LEU A 662 " --> pdb=" O LYS A 506 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1121 Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.885A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A1158 " --> pdb=" O VAL A1149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.885A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS A1158 " --> pdb=" O VAL A1149 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) 434 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 84 hydrogen bonds 164 hydrogen bond angles 0 basepair planarities 34 basepair parallelities 63 stacking parallelities Total time for adding SS restraints: 2.45 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.31: 1674 1.31 - 1.49: 5288 1.49 - 1.67: 4616 1.67 - 1.85: 33 1.85 - 2.02: 6 Bond restraints: 11617 Sorted by residual: bond pdb=" CZ ARG A 557 " pdb=" NH1 ARG A 557 " ideal model delta sigma weight residual 1.323 2.024 -0.701 1.40e-02 5.10e+03 2.51e+03 bond pdb=" CZ ARG A 691 " pdb=" NH1 ARG A 691 " ideal model delta sigma weight residual 1.323 2.024 -0.701 1.40e-02 5.10e+03 2.50e+03 bond pdb=" CZ ARG A 586 " pdb=" NH1 ARG A 586 " ideal model delta sigma weight residual 1.323 1.976 -0.653 1.40e-02 5.10e+03 2.17e+03 bond pdb=" CZ ARG A 654 " pdb=" NH2 ARG A 654 " ideal model delta sigma weight residual 1.330 1.898 -0.568 1.30e-02 5.92e+03 1.91e+03 bond pdb=" CD GLN A 194 " pdb=" NE2 GLN A 194 " ideal model delta sigma weight residual 1.328 1.976 -0.648 2.10e-02 2.27e+03 9.52e+02 ... (remaining 11612 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.97: 16169 7.97 - 15.93: 26 15.93 - 23.90: 10 23.90 - 31.86: 2 31.86 - 39.83: 1 Bond angle restraints: 16208 Sorted by residual: angle pdb=" NH1 ARG A 557 " pdb=" CZ ARG A 557 " pdb=" NH2 ARG A 557 " ideal model delta sigma weight residual 119.30 159.13 -39.83 1.30e+00 5.92e-01 9.38e+02 angle pdb=" N6 A B 12 " pdb=" C6 A B 12 " pdb=" N1 A B 12 " ideal model delta sigma weight residual 118.60 135.88 -17.28 6.00e-01 2.78e+00 8.29e+02 angle pdb=" NE ARG A 557 " pdb=" CZ ARG A 557 " pdb=" NH2 ARG A 557 " ideal model delta sigma weight residual 119.20 95.45 23.75 9.00e-01 1.23e+00 6.97e+02 angle pdb=" C5 A B 12 " pdb=" C6 A B 12 " pdb=" N6 A B 12 " ideal model delta sigma weight residual 123.70 102.82 20.88 8.00e-01 1.56e+00 6.81e+02 angle pdb=" NE ARG A 494 " pdb=" CZ ARG A 494 " pdb=" NH1 ARG A 494 " ideal model delta sigma weight residual 121.50 146.63 -25.13 1.00e+00 1.00e+00 6.32e+02 ... (remaining 16203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.67: 6493 29.67 - 59.35: 470 59.35 - 89.02: 93 89.02 - 118.69: 0 118.69 - 148.36: 1 Dihedral angle restraints: 7057 sinusoidal: 3798 harmonic: 3259 Sorted by residual: dihedral pdb=" C ASP A 284 " pdb=" N ASP A 284 " pdb=" CA ASP A 284 " pdb=" CB ASP A 284 " ideal model delta harmonic sigma weight residual -122.60 -139.46 16.86 0 2.50e+00 1.60e-01 4.55e+01 dihedral pdb=" N ASP A 284 " pdb=" C ASP A 284 " pdb=" CA ASP A 284 " pdb=" CB ASP A 284 " ideal model delta harmonic sigma weight residual 122.80 139.16 -16.36 0 2.50e+00 1.60e-01 4.28e+01 dihedral pdb=" C ASP A 645 " pdb=" N ASP A 645 " pdb=" CA ASP A 645 " pdb=" CB ASP A 645 " ideal model delta harmonic sigma weight residual -122.60 -133.64 11.04 0 2.50e+00 1.60e-01 1.95e+01 ... (remaining 7054 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.129: 1792 0.129 - 0.259: 97 0.259 - 0.388: 7 0.388 - 0.517: 0 0.517 - 0.647: 1 Chirality restraints: 1897 Sorted by residual: chirality pdb=" CA ASP A 284 " pdb=" N ASP A 284 " pdb=" C ASP A 284 " pdb=" CB ASP A 284 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.05e+01 chirality pdb=" CA TYR A1201 " pdb=" N TYR A1201 " pdb=" C TYR A1201 " pdb=" CB TYR A1201 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" P G B 11 " pdb=" OP1 G B 11 " pdb=" OP2 G B 11 " pdb=" O5' G B 11 " both_signs ideal model delta sigma weight residual True 2.41 -2.71 -0.30 2.00e-01 2.50e+01 2.24e+00 ... (remaining 1894 not shown) Planarity restraints: 1668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G B 62 " -0.220 2.00e-02 2.50e+03 9.27e-02 2.58e+02 pdb=" N9 G B 62 " 0.047 2.00e-02 2.50e+03 pdb=" C8 G B 62 " 0.027 2.00e-02 2.50e+03 pdb=" N7 G B 62 " 0.051 2.00e-02 2.50e+03 pdb=" C5 G B 62 " 0.072 2.00e-02 2.50e+03 pdb=" C6 G B 62 " -0.010 2.00e-02 2.50e+03 pdb=" O6 G B 62 " -0.151 2.00e-02 2.50e+03 pdb=" N1 G B 62 " -0.018 2.00e-02 2.50e+03 pdb=" C2 G B 62 " 0.044 2.00e-02 2.50e+03 pdb=" N2 G B 62 " -0.030 2.00e-02 2.50e+03 pdb=" N3 G B 62 " 0.088 2.00e-02 2.50e+03 pdb=" C4 G B 62 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 20 " 0.127 2.00e-02 2.50e+03 5.55e-02 9.24e+01 pdb=" N9 DG C 20 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DG C 20 " -0.015 2.00e-02 2.50e+03 pdb=" N7 DG C 20 " -0.018 2.00e-02 2.50e+03 pdb=" C5 DG C 20 " -0.036 2.00e-02 2.50e+03 pdb=" C6 DG C 20 " 0.001 2.00e-02 2.50e+03 pdb=" O6 DG C 20 " 0.070 2.00e-02 2.50e+03 pdb=" N1 DG C 20 " 0.034 2.00e-02 2.50e+03 pdb=" C2 DG C 20 " -0.022 2.00e-02 2.50e+03 pdb=" N2 DG C 20 " 0.029 2.00e-02 2.50e+03 pdb=" N3 DG C 20 " -0.082 2.00e-02 2.50e+03 pdb=" C4 DG C 20 " -0.067 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 464 " -0.103 2.00e-02 2.50e+03 4.99e-02 6.22e+01 pdb=" CG TRP A 464 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP A 464 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 464 " 0.045 2.00e-02 2.50e+03 pdb=" NE1 TRP A 464 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TRP A 464 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 464 " 0.061 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 464 " -0.061 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 464 " 0.018 2.00e-02 2.50e+03 pdb=" CH2 TRP A 464 " -0.044 2.00e-02 2.50e+03 ... (remaining 1665 not shown) Histogram of nonbonded interaction distances: 1.56 - 2.22: 8 2.22 - 2.89: 3965 2.89 - 3.56: 16095 3.56 - 4.23: 27838 4.23 - 4.90: 43946 Nonbonded interactions: 91852 Sorted by model distance: nonbonded pdb=" O VAL A 452 " pdb=" SD MET A 465 " model vdw 1.556 3.400 nonbonded pdb=" CG1 VAL A 452 " pdb=" CE MET A 465 " model vdw 1.595 3.880 nonbonded pdb=" O VAL A 452 " pdb=" CG MET A 465 " model vdw 1.949 3.440 nonbonded pdb=" CG GLN A 342 " pdb=" CE MET A 383 " model vdw 1.987 3.860 nonbonded pdb=" C VAL A 452 " pdb=" SD MET A 465 " model vdw 2.076 3.630 ... (remaining 91847 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.010 Process input model: 12.080 Find NCS groups from input model: 0.050 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4511 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 : 0.017 0.701 11618 Z= 1.163 Angle : 1.322 39.825 16208 Z= 1.034 Chirality : 0.063 0.647 1897 Planarity : 0.009 0.106 1668 Dihedral : 18.660 148.364 4943 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.64 % Allowed : 17.66 % Favored : 81.70 % Cbeta Deviations : 0.28 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.23), residues: 1098 helix: -0.94 (0.20), residues: 529 sheet: -0.69 (0.52), residues: 105 loop : -0.64 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 951 TYR 0.095 0.005 TYR A 451 PHE 0.058 0.005 PHE A 491 TRP 0.103 0.012 TRP A 464 HIS 0.019 0.002 HIS A1297 Details of bonding type rmsd/Z covalent geometry : bond 0.01724 / 1.14 (11617) covalent geometry : angle 1.32209 / 1.03 (16208) hydrogen bonds : bond 0.14216 / 9.83 ( 509) hydrogen bonds : angle 6.72659 / 4.82 ( 1427) Misc. bond : bond 0.26246 / 13.81 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LEU cc_start: -0.0396 (tp) cc_final: -0.0962 (tp) REVERT: A 497 ASN cc_start: -0.3462 (OUTLIER) cc_final: -0.3938 (m110) REVERT: A 501 ASN cc_start: 0.1665 (m-40) cc_final: 0.0360 (m110) REVERT: A 515 TYR cc_start: -0.0495 (t80) cc_final: -0.0831 (t80) REVERT: A 524 LEU cc_start: 0.1022 (mm) cc_final: -0.0692 (mp) REVERT: A 666 LEU cc_start: 0.0547 (tp) cc_final: -0.0591 (tp) REVERT: A 740 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8615 (t) outliers start: 6 outliers final: 1 residues processed: 101 average time/residue: 0.1299 time to fit residues: 18.2601 Evaluate side-chains 75 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 740 THR Chi-restraints excluded: chain A residue 1326 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 108 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 77 ASN ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 712 GLN A 723 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.116152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.079255 restraints weight = 27761.450| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.25 r_work: 0.3230 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 11618 Z= 0.203 Angle : 0.650 12.790 16208 Z= 0.349 Chirality : 0.042 0.241 1897 Planarity : 0.005 0.044 1668 Dihedral : 19.074 151.153 2782 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.87 % Allowed : 14.15 % Favored : 82.98 % 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: -0.43 (0.24), residues: 1098 helix: 0.09 (0.21), residues: 541 sheet: -0.62 (0.49), residues: 117 loop : -0.47 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 557 TYR 0.025 0.002 TYR A 594 PHE 0.022 0.002 PHE A1105 TRP 0.015 0.001 TRP A 464 HIS 0.009 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.20 (11617) covalent geometry : angle 0.64991 / 0.35 (16208) hydrogen bonds : bond 0.04819 / 3.40 ( 509) hydrogen bonds : angle 5.16789 / 3.65 ( 1427) Misc. bond : bond 0.00920 / 0.48 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 72 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8541 (tm-30) cc_final: 0.8144 (tm-30) REVERT: A 383 MET cc_start: 0.7722 (mtp) cc_final: 0.7463 (mtp) REVERT: A 497 ASN cc_start: 0.7373 (OUTLIER) cc_final: 0.7082 (m-40) REVERT: A 604 LYS cc_start: 0.9317 (mmtm) cc_final: 0.8959 (mmmt) REVERT: A 625 LEU cc_start: 0.8683 (mt) cc_final: 0.8467 (mt) REVERT: A 648 MET cc_start: 0.8399 (mpp) cc_final: 0.7760 (mpp) REVERT: A 694 MET cc_start: 0.8651 (tpt) cc_final: 0.8434 (tpt) REVERT: A 939 MET cc_start: 0.8746 (mmp) cc_final: 0.8424 (mmp) outliers start: 27 outliers final: 13 residues processed: 95 average time/residue: 0.0988 time to fit residues: 14.0921 Evaluate side-chains 75 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 723 HIS Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1116 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 7 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 119 optimal weight: 9.9990 chunk 103 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 102 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** 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 = 0.4028 r_free = 0.4028 target = 0.114903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.079168 restraints weight = 27327.810| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 3.14 r_work: 0.3216 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11618 Z= 0.172 Angle : 0.578 12.498 16208 Z= 0.315 Chirality : 0.040 0.244 1897 Planarity : 0.004 0.042 1668 Dihedral : 18.979 151.976 2779 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.66 % Allowed : 15.11 % Favored : 82.23 % 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: -0.11 (0.25), residues: 1098 helix: 0.44 (0.22), residues: 540 sheet: -0.55 (0.50), residues: 117 loop : -0.41 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 951 TYR 0.021 0.002 TYR A 594 PHE 0.029 0.002 PHE A 693 TRP 0.008 0.001 TRP A 464 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.17 (11617) covalent geometry : angle 0.57804 / 0.31 (16208) hydrogen bonds : bond 0.04301 / 3.00 ( 509) hydrogen bonds : angle 4.93140 / 3.49 ( 1427) Misc. bond : bond 0.00314 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 604 LYS cc_start: 0.9357 (mmtm) cc_final: 0.8900 (mmtm) REVERT: A 625 LEU cc_start: 0.8646 (mt) cc_final: 0.8422 (mt) REVERT: A 648 MET cc_start: 0.8417 (mpp) cc_final: 0.7754 (mpp) REVERT: A 693 PHE cc_start: 0.9044 (p90) cc_final: 0.8753 (p90) REVERT: A 739 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.7157 (mp-120) REVERT: A 1307 GLU cc_start: 0.7137 (tp30) cc_final: 0.6524 (tp30) outliers start: 25 outliers final: 16 residues processed: 88 average time/residue: 0.1015 time to fit residues: 13.5306 Evaluate side-chains 79 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 62 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1309 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 61 optimal weight: 0.5980 chunk 56 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 99 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1261 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.114292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.078152 restraints weight = 27450.141| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.18 r_work: 0.3198 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 11618 Z= 0.163 Angle : 0.553 14.053 16208 Z= 0.298 Chirality : 0.039 0.243 1897 Planarity : 0.003 0.041 1668 Dihedral : 18.949 151.841 2777 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.87 % Allowed : 15.96 % Favored : 81.17 % 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: 0.05 (0.25), residues: 1098 helix: 0.62 (0.22), residues: 541 sheet: -0.55 (0.51), residues: 117 loop : -0.40 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 139 TYR 0.028 0.002 TYR A 450 PHE 0.018 0.001 PHE A1105 TRP 0.006 0.001 TRP A 18 HIS 0.039 0.002 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (11617) covalent geometry : angle 0.55307 / 0.30 (16208) hydrogen bonds : bond 0.04081 / 2.86 ( 509) hydrogen bonds : angle 4.76556 / 3.38 ( 1427) Misc. bond : bond 0.00899 / 0.47 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8093 (tm-30) REVERT: A 625 LEU cc_start: 0.8654 (mt) cc_final: 0.8407 (mt) REVERT: A 648 MET cc_start: 0.8497 (mpp) cc_final: 0.7804 (mpp) REVERT: A 739 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7197 (mp-120) REVERT: A 1300 LYS cc_start: 0.7730 (mmtp) cc_final: 0.7469 (mptp) REVERT: A 1307 GLU cc_start: 0.7293 (tp30) cc_final: 0.6688 (tp30) outliers start: 27 outliers final: 18 residues processed: 88 average time/residue: 0.1008 time to fit residues: 13.2724 Evaluate side-chains 80 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1245 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 1.9990 chunk 98 optimal weight: 10.0000 chunk 42 optimal weight: 0.0000 chunk 26 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 45 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 ASN ** A 933 GLN ** 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 = 0.3933 r_free = 0.3933 target = 0.111896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.074809 restraints weight = 27072.713| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.28 r_work: 0.3105 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11618 Z= 0.187 Angle : 0.644 39.642 16208 Z= 0.322 Chirality : 0.041 0.258 1897 Planarity : 0.004 0.039 1668 Dihedral : 18.944 152.263 2777 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.62 % Allowed : 15.00 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.25), residues: 1098 helix: 0.74 (0.22), residues: 548 sheet: -0.62 (0.51), residues: 117 loop : -0.57 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.026 0.002 TYR A 450 PHE 0.020 0.002 PHE A1105 TRP 0.006 0.001 TRP A 18 HIS 0.009 0.002 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.19 (11617) covalent geometry : angle 0.64359 / 0.32 (16208) hydrogen bonds : bond 0.04170 / 2.94 ( 509) hydrogen bonds : angle 4.70446 / 3.32 ( 1427) Misc. bond : bond 0.00711 / 0.37 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 65 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8559 (tm-30) cc_final: 0.7985 (tm-30) REVERT: A 594 TYR cc_start: 0.8735 (t80) cc_final: 0.7990 (t80) REVERT: A 606 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7284 (t80) REVERT: A 625 LEU cc_start: 0.8592 (mt) cc_final: 0.8328 (mt) REVERT: A 648 MET cc_start: 0.8509 (mpp) cc_final: 0.7850 (mpp) REVERT: A 739 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7136 (mp-120) REVERT: A 763 MET cc_start: 0.2334 (OUTLIER) cc_final: 0.2108 (tpt) REVERT: A 1300 LYS cc_start: 0.7607 (mmtp) cc_final: 0.7323 (mptp) REVERT: A 1307 GLU cc_start: 0.7320 (tp30) cc_final: 0.6716 (tp30) outliers start: 34 outliers final: 22 residues processed: 94 average time/residue: 0.1018 time to fit residues: 14.1802 Evaluate side-chains 86 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 61 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1280 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 51 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 933 GLN ** 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 = 0.3932 r_free = 0.3932 target = 0.111793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.074765 restraints weight = 27217.938| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 3.28 r_work: 0.3102 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11618 Z= 0.176 Angle : 0.634 38.466 16208 Z= 0.315 Chirality : 0.040 0.249 1897 Planarity : 0.003 0.039 1668 Dihedral : 18.954 151.906 2777 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.83 % Allowed : 15.11 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.25), residues: 1098 helix: 0.73 (0.22), residues: 548 sheet: -0.69 (0.51), residues: 117 loop : -0.59 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 671 TYR 0.022 0.002 TYR A 450 PHE 0.018 0.002 PHE A1105 TRP 0.006 0.001 TRP A 18 HIS 0.020 0.002 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.18 (11617) covalent geometry : angle 0.63429 / 0.31 (16208) hydrogen bonds : bond 0.04050 / 2.83 ( 509) hydrogen bonds : angle 4.64324 / 3.28 ( 1427) Misc. bond : bond 0.00760 / 0.40 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 66 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8532 (tm-30) cc_final: 0.7977 (tm-30) REVERT: A 625 LEU cc_start: 0.8576 (mt) cc_final: 0.8304 (mt) REVERT: A 648 MET cc_start: 0.8551 (mpp) cc_final: 0.7932 (mpp) REVERT: A 739 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7133 (mp-120) REVERT: A 763 MET cc_start: 0.2729 (OUTLIER) cc_final: 0.2468 (tpt) REVERT: A 1188 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8470 (mtmm) REVERT: A 1307 GLU cc_start: 0.7406 (tp30) cc_final: 0.6843 (tp30) outliers start: 36 outliers final: 23 residues processed: 96 average time/residue: 0.0984 time to fit residues: 14.1840 Evaluate side-chains 88 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 62 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 960 SER Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1245 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 0.8980 chunk 65 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 chunk 9 optimal weight: 0.6980 chunk 119 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** 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 = 0.3943 r_free = 0.3943 target = 0.112483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.075758 restraints weight = 26899.106| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 3.27 r_work: 0.3123 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11618 Z= 0.126 Angle : 0.586 31.968 16208 Z= 0.295 Chirality : 0.039 0.275 1897 Planarity : 0.003 0.039 1668 Dihedral : 18.934 151.357 2777 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.09 % Allowed : 16.70 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.25), residues: 1098 helix: 0.82 (0.22), residues: 551 sheet: -0.66 (0.51), residues: 117 loop : -0.51 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 671 TYR 0.027 0.001 TYR A 594 PHE 0.014 0.001 PHE A1105 TRP 0.007 0.001 TRP A 476 HIS 0.008 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (11617) covalent geometry : angle 0.58552 / 0.30 (16208) hydrogen bonds : bond 0.03775 / 2.65 ( 509) hydrogen bonds : angle 4.53549 / 3.21 ( 1427) Misc. bond : bond 0.00694 / 0.37 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 66 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8464 (tm-30) cc_final: 0.7988 (tm-30) REVERT: A 594 TYR cc_start: 0.8827 (t80) cc_final: 0.7953 (t80) REVERT: A 625 LEU cc_start: 0.8596 (mt) cc_final: 0.8336 (mt) REVERT: A 639 TYR cc_start: 0.8923 (m-10) cc_final: 0.8700 (m-80) REVERT: A 648 MET cc_start: 0.8645 (mpp) cc_final: 0.8013 (mpp) REVERT: A 739 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7094 (mp-120) REVERT: A 763 MET cc_start: 0.2727 (OUTLIER) cc_final: 0.2441 (tpt) REVERT: A 1188 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8435 (mtmm) REVERT: A 1307 GLU cc_start: 0.7376 (tp30) cc_final: 0.6829 (tp30) outliers start: 29 outliers final: 22 residues processed: 88 average time/residue: 0.1129 time to fit residues: 14.5478 Evaluate side-chains 88 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1309 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 0 optimal weight: 4.9990 chunk 18 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 79 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** 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 = 0.3930 r_free = 0.3930 target = 0.111442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.074735 restraints weight = 27062.829| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 3.27 r_work: 0.3096 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11618 Z= 0.158 Angle : 0.603 33.769 16208 Z= 0.301 Chirality : 0.039 0.248 1897 Planarity : 0.003 0.039 1668 Dihedral : 18.907 151.337 2777 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.09 % Allowed : 17.23 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.12 (0.25), residues: 1098 helix: 0.82 (0.22), residues: 552 sheet: -0.65 (0.51), residues: 117 loop : -0.55 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1114 TYR 0.022 0.002 TYR A 594 PHE 0.051 0.002 PHE A 185 TRP 0.005 0.001 TRP A 476 HIS 0.008 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (11617) covalent geometry : angle 0.60328 / 0.30 (16208) hydrogen bonds : bond 0.03906 / 2.74 ( 509) hydrogen bonds : angle 4.53747 / 3.20 ( 1427) Misc. bond : bond 0.00575 / 0.30 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 62 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8480 (tm-30) cc_final: 0.8035 (tm-30) REVERT: A 517 TYR cc_start: 0.6664 (t80) cc_final: 0.6416 (t80) REVERT: A 594 TYR cc_start: 0.8775 (t80) cc_final: 0.7997 (t80) REVERT: A 625 LEU cc_start: 0.8562 (mt) cc_final: 0.8265 (mt) REVERT: A 648 MET cc_start: 0.8709 (mpp) cc_final: 0.8115 (mpp) REVERT: A 739 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7135 (mp-120) REVERT: A 763 MET cc_start: 0.2819 (OUTLIER) cc_final: 0.2557 (tpt) REVERT: A 1188 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8461 (mtmm) REVERT: A 1307 GLU cc_start: 0.7441 (tp30) cc_final: 0.6887 (tp30) outliers start: 29 outliers final: 22 residues processed: 84 average time/residue: 0.1130 time to fit residues: 13.8063 Evaluate side-chains 85 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 763 MET Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1280 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 114 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 16 optimal weight: 0.0570 chunk 23 optimal weight: 5.9990 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 20 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 412 HIS A 563 GLN ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.112124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.075728 restraints weight = 26834.157| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 3.23 r_work: 0.3122 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.2971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11618 Z= 0.126 Angle : 0.572 30.031 16208 Z= 0.287 Chirality : 0.038 0.242 1897 Planarity : 0.003 0.039 1668 Dihedral : 18.894 150.604 2777 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.55 % Allowed : 17.66 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.28 (0.26), residues: 1098 helix: 0.93 (0.23), residues: 552 sheet: -0.57 (0.51), residues: 117 loop : -0.46 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 671 TYR 0.022 0.001 TYR A 594 PHE 0.030 0.001 PHE A 185 TRP 0.006 0.001 TRP A 476 HIS 0.005 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (11617) covalent geometry : angle 0.57169 / 0.29 (16208) hydrogen bonds : bond 0.03644 / 2.55 ( 509) hydrogen bonds : angle 4.45210 / 3.15 ( 1427) Misc. bond : bond 0.00619 / 0.33 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8426 (tm-30) cc_final: 0.7992 (tm-30) REVERT: A 594 TYR cc_start: 0.8754 (t80) cc_final: 0.7931 (t80) REVERT: A 625 LEU cc_start: 0.8535 (mt) cc_final: 0.8245 (mt) REVERT: A 648 MET cc_start: 0.8698 (mpp) cc_final: 0.8141 (mpp) REVERT: A 739 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7087 (mp-120) REVERT: A 746 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7471 (tp30) REVERT: A 1188 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8437 (mtmm) REVERT: A 1307 GLU cc_start: 0.7444 (tp30) cc_final: 0.6889 (tp30) outliers start: 24 outliers final: 19 residues processed: 83 average time/residue: 0.0851 time to fit residues: 10.5742 Evaluate side-chains 84 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 758 ASN Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1309 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 16 optimal weight: 0.7980 chunk 93 optimal weight: 0.0570 chunk 21 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 1 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 116 optimal weight: 11.9990 chunk 119 optimal weight: 10.0000 chunk 38 optimal weight: 0.0470 chunk 57 optimal weight: 10.0000 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** 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 = 0.3941 r_free = 0.3941 target = 0.112068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.075495 restraints weight = 27039.607| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.27 r_work: 0.3122 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11618 Z= 0.125 Angle : 0.521 8.682 16208 Z= 0.278 Chirality : 0.038 0.312 1897 Planarity : 0.003 0.038 1668 Dihedral : 18.880 150.601 2777 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.55 % Allowed : 17.77 % Favored : 79.68 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.32 (0.25), residues: 1098 helix: 0.96 (0.23), residues: 552 sheet: -0.50 (0.51), residues: 117 loop : -0.45 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1337 TYR 0.022 0.002 TYR A 639 PHE 0.035 0.001 PHE A 185 TRP 0.005 0.001 TRP A 476 HIS 0.011 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (11617) covalent geometry : angle 0.52100 / 0.28 (16208) hydrogen bonds : bond 0.03728 / 2.61 ( 509) hydrogen bonds : angle 4.45801 / 3.15 ( 1427) Misc. bond : bond 0.01226 / 0.65 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 64 time to evaluate : 0.301 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8404 (tm-30) cc_final: 0.7991 (tm-30) REVERT: A 594 TYR cc_start: 0.8769 (t80) cc_final: 0.7978 (t80) REVERT: A 625 LEU cc_start: 0.8515 (mt) cc_final: 0.8213 (mt) REVERT: A 628 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7179 (p0) REVERT: A 648 MET cc_start: 0.8721 (mpp) cc_final: 0.8151 (mpp) REVERT: A 739 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7007 (mp-120) REVERT: A 763 MET cc_start: 0.2758 (tpp) cc_final: 0.2521 (tpt) REVERT: A 1188 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8408 (mtmm) REVERT: A 1307 GLU cc_start: 0.7463 (tp30) cc_final: 0.6914 (tp30) outliers start: 24 outliers final: 18 residues processed: 84 average time/residue: 0.0797 time to fit residues: 9.9353 Evaluate side-chains 82 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 739 GLN Chi-restraints excluded: chain A residue 746 GLU Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1236 LEU Chi-restraints excluded: chain A residue 1242 TYR Chi-restraints excluded: chain A residue 1245 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 74 optimal weight: 5.9990 chunk 73 optimal weight: 0.0980 chunk 47 optimal weight: 0.2980 chunk 114 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 104 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 61 optimal weight: 0.0050 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 933 GLN ** 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 = 0.3948 r_free = 0.3948 target = 0.112483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.076084 restraints weight = 27293.100| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.27 r_work: 0.3134 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 11618 Z= 0.119 Angle : 0.531 11.470 16208 Z= 0.285 Chirality : 0.038 0.323 1897 Planarity : 0.003 0.039 1668 Dihedral : 18.885 150.186 2777 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.55 % Allowed : 17.77 % Favored : 79.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.36 (0.26), residues: 1098 helix: 0.96 (0.23), residues: 552 sheet: -0.47 (0.51), residues: 117 loop : -0.38 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1337 TYR 0.022 0.001 TYR A 594 PHE 0.031 0.001 PHE A 185 TRP 0.006 0.001 TRP A 476 HIS 0.014 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (11617) covalent geometry : angle 0.53145 / 0.29 (16208) hydrogen bonds : bond 0.03851 / 2.65 ( 509) hydrogen bonds : angle 4.50618 / 3.17 ( 1427) Misc. bond : bond 0.00568 / 0.30 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3035.25 seconds wall clock time: 52 minutes 48.18 seconds (3168.18 seconds total)