Starting phenix.real_space_refine on Sat May 17 11:27:57 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6p_41074/05_2025/8t6p_41074.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6p_41074/05_2025/8t6p_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6p_41074/05_2025/8t6p_41074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6p_41074/05_2025/8t6p_41074.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6p_41074/05_2025/8t6p_41074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6p_41074/05_2025/8t6p_41074.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'ASP:plan': 5, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 8} 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: 7.49, per 1000 atoms: 0.67 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: 2.91 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 4.01 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: 5.22 Time building geometry restraints manager: 3.38 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=" 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=" 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 angle pdb=" NH1 ARG A 494 " pdb=" CZ ARG A 494 " pdb=" NH2 ARG A 494 " ideal model delta sigma weight residual 119.30 93.19 26.11 1.30e+00 5.92e-01 4.03e+02 angle pdb=" OD1 ASN A 668 " pdb=" CG ASN A 668 " pdb=" ND2 ASN A 668 " ideal model delta sigma weight residual 122.60 102.72 19.88 1.00e+00 1.00e+00 3.95e+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: 1832 0.129 - 0.259: 57 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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 32.010 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4428 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= 1.116 Angle : 1.284 39.825 16208 Z= 0.858 Chirality : 0.057 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.103 0.012 TRP A 464 HIS 0.019 0.002 HIS A1297 PHE 0.058 0.005 PHE A 491 TYR 0.095 0.005 TYR A 451 ARG 0.014 0.001 ARG A 951 Details of bonding type rmsd hydrogen bonds : bond 0.14216 ( 509) hydrogen bonds : angle 6.72659 ( 1427) covalent geometry : bond 0.01718 (11617) covalent geometry : angle 1.28355 (16208) Misc. bond : bond 0.26246 ( 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 : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 LEU cc_start: -0.0396 (tp) cc_final: -0.1027 (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: 0.0361 (m110) REVERT: A 515 TYR cc_start: -0.0495 (t80) cc_final: -0.0820 (t80) REVERT: A 524 LEU cc_start: 0.1022 (mm) cc_final: -0.0663 (mp) REVERT: A 666 LEU cc_start: 0.0547 (tp) cc_final: -0.0604 (tp) REVERT: A 740 THR cc_start: 0.8835 (OUTLIER) cc_final: 0.8616 (t) outliers start: 6 outliers final: 1 residues processed: 101 average time/residue: 0.2753 time to fit residues: 38.2599 Evaluate side-chains 74 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 71 time to evaluate : 1.189 ------------------------------------------------------------------------------- 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 101 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 70 optimal weight: 0.5980 chunk 108 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 723 HIS ** 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 = 0.4041 r_free = 0.4041 target = 0.115846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.079913 restraints weight = 26958.203| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 3.10 r_work: 0.3242 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11618 Z= 0.158 Angle : 0.588 14.487 16208 Z= 0.310 Chirality : 0.039 0.210 1897 Planarity : 0.004 0.042 1668 Dihedral : 18.908 153.917 2782 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.55 % Allowed : 15.11 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1098 helix: 0.26 (0.22), residues: 544 sheet: -0.63 (0.53), residues: 109 loop : -0.35 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 464 HIS 0.005 0.002 HIS A 328 PHE 0.016 0.001 PHE A1105 TYR 0.017 0.001 TYR A 594 ARG 0.005 0.001 ARG A 951 Details of bonding type rmsd hydrogen bonds : bond 0.03967 ( 509) hydrogen bonds : angle 4.92872 ( 1427) covalent geometry : bond 0.00341 (11617) covalent geometry : angle 0.58753 (16208) Misc. bond : bond 0.00571 ( 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: 24 poor density : 75 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8108 (tm-30) REVERT: A 497 ASN cc_start: 0.7372 (OUTLIER) cc_final: 0.6876 (m110) REVERT: A 625 LEU cc_start: 0.8662 (mt) cc_final: 0.8439 (mt) REVERT: A 648 MET cc_start: 0.8440 (mpp) cc_final: 0.7792 (mpp) REVERT: A 654 ARG cc_start: 0.8309 (tpp-160) cc_final: 0.8004 (tpp-160) REVERT: A 723 HIS cc_start: 0.6964 (OUTLIER) cc_final: 0.6403 (t-170) REVERT: A 1263 LYS cc_start: 0.8812 (pptt) cc_final: 0.8310 (ttmm) REVERT: A 1307 GLU cc_start: 0.7207 (tp30) cc_final: 0.6593 (tp30) outliers start: 24 outliers final: 12 residues processed: 96 average time/residue: 0.2341 time to fit residues: 32.9004 Evaluate side-chains 77 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 63 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 497 ASN Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 723 HIS 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 1105 PHE Chi-restraints excluded: chain A residue 1106 SER Chi-restraints excluded: chain A residue 1116 SER Chi-restraints excluded: chain A residue 1179 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 50 optimal weight: 0.9980 chunk 25 optimal weight: 8.9990 chunk 119 optimal weight: 4.9990 chunk 31 optimal weight: 0.9980 chunk 99 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN A 511 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3921 r_free = 0.3921 target = 0.111127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.074077 restraints weight = 27121.586| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 3.27 r_work: 0.3085 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11618 Z= 0.222 Angle : 0.604 9.495 16208 Z= 0.317 Chirality : 0.040 0.208 1897 Planarity : 0.004 0.040 1668 Dihedral : 18.941 153.991 2779 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.09 % Allowed : 15.21 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1098 helix: 0.58 (0.22), residues: 549 sheet: -0.68 (0.54), residues: 109 loop : -0.44 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 18 HIS 0.031 0.002 HIS A 723 PHE 0.020 0.002 PHE A 98 TYR 0.021 0.002 TYR A 594 ARG 0.005 0.001 ARG A 403 Details of bonding type rmsd hydrogen bonds : bond 0.04099 ( 509) hydrogen bonds : angle 4.73552 ( 1427) covalent geometry : bond 0.00490 (11617) covalent geometry : angle 0.60446 (16208) Misc. bond : bond 0.00967 ( 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 93 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 64 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8025 (tm-30) REVERT: A 594 TYR cc_start: 0.8631 (t80) cc_final: 0.8414 (t80) REVERT: A 625 LEU cc_start: 0.8483 (mt) cc_final: 0.8213 (mt) REVERT: A 648 MET cc_start: 0.8462 (mpp) cc_final: 0.7838 (mpp) REVERT: A 654 ARG cc_start: 0.8254 (tpp-160) cc_final: 0.7976 (tpp-160) REVERT: A 739 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.7065 (mp-120) REVERT: A 1258 PHE cc_start: 0.8199 (t80) cc_final: 0.7942 (t80) REVERT: A 1307 GLU cc_start: 0.7324 (tp30) cc_final: 0.6667 (tp30) outliers start: 29 outliers final: 20 residues processed: 90 average time/residue: 0.2302 time to fit residues: 30.9539 Evaluate side-chains 83 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 62 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 322 ILE Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 724 ILE Chi-restraints excluded: chain A residue 727 LEU Chi-restraints excluded: chain A residue 739 GLN 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 1193 ASP Chi-restraints excluded: chain A residue 1205 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 100 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 88 optimal weight: 0.6980 chunk 27 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 2 optimal weight: 0.7980 chunk 62 optimal weight: 9.9990 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 GLN ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3940 r_free = 0.3940 target = 0.112153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.075406 restraints weight = 26884.106| |-----------------------------------------------------------------------------| r_work (start): 0.3279 rms_B_bonded: 3.27 r_work: 0.3113 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11618 Z= 0.140 Angle : 0.532 12.330 16208 Z= 0.279 Chirality : 0.037 0.210 1897 Planarity : 0.003 0.039 1668 Dihedral : 18.845 152.753 2777 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.34 % Allowed : 16.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.25), residues: 1098 helix: 0.83 (0.22), residues: 549 sheet: -0.59 (0.51), residues: 117 loop : -0.42 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.006 0.001 HIS A 328 PHE 0.031 0.001 PHE A 693 TYR 0.020 0.001 TYR A 594 ARG 0.003 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03593 ( 509) hydrogen bonds : angle 4.49316 ( 1427) covalent geometry : bond 0.00302 (11617) covalent geometry : angle 0.53246 (16208) Misc. bond : bond 0.00640 ( 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 88 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 1.053 Fit side-chains REVERT: A 60 GLU cc_start: 0.8463 (tm-30) cc_final: 0.7938 (tm-30) REVERT: A 594 TYR cc_start: 0.8648 (t80) cc_final: 0.8005 (t80) REVERT: A 625 LEU cc_start: 0.8467 (mt) cc_final: 0.8181 (mt) REVERT: A 654 ARG cc_start: 0.8311 (tpp-160) cc_final: 0.7996 (tpp-160) REVERT: A 739 GLN cc_start: 0.8300 (OUTLIER) cc_final: 0.7044 (mp-120) REVERT: A 763 MET cc_start: 0.2826 (tpp) cc_final: 0.2616 (tpt) REVERT: A 1188 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8426 (mtmm) REVERT: A 1307 GLU cc_start: 0.7365 (tp30) cc_final: 0.6832 (tp30) outliers start: 22 outliers final: 14 residues processed: 84 average time/residue: 0.2658 time to fit residues: 32.3881 Evaluate side-chains 74 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 368 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 960 SER Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1095 VAL 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 1236 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 68 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** A 712 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 933 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.111242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.074698 restraints weight = 27068.756| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 3.25 r_work: 0.3100 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11618 Z= 0.158 Angle : 0.611 33.706 16208 Z= 0.301 Chirality : 0.038 0.269 1897 Planarity : 0.003 0.039 1668 Dihedral : 18.829 152.717 2777 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 4.15 % Allowed : 15.53 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.26), residues: 1098 helix: 0.91 (0.23), residues: 552 sheet: -0.60 (0.51), residues: 117 loop : -0.40 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 18 HIS 0.007 0.001 HIS A 328 PHE 0.018 0.002 PHE A 693 TYR 0.017 0.001 TYR A 450 ARG 0.005 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.03679 ( 509) hydrogen bonds : angle 4.45739 ( 1427) covalent geometry : bond 0.00346 (11617) covalent geometry : angle 0.61051 (16208) Misc. bond : bond 0.00867 ( 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 103 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 64 time to evaluate : 1.103 Fit side-chains REVERT: A 60 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7900 (tm-30) REVERT: A 383 MET cc_start: 0.7961 (ptp) cc_final: 0.7681 (ptm) REVERT: A 594 TYR cc_start: 0.8650 (t80) cc_final: 0.7904 (t80) REVERT: A 654 ARG cc_start: 0.8293 (tpp-160) cc_final: 0.7976 (tpp-160) REVERT: A 739 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.7093 (mp-120) REVERT: A 763 MET cc_start: 0.2770 (tpp) cc_final: 0.2565 (tpt) REVERT: A 1188 LYS cc_start: 0.8606 (OUTLIER) cc_final: 0.8217 (mtmm) REVERT: A 1307 GLU cc_start: 0.7487 (tp30) cc_final: 0.6958 (tp30) outliers start: 39 outliers final: 22 residues processed: 96 average time/residue: 0.2342 time to fit residues: 33.3192 Evaluate side-chains 83 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 1.123 ------------------------------------------------------------------------------- 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 338 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 368 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 960 SER 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 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 1245 LEU 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 0 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 73 optimal weight: 0.0670 chunk 106 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 112 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 65 optimal weight: 0.0570 overall best weight: 0.7438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 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 = 0.3944 r_free = 0.3944 target = 0.112021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.075824 restraints weight = 27161.872| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 3.25 r_work: 0.3129 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11618 Z= 0.128 Angle : 0.546 16.736 16208 Z= 0.280 Chirality : 0.038 0.321 1897 Planarity : 0.003 0.038 1668 Dihedral : 18.787 151.694 2777 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.66 % Allowed : 16.38 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1098 helix: 0.96 (0.23), residues: 553 sheet: -0.57 (0.51), residues: 117 loop : -0.35 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 18 HIS 0.035 0.002 HIS A 415 PHE 0.013 0.001 PHE A1105 TYR 0.015 0.001 TYR A 594 ARG 0.007 0.000 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.03529 ( 509) hydrogen bonds : angle 4.36634 ( 1427) covalent geometry : bond 0.00276 (11617) covalent geometry : angle 0.54575 (16208) Misc. bond : bond 0.01531 ( 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 94 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8382 (tm-30) cc_final: 0.7897 (tm-30) REVERT: A 383 MET cc_start: 0.8102 (ptp) cc_final: 0.7888 (ptm) REVERT: A 594 TYR cc_start: 0.8638 (t80) cc_final: 0.7890 (t80) REVERT: A 625 LEU cc_start: 0.8400 (mt) cc_final: 0.8186 (mt) REVERT: A 654 ARG cc_start: 0.8321 (tpp-160) cc_final: 0.8023 (tpp-160) REVERT: A 739 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7099 (mp-120) outliers start: 25 outliers final: 17 residues processed: 90 average time/residue: 0.2219 time to fit residues: 29.4157 Evaluate side-chains 78 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 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 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 1116 SER Chi-restraints excluded: chain A residue 1193 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 33 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 712 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 = 0.3897 r_free = 0.3897 target = 0.109101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.072631 restraints weight = 27448.326| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 3.25 r_work: 0.3061 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11618 Z= 0.201 Angle : 0.591 16.710 16208 Z= 0.305 Chirality : 0.040 0.330 1897 Planarity : 0.003 0.039 1668 Dihedral : 18.903 153.459 2777 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.40 % Allowed : 15.74 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1098 helix: 0.86 (0.22), residues: 553 sheet: -0.65 (0.51), residues: 117 loop : -0.48 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.007 0.001 HIS A 160 PHE 0.016 0.002 PHE A1105 TYR 0.023 0.002 TYR A 450 ARG 0.003 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 509) hydrogen bonds : angle 4.49938 ( 1427) covalent geometry : bond 0.00442 (11617) covalent geometry : angle 0.59063 (16208) Misc. bond : bond 0.01365 ( 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 91 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8027 (tm-30) REVERT: A 383 MET cc_start: 0.8083 (ptp) cc_final: 0.7815 (ptm) REVERT: A 594 TYR cc_start: 0.8699 (t80) cc_final: 0.8279 (t80) REVERT: A 628 ASP cc_start: 0.7729 (OUTLIER) cc_final: 0.7311 (p0) REVERT: A 654 ARG cc_start: 0.8257 (tpp-160) cc_final: 0.7957 (tpp-160) REVERT: A 739 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7260 (mp-120) REVERT: A 1188 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8204 (mtmm) outliers start: 32 outliers final: 22 residues processed: 85 average time/residue: 0.2251 time to fit residues: 28.6815 Evaluate side-chains 79 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 54 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 338 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 368 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 28 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 74 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 98 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN ** 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 = 0.3892 r_free = 0.3892 target = 0.108586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.072383 restraints weight = 27108.215| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 3.20 r_work: 0.3060 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11618 Z= 0.201 Angle : 0.594 19.588 16208 Z= 0.305 Chirality : 0.040 0.336 1897 Planarity : 0.003 0.038 1668 Dihedral : 18.934 153.345 2777 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.51 % Allowed : 15.96 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1098 helix: 0.90 (0.22), residues: 551 sheet: -0.78 (0.49), residues: 121 loop : -0.48 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 18 HIS 0.007 0.001 HIS A 328 PHE 0.018 0.002 PHE A 693 TYR 0.018 0.002 TYR A 450 ARG 0.003 0.000 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.03868 ( 509) hydrogen bonds : angle 4.51074 ( 1427) covalent geometry : bond 0.00441 (11617) covalent geometry : angle 0.59380 (16208) Misc. bond : bond 0.02116 ( 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 93 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 60 time to evaluate : 1.154 Fit side-chains REVERT: A 60 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8032 (tm-30) REVERT: A 594 TYR cc_start: 0.8650 (t80) cc_final: 0.7903 (t80) REVERT: A 628 ASP cc_start: 0.7738 (OUTLIER) cc_final: 0.7301 (p0) REVERT: A 654 ARG cc_start: 0.8257 (tpp-160) cc_final: 0.8029 (tpp-160) REVERT: A 739 GLN cc_start: 0.8457 (OUTLIER) cc_final: 0.7260 (mp-120) REVERT: A 1188 LYS cc_start: 0.8564 (OUTLIER) cc_final: 0.8176 (mtmm) REVERT: A 1307 GLU cc_start: 0.7672 (tp30) cc_final: 0.7177 (mt-10) outliers start: 33 outliers final: 23 residues processed: 89 average time/residue: 0.2178 time to fit residues: 29.1862 Evaluate side-chains 85 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 59 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 338 LEU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 368 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 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 1116 SER Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1205 GLU 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 50 optimal weight: 6.9990 chunk 64 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3871 r_free = 0.3871 target = 0.107210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.070923 restraints weight = 27105.681| |-----------------------------------------------------------------------------| r_work (start): 0.3190 rms_B_bonded: 3.21 r_work: 0.3026 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 11618 Z= 0.264 Angle : 0.653 14.527 16208 Z= 0.342 Chirality : 0.043 0.568 1897 Planarity : 0.004 0.038 1668 Dihedral : 19.037 154.231 2777 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.40 % Allowed : 16.06 % Favored : 80.53 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.25), residues: 1098 helix: 0.79 (0.22), residues: 552 sheet: -0.82 (0.50), residues: 119 loop : -0.57 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 18 HIS 0.014 0.002 HIS A 415 PHE 0.023 0.002 PHE A1105 TYR 0.024 0.002 TYR A 450 ARG 0.007 0.001 ARG A 967 Details of bonding type rmsd hydrogen bonds : bond 0.04593 ( 509) hydrogen bonds : angle 4.70337 ( 1427) covalent geometry : bond 0.00581 (11617) covalent geometry : angle 0.65308 (16208) Misc. bond : bond 0.00526 ( 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 92 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 60 time to evaluate : 1.101 Fit side-chains REVERT: A 60 GLU cc_start: 0.8500 (tm-30) cc_final: 0.8085 (tm-30) REVERT: A 161 MET cc_start: 0.5247 (ptp) cc_final: 0.4356 (ptp) REVERT: A 187 GLN cc_start: 0.9239 (tt0) cc_final: 0.8878 (mm-40) REVERT: A 415 HIS cc_start: 0.6022 (m90) cc_final: 0.5502 (t-170) REVERT: A 594 TYR cc_start: 0.8685 (t80) cc_final: 0.8319 (t80) REVERT: A 628 ASP cc_start: 0.7814 (OUTLIER) cc_final: 0.7343 (p0) REVERT: A 739 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7301 (mp-120) REVERT: A 1188 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8205 (mtmm) REVERT: A 1307 GLU cc_start: 0.7718 (tp30) cc_final: 0.7235 (mt-10) outliers start: 32 outliers final: 23 residues processed: 87 average time/residue: 0.2180 time to fit residues: 28.4885 Evaluate side-chains 84 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 1.076 ------------------------------------------------------------------------------- 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 322 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 368 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 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 1116 SER Chi-restraints excluded: chain A residue 1188 LYS Chi-restraints excluded: chain A residue 1193 ASP Chi-restraints excluded: chain A residue 1205 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 13 optimal weight: 0.3980 chunk 96 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 102 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3929 r_free = 0.3929 target = 0.110826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.074837 restraints weight = 27190.048| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 3.23 r_work: 0.3115 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11618 Z= 0.120 Angle : 0.558 12.623 16208 Z= 0.291 Chirality : 0.038 0.420 1897 Planarity : 0.003 0.037 1668 Dihedral : 18.890 150.984 2777 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.66 % Allowed : 16.91 % Favored : 80.43 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.26), residues: 1098 helix: 1.09 (0.23), residues: 550 sheet: -0.63 (0.51), residues: 117 loop : -0.43 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 464 HIS 0.016 0.001 HIS A 415 PHE 0.022 0.001 PHE A 693 TYR 0.019 0.001 TYR A 639 ARG 0.003 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 509) hydrogen bonds : angle 4.50739 ( 1427) covalent geometry : bond 0.00252 (11617) covalent geometry : angle 0.55784 (16208) Misc. bond : bond 0.00645 ( 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 101 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 1.187 Fit side-chains REVERT: A 60 GLU cc_start: 0.8347 (tm-30) cc_final: 0.7891 (tm-30) REVERT: A 161 MET cc_start: 0.5053 (ptp) cc_final: 0.4809 (ptp) REVERT: A 187 GLN cc_start: 0.9183 (tt0) cc_final: 0.8827 (mm-40) REVERT: A 415 HIS cc_start: 0.5835 (m90) cc_final: 0.5483 (t-90) REVERT: A 594 TYR cc_start: 0.8680 (t80) cc_final: 0.7965 (t80) REVERT: A 654 ARG cc_start: 0.8316 (tpp-160) cc_final: 0.8078 (tpp-160) REVERT: A 739 GLN cc_start: 0.8227 (OUTLIER) cc_final: 0.7042 (mp-120) REVERT: A 746 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7473 (tp30) REVERT: A 1188 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8160 (mtmm) REVERT: A 1307 GLU cc_start: 0.7557 (tp30) cc_final: 0.7083 (tp30) outliers start: 25 outliers final: 17 residues processed: 95 average time/residue: 0.2533 time to fit residues: 34.3892 Evaluate side-chains 87 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 67 time to evaluate : 1.069 ------------------------------------------------------------------------------- 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 338 LEU Chi-restraints excluded: chain A residue 368 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 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 1116 SER Chi-restraints excluded: chain A residue 1188 LYS 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 82 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 100 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 20 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 55 optimal weight: 0.0170 chunk 113 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 overall best weight: 3.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 497 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3841 r_free = 0.3841 target = 0.106264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.069344 restraints weight = 27495.072| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 3.37 r_work: 0.2977 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 11618 Z= 0.346 Angle : 0.726 12.994 16208 Z= 0.376 Chirality : 0.046 0.517 1897 Planarity : 0.004 0.041 1668 Dihedral : 19.187 155.140 2777 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.77 % Allowed : 17.02 % Favored : 80.21 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.25), residues: 1098 helix: 0.69 (0.22), residues: 557 sheet: -0.89 (0.50), residues: 119 loop : -0.74 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 18 HIS 0.011 0.002 HIS A 415 PHE 0.034 0.002 PHE A1105 TYR 0.034 0.003 TYR A 450 ARG 0.006 0.001 ARG A 100 Details of bonding type rmsd hydrogen bonds : bond 0.05065 ( 509) hydrogen bonds : angle 4.87603 ( 1427) covalent geometry : bond 0.00762 (11617) covalent geometry : angle 0.72591 (16208) Misc. bond : bond 0.00802 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6206.50 seconds wall clock time: 108 minutes 6.56 seconds (6486.56 seconds total)