Starting phenix.real_space_refine on Fri Jul 3 18:48:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6p_41074/07_2026/8t6p_41074.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6p_41074/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6p_41074/07_2026/8t6p_41074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6p_41074/07_2026/8t6p_41074.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6p_41074/07_2026/8t6p_41074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6p_41074/07_2026/8t6p_41074.cif" } 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-dev-6108/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: 2.35, per 1000 atoms: 0.21 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: 0.77 Conformation dependent library (CDL) restraints added in 429.4 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: 1.21 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: 3.19 Time building geometry restraints manager: 0.97 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: 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: 5.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.780 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.030 ------------------------------------------------------------------------------- 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= 1.158 Angle : 1.292 39.825 16208 Z= 1.005 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 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 0.01722 / 1.13 (11617) covalent geometry : angle 1.29211 / 1.00 (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 : 0.328 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: 0.1311 time to fit residues: 18.0132 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 : 0.382 ------------------------------------------------------------------------------- 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: 6.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 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: 1.5584 ------------------------------------------------------------------------------- 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 = 0.116169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.079304 restraints weight = 27745.997| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 3.26 r_work: 0.3227 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1245 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= 0.202 Angle : 0.640 13.487 16208 Z= 0.350 Chirality : 0.042 0.212 1897 Planarity : 0.004 0.042 1668 Dihedral : 19.162 153.182 2782 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.87 % Allowed : 14.57 % Favored : 82.55 % 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: -0.42 (0.24), residues: 1098 helix: 0.08 (0.21), residues: 541 sheet: -0.62 (0.49), residues: 117 loop : -0.43 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 671 TYR 0.023 0.002 TYR A 594 PHE 0.021 0.002 PHE A1105 TRP 0.016 0.001 TRP A 464 HIS 0.009 0.002 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00426 / 0.20 (11617) covalent geometry : angle 0.64016 / 0.35 (16208) hydrogen bonds : bond 0.04965 / 3.51 ( 509) hydrogen bonds : angle 5.18015 / 3.66 ( 1427) Misc. bond : bond 0.01909 / 1.00 ( 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 : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8124 (tm-30) REVERT: A 383 MET cc_start: 0.7739 (mtp) cc_final: 0.7476 (mtp) REVERT: A 497 ASN cc_start: 0.7425 (OUTLIER) cc_final: 0.7130 (m-40) REVERT: A 625 LEU cc_start: 0.8687 (mt) cc_final: 0.8473 (mt) REVERT: A 648 MET cc_start: 0.8389 (mpp) cc_final: 0.7749 (mpp) REVERT: A 694 MET cc_start: 0.8638 (tpt) cc_final: 0.8418 (tpt) REVERT: A 939 MET cc_start: 0.8749 (mmp) cc_final: 0.8429 (mmp) outliers start: 27 outliers final: 13 residues processed: 95 average time/residue: 0.0974 time to fit residues: 13.9378 Evaluate side-chains 74 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 511 HIS A 723 HIS ** A1261 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 = 0.4031 r_free = 0.4031 target = 0.115212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.078475 restraints weight = 27965.040| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.25 r_work: 0.3207 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11618 Z= 0.182 Angle : 0.582 9.447 16208 Z= 0.318 Chirality : 0.040 0.197 1897 Planarity : 0.004 0.042 1668 Dihedral : 19.073 153.427 2779 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.66 % Allowed : 14.89 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.15 (0.25), residues: 1098 helix: 0.38 (0.22), residues: 540 sheet: -0.59 (0.50), residues: 117 loop : -0.39 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 139 TYR 0.026 0.002 TYR A 594 PHE 0.029 0.002 PHE A 693 TRP 0.008 0.001 TRP A 464 HIS 0.009 0.002 HIS A 723 Details of bonding type rmsd/Z covalent geometry : bond 0.00389 / 0.18 (11617) covalent geometry : angle 0.58154 / 0.32 (16208) hydrogen bonds : bond 0.04318 / 3.01 ( 509) hydrogen bonds : angle 4.97892 / 3.53 ( 1427) Misc. bond : bond 0.02470 / 1.30 ( 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 : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8173 (tm-30) REVERT: A 594 TYR cc_start: 0.8556 (t80) cc_final: 0.8179 (t80) REVERT: A 625 LEU cc_start: 0.8675 (mt) cc_final: 0.8455 (mt) REVERT: A 648 MET cc_start: 0.8433 (mpp) cc_final: 0.7758 (mpp) REVERT: A 693 PHE cc_start: 0.9012 (p90) cc_final: 0.8719 (p90) REVERT: A 739 GLN cc_start: 0.8550 (OUTLIER) cc_final: 0.7244 (mp-120) REVERT: A 1307 GLU cc_start: 0.7184 (tp30) cc_final: 0.6571 (tp30) outliers start: 25 outliers final: 18 residues processed: 89 average time/residue: 0.0976 time to fit residues: 12.9044 Evaluate side-chains 81 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 512 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 623 LEU 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 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: 0.8980 chunk 56 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 89 optimal weight: 0.2980 chunk 55 optimal weight: 0.0980 chunk 88 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 31 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 30 optimal weight: 0.0570 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 224 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 = 0.4044 r_free = 0.4044 target = 0.115878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.080095 restraints weight = 27168.245| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 3.17 r_work: 0.3246 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.091 11618 Z= 0.117 Angle : 0.523 14.016 16208 Z= 0.286 Chirality : 0.038 0.220 1897 Planarity : 0.003 0.043 1668 Dihedral : 19.005 152.646 2777 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.02 % Allowed : 15.96 % Favored : 82.02 % 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: 0.06 (0.25), residues: 1098 helix: 0.58 (0.22), residues: 542 sheet: -0.51 (0.51), residues: 117 loop : -0.32 (0.29), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 951 TYR 0.025 0.001 TYR A 450 PHE 0.014 0.001 PHE A 693 TRP 0.006 0.001 TRP A 464 HIS 0.032 0.002 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (11617) covalent geometry : angle 0.52341 / 0.29 (16208) hydrogen bonds : bond 0.03890 / 2.72 ( 509) hydrogen bonds : angle 4.73820 / 3.37 ( 1427) Misc. bond : bond 0.01150 / 0.61 ( 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 90 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8044 (tm-30) REVERT: A 594 TYR cc_start: 0.8408 (t80) cc_final: 0.8032 (t80) REVERT: A 625 LEU cc_start: 0.8662 (mt) cc_final: 0.8420 (mt) REVERT: A 648 MET cc_start: 0.8478 (mpp) cc_final: 0.7773 (mpp) REVERT: A 739 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7174 (mp-120) REVERT: A 746 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7568 (tp30) REVERT: A 1300 LYS cc_start: 0.7705 (mmtp) cc_final: 0.7471 (mptp) outliers start: 19 outliers final: 9 residues processed: 86 average time/residue: 0.0932 time to fit residues: 12.1382 Evaluate side-chains 73 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 62 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 623 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 1245 LEU Chi-restraints excluded: chain A residue 1309 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 1 optimal weight: 2.9990 chunk 98 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 20.0000 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.3928 r_free = 0.3928 target = 0.111601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.074440 restraints weight = 27203.437| |-----------------------------------------------------------------------------| r_work (start): 0.3255 rms_B_bonded: 3.32 r_work: 0.3087 rms_B_bonded: 4.29 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 11618 Z= 0.236 Angle : 0.668 39.040 16208 Z= 0.339 Chirality : 0.041 0.259 1897 Planarity : 0.004 0.041 1668 Dihedral : 18.992 154.074 2777 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.51 % Allowed : 14.89 % Favored : 81.60 % 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: -0.04 (0.25), residues: 1098 helix: 0.60 (0.22), residues: 549 sheet: -0.58 (0.51), residues: 117 loop : -0.53 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.021 0.002 TYR A 450 PHE 0.024 0.002 PHE A1105 TRP 0.007 0.001 TRP A 18 HIS 0.007 0.002 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00515 / 0.24 (11617) covalent geometry : angle 0.66820 / 0.34 (16208) hydrogen bonds : bond 0.04431 / 3.14 ( 509) hydrogen bonds : angle 4.77940 / 3.37 ( 1427) Misc. bond : bond 0.00812 / 0.43 ( 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 95 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 62 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8004 (tm-30) REVERT: A 594 TYR cc_start: 0.8434 (t80) cc_final: 0.8140 (t80) REVERT: A 625 LEU cc_start: 0.8592 (mt) cc_final: 0.8323 (mt) REVERT: A 648 MET cc_start: 0.8422 (mpp) cc_final: 0.7763 (mpp) REVERT: A 739 GLN cc_start: 0.8495 (OUTLIER) cc_final: 0.7066 (mp-120) REVERT: A 763 MET cc_start: 0.2225 (OUTLIER) cc_final: 0.2022 (tpt) REVERT: A 1258 PHE cc_start: 0.8142 (t80) cc_final: 0.7917 (t80) REVERT: A 1307 GLU cc_start: 0.7264 (tp30) cc_final: 0.6663 (tp30) outliers start: 33 outliers final: 21 residues processed: 88 average time/residue: 0.0866 time to fit residues: 11.3563 Evaluate side-chains 83 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 339 VAL Chi-restraints excluded: chain A residue 368 SER Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 607 LEU 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 51 optimal weight: 0.7980 chunk 85 optimal weight: 0.0970 chunk 48 optimal weight: 0.9990 chunk 45 optimal weight: 0.0570 chunk 108 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 34 optimal weight: 0.0870 chunk 5 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 7.9990 overall best weight: 0.3274 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.113734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.077016 restraints weight = 27121.971| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 3.31 r_work: 0.3147 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 11618 Z= 0.109 Angle : 0.522 13.484 16208 Z= 0.280 Chirality : 0.037 0.242 1897 Planarity : 0.003 0.040 1668 Dihedral : 18.989 152.289 2777 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.66 % Allowed : 16.06 % Favored : 81.28 % 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: 0.13 (0.25), residues: 1098 helix: 0.75 (0.22), residues: 549 sheet: -0.56 (0.51), residues: 117 loop : -0.44 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 951 TYR 0.023 0.001 TYR A 450 PHE 0.014 0.001 PHE A 682 TRP 0.007 0.001 TRP A 476 HIS 0.007 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (11617) covalent geometry : angle 0.52203 / 0.28 (16208) hydrogen bonds : bond 0.03733 / 2.58 ( 509) hydrogen bonds : angle 4.57118 / 3.24 ( 1427) Misc. bond : bond 0.00803 / 0.42 ( 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 92 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 67 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8479 (tm-30) cc_final: 0.7945 (tm-30) REVERT: A 594 TYR cc_start: 0.8406 (t80) cc_final: 0.8058 (t80) REVERT: A 625 LEU cc_start: 0.8572 (mt) cc_final: 0.8321 (mt) REVERT: A 648 MET cc_start: 0.8495 (mpp) cc_final: 0.7863 (mpp) REVERT: A 739 GLN cc_start: 0.8293 (OUTLIER) cc_final: 0.7028 (mp-120) REVERT: A 744 VAL cc_start: 0.8878 (t) cc_final: 0.8672 (p) REVERT: A 746 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7490 (tp30) REVERT: A 1307 GLU cc_start: 0.7243 (tp30) cc_final: 0.6650 (tp30) outliers start: 25 outliers final: 16 residues processed: 87 average time/residue: 0.0888 time to fit residues: 11.3496 Evaluate side-chains 79 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 607 LEU 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 1193 ASP Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1309 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 71 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 118 optimal weight: 20.0000 chunk 9 optimal weight: 0.9990 chunk 119 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 17 optimal weight: 0.0980 chunk 47 optimal weight: 0.4980 chunk 109 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3960 r_free = 0.3960 target = 0.113566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.076873 restraints weight = 26901.452| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 3.28 r_work: 0.3143 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11618 Z= 0.122 Angle : 0.523 11.364 16208 Z= 0.282 Chirality : 0.038 0.262 1897 Planarity : 0.003 0.040 1668 Dihedral : 18.926 152.516 2777 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.34 % Allowed : 16.70 % 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 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: 0.23 (0.25), residues: 1098 helix: 0.86 (0.22), residues: 549 sheet: -0.57 (0.51), residues: 117 loop : -0.42 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 671 TYR 0.023 0.001 TYR A 517 PHE 0.015 0.001 PHE A1105 TRP 0.005 0.001 TRP A 476 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (11617) covalent geometry : angle 0.52271 / 0.28 (16208) hydrogen bonds : bond 0.03796 / 2.65 ( 509) hydrogen bonds : angle 4.52518 / 3.20 ( 1427) Misc. bond : bond 0.00875 / 0.46 ( 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 88 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8455 (tm-30) cc_final: 0.7969 (tm-30) REVERT: A 594 TYR cc_start: 0.8390 (t80) cc_final: 0.8010 (t80) REVERT: A 625 LEU cc_start: 0.8582 (mt) cc_final: 0.8320 (mt) REVERT: A 648 MET cc_start: 0.8605 (mpp) cc_final: 0.8010 (mpp) REVERT: A 739 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7052 (mp-120) REVERT: A 746 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7475 (tp30) REVERT: A 1307 GLU cc_start: 0.7284 (tp30) cc_final: 0.6746 (tp30) outliers start: 22 outliers final: 15 residues processed: 85 average time/residue: 0.0789 time to fit residues: 10.0289 Evaluate side-chains 80 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 63 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 607 LEU 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 1245 LEU 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: 0.5980 chunk 70 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 48 optimal weight: 0.0270 chunk 79 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 overall best weight: 0.8640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.3955 r_free = 0.3955 target = 0.113077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.076378 restraints weight = 27019.489| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 3.29 r_work: 0.3137 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 11618 Z= 0.137 Angle : 0.544 18.639 16208 Z= 0.291 Chirality : 0.038 0.323 1897 Planarity : 0.003 0.040 1668 Dihedral : 18.935 152.258 2777 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.55 % Allowed : 16.60 % 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 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: 0.24 (0.25), residues: 1098 helix: 0.91 (0.23), residues: 547 sheet: -0.60 (0.51), residues: 117 loop : -0.45 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 671 TYR 0.017 0.001 TYR A 639 PHE 0.048 0.001 PHE A 185 TRP 0.004 0.001 TRP A 476 HIS 0.033 0.002 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 (11617) covalent geometry : angle 0.54390 / 0.29 (16208) hydrogen bonds : bond 0.03913 / 2.73 ( 509) hydrogen bonds : angle 4.56808 / 3.22 ( 1427) Misc. bond : bond 0.00246 / 0.13 ( 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 89 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 65 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7976 (tm-30) REVERT: A 517 TYR cc_start: 0.6393 (t80) cc_final: 0.6187 (t80) REVERT: A 594 TYR cc_start: 0.8331 (t80) cc_final: 0.7997 (t80) REVERT: A 625 LEU cc_start: 0.8561 (mt) cc_final: 0.8297 (mt) REVERT: A 648 MET cc_start: 0.8665 (mpp) cc_final: 0.8046 (mpp) REVERT: A 739 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7022 (mp-120) REVERT: A 744 VAL cc_start: 0.8835 (t) cc_final: 0.8626 (p) REVERT: A 746 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7485 (tp30) REVERT: A 1188 LYS cc_start: 0.8703 (OUTLIER) cc_final: 0.8450 (mtmm) REVERT: A 1307 GLU cc_start: 0.7366 (tp30) cc_final: 0.6811 (tp30) outliers start: 24 outliers final: 19 residues processed: 86 average time/residue: 0.0943 time to fit residues: 12.0018 Evaluate side-chains 82 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 370 GLU Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 607 LEU 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 1245 LEU Chi-restraints excluded: chain A residue 1309 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 120 random chunks: chunk 114 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 23 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 5 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS ** A 563 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 = 0.3954 r_free = 0.3954 target = 0.113001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.076373 restraints weight = 26974.102| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 3.25 r_work: 0.3136 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 11618 Z= 0.137 Angle : 0.534 12.902 16208 Z= 0.295 Chirality : 0.038 0.336 1897 Planarity : 0.003 0.040 1668 Dihedral : 18.953 152.215 2777 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.98 % Allowed : 16.38 % Favored : 80.64 % 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: 0.25 (0.26), residues: 1098 helix: 0.89 (0.23), residues: 549 sheet: -0.61 (0.51), residues: 117 loop : -0.42 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 671 TYR 0.017 0.001 TYR A1237 PHE 0.036 0.001 PHE A 185 TRP 0.004 0.001 TRP A 476 HIS 0.022 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (11617) covalent geometry : angle 0.53390 / 0.30 (16208) hydrogen bonds : bond 0.04092 / 2.83 ( 509) hydrogen bonds : angle 4.64421 / 3.27 ( 1427) Misc. bond : bond 0.01372 / 0.72 ( 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 94 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 66 time to evaluate : 0.272 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: 0.8445 (tm-30) cc_final: 0.7992 (tm-30) REVERT: A 594 TYR cc_start: 0.8319 (t80) cc_final: 0.7910 (t80) REVERT: A 607 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8421 (mp) REVERT: A 625 LEU cc_start: 0.8503 (mt) cc_final: 0.8225 (mt) REVERT: A 639 TYR cc_start: 0.8912 (m-10) cc_final: 0.8611 (m-10) REVERT: A 648 MET cc_start: 0.8706 (mpp) cc_final: 0.8113 (mpp) REVERT: A 739 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7029 (mp-120) REVERT: A 744 VAL cc_start: 0.8843 (t) cc_final: 0.8633 (p) REVERT: A 746 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7499 (tp30) REVERT: A 1188 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8460 (mtmm) REVERT: A 1307 GLU cc_start: 0.7390 (tp30) cc_final: 0.6836 (tp30) outliers start: 28 outliers final: 22 residues processed: 89 average time/residue: 0.0886 time to fit residues: 11.8104 Evaluate side-chains 89 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 339 VAL Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 607 LEU 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 1236 LEU Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1280 VAL 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: 2.9990 chunk 93 optimal weight: 0.0570 chunk 21 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 66 optimal weight: 20.0000 chunk 1 optimal weight: 0.0970 chunk 44 optimal weight: 1.9990 chunk 116 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 38 optimal weight: 0.1980 chunk 57 optimal weight: 7.9990 overall best weight: 1.0700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 563 GLN ** A 723 HIS ** 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 = 0.3942 r_free = 0.3942 target = 0.112120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.075392 restraints weight = 27033.491| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.28 r_work: 0.3118 rms_B_bonded: 4.25 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 11618 Z= 0.151 Angle : 0.549 14.664 16208 Z= 0.301 Chirality : 0.039 0.381 1897 Planarity : 0.003 0.040 1668 Dihedral : 18.987 152.457 2777 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.66 % Allowed : 16.81 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.25), residues: 1098 helix: 0.93 (0.22), residues: 549 sheet: -0.64 (0.51), residues: 117 loop : -0.47 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 671 TYR 0.017 0.001 TYR A 450 PHE 0.036 0.002 PHE A 185 TRP 0.005 0.001 TRP A 18 HIS 0.029 0.002 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (11617) covalent geometry : angle 0.54911 / 0.30 (16208) hydrogen bonds : bond 0.04092 / 2.85 ( 509) hydrogen bonds : angle 4.61707 / 3.26 ( 1427) Misc. bond : bond 0.01408 / 0.74 ( 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: 25 poor density : 63 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.8442 (tm-30) cc_final: 0.8009 (tm-30) REVERT: A 594 TYR cc_start: 0.8353 (t80) cc_final: 0.7942 (t80) REVERT: A 607 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8452 (mp) REVERT: A 625 LEU cc_start: 0.8516 (mt) cc_final: 0.8225 (mt) REVERT: A 648 MET cc_start: 0.8741 (mpp) cc_final: 0.8179 (mpp) REVERT: A 739 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.7102 (mp-120) REVERT: A 746 GLU cc_start: 0.7740 (OUTLIER) cc_final: 0.7474 (tp30) REVERT: A 1188 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8445 (mtmm) REVERT: A 1307 GLU cc_start: 0.7416 (tp30) cc_final: 0.6859 (tp30) outliers start: 25 outliers final: 19 residues processed: 85 average time/residue: 0.0937 time to fit residues: 11.8522 Evaluate side-chains 86 residues out of total 996 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 63 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 181 VAL Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain A residue 607 LEU 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 1236 LEU 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 74 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 47 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 104 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3951 r_free = 0.3951 target = 0.112652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.076089 restraints weight = 27274.722| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 3.29 r_work: 0.3134 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 11618 Z= 0.133 Angle : 0.549 15.715 16208 Z= 0.305 Chirality : 0.038 0.337 1897 Planarity : 0.004 0.070 1668 Dihedral : 18.981 151.926 2777 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.77 % Allowed : 16.81 % 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 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: 0.34 (0.26), residues: 1098 helix: 0.99 (0.23), residues: 548 sheet: -0.60 (0.50), residues: 117 loop : -0.39 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 671 TYR 0.018 0.001 TYR A 450 PHE 0.033 0.001 PHE A 185 TRP 0.005 0.001 TRP A 476 HIS 0.014 0.001 HIS A 415 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.13 (11617) covalent geometry : angle 0.54853 / 0.30 (16208) hydrogen bonds : bond 0.04115 / 2.82 ( 509) hydrogen bonds : angle 4.62389 / 3.26 ( 1427) Misc. bond : bond 0.02071 / 1.09 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2914.40 seconds wall clock time: 50 minutes 33.69 seconds (3033.69 seconds total)