Starting phenix.real_space_refine on Wed Aug 5 19:26:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w7t_65732/08_2026/9w7t_65732.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w7t_65732/08_2026/9w7t_65732.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w7t_65732/08_2026/9w7t_65732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w7t_65732/08_2026/9w7t_65732.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w7t_65732/08_2026/9w7t_65732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w7t_65732/08_2026/9w7t_65732.map" } resolution = 3.91 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= 0.005 sd= 0.045 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 144 5.49 5 S 19 5.16 5 C 6614 2.51 5 N 1982 2.21 5 O 2475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11234 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 993, 8142 Classifications: {'peptide': 993} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 966} Chain breaks: 3 Chain: "B" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 698 Classifications: {'DNA': 34} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 33} Chain: "C" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 305 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "D" Number of atoms: 2089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 2089 Classifications: {'RNA': 98} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 48, 'rna3p_pyr': 38} Link IDs: {'rna2p': 11, 'rna3p': 86} Time building chain proxies: 1.73, per 1000 atoms: 0.15 Number of scatterers: 11234 At special positions: 0 Unit cell: (120.736, 102.41, 140.14, 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 19 16.00 P 144 15.00 O 2475 8.00 N 1982 7.00 C 6614 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.58 Conformation dependent library (CDL) restraints added in 263.9 milliseconds 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1886 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 8 sheets defined 54.2% alpha, 10.2% beta 49 base pairs and 87 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.712A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.581A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 removed outlier: 3.637A pdb=" N PHE A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 346 through 353 removed outlier: 3.543A pdb=" N ASP A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 382 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.614A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.277A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.935A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 435 " --> pdb=" O PRO A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 483 through 495 removed outlier: 4.196A pdb=" N MET A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.092A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 552 Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 601 Processing helix chain 'A' and resid 603 through 608 removed outlier: 3.538A pdb=" N LEU A 607 " --> pdb=" O ASP A 603 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 638 through 643 removed outlier: 4.599A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 664 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 702 through 711 removed outlier: 4.338A pdb=" N GLU A 706 " --> pdb=" O LEU A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.532A pdb=" N LYS A 734 " --> pdb=" O SER A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 Processing helix chain 'A' and resid 959 through 971 removed outlier: 4.090A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 999 removed outlier: 4.423A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 Processing helix chain 'A' and resid 1177 through 1185 removed outlier: 3.513A pdb=" N LYS A1185 " --> pdb=" O PHE A1181 " (cutoff:3.500A) Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1241 Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.551A pdb=" N HIS A1262 " --> pdb=" O PHE A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.657A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1314 through 1316 No H-bonds generated for 'chain 'A' and resid 1314 through 1316' Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.681A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 6.479A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N TYR A 5 " --> pdb=" O ASN A 758 " (cutoff:3.500A) removed outlier: 8.741A pdb=" N VAL A 760 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N LEU A 9 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.606A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 507 through 509 removed outlier: 5.428A pdb=" N LEU A 508 " --> pdb=" O GLY A 660 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.510A pdb=" N TYR A 529 " --> pdb=" O ALA A 538 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS A 528 " --> pdb=" O SER A 581 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1106 through 1111 removed outlier: 6.692A pdb=" N LYS A1107 " --> pdb=" O PRO A1137 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N SER A1109 " --> pdb=" O ASP A1135 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP A1135 " --> pdb=" O SER A1109 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A1133 " --> pdb=" O LEU A1111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.532A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU A1164 " --> pdb=" O VAL A1143 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1324 through 1326 379 hydrogen bonds defined for protein. 1095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 124 hydrogen bonds 236 hydrogen bond angles 0 basepair planarities 49 basepair parallelities 87 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2703 1.33 - 1.45: 2946 1.45 - 1.57: 5783 1.57 - 1.69: 288 1.69 - 1.81: 36 Bond restraints: 11756 Sorted by residual: bond pdb=" C3' DA B 8 " pdb=" C2' DA B 8 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DC C 8 " pdb=" C2' DC C 8 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG B 7 " pdb=" C2' DG B 7 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DC B 16 " pdb=" C2' DC B 16 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DC C 10 " pdb=" C2' DC C 10 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.88e+00 ... (remaining 11751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 15093 0.95 - 1.90: 947 1.90 - 2.85: 442 2.85 - 3.80: 24 3.80 - 4.75: 3 Bond angle restraints: 16509 Sorted by residual: angle pdb=" O4' DG B 18 " pdb=" C4' DG B 18 " pdb=" C3' DG B 18 " ideal model delta sigma weight residual 106.00 102.94 3.06 6.00e-01 2.78e+00 2.61e+01 angle pdb=" O4' DT B 19 " pdb=" C4' DT B 19 " pdb=" C3' DT B 19 " ideal model delta sigma weight residual 106.00 103.16 2.84 6.00e-01 2.78e+00 2.23e+01 angle pdb=" O4' DG B 25 " pdb=" C4' DG B 25 " pdb=" C3' DG B 25 " ideal model delta sigma weight residual 106.00 103.51 2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT B 31 " pdb=" C4 DT B 31 " pdb=" O4 DT B 31 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT B 4 " pdb=" C4 DT B 4 " pdb=" O4 DT B 4 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.70e+01 ... (remaining 16504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.59: 6755 34.59 - 69.17: 317 69.17 - 103.75: 26 103.75 - 138.34: 0 138.34 - 172.92: 1 Dihedral angle restraints: 7099 sinusoidal: 4184 harmonic: 2915 Sorted by residual: dihedral pdb=" C4' DG B 7 " pdb=" C3' DG B 7 " pdb=" O3' DG B 7 " pdb=" P DA B 8 " ideal model delta sinusoidal sigma weight residual 220.00 47.08 172.92 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA PHE A 446 " pdb=" C PHE A 446 " pdb=" N ARG A 447 " pdb=" CA ARG A 447 " ideal model delta harmonic sigma weight residual 180.00 163.59 16.41 0 5.00e+00 4.00e-02 1.08e+01 dihedral pdb=" CG ARG A1359 " pdb=" CD ARG A1359 " pdb=" NE ARG A1359 " pdb=" CZ ARG A1359 " ideal model delta sinusoidal sigma weight residual -180.00 -136.83 -43.17 2 1.50e+01 4.44e-03 9.99e+00 ... (remaining 7096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1215 0.029 - 0.059: 375 0.059 - 0.088: 148 0.088 - 0.118: 71 0.118 - 0.147: 95 Chirality restraints: 1904 Sorted by residual: chirality pdb=" C3' DG B 7 " pdb=" C4' DG B 7 " pdb=" O3' DG B 7 " pdb=" C2' DG B 7 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" C2' G D 73 " pdb=" C3' G D 73 " pdb=" O2' G D 73 " pdb=" C1' G D 73 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.23e-01 chirality pdb=" C1' A D 74 " pdb=" O4' A D 74 " pdb=" C2' A D 74 " pdb=" N9 A D 74 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 5.12e-01 ... (remaining 1901 not shown) Planarity restraints: 1565 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D 74 " -0.023 2.00e-02 2.50e+03 1.03e-02 2.92e+00 pdb=" N9 A D 74 " 0.024 2.00e-02 2.50e+03 pdb=" C8 A D 74 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A D 74 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A D 74 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A D 74 " -0.002 2.00e-02 2.50e+03 pdb=" N6 A D 74 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A D 74 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A D 74 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A D 74 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A D 74 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A1228 " -0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO A1229 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A1229 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A1229 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A D 34 " 0.019 2.00e-02 2.50e+03 8.76e-03 2.11e+00 pdb=" N9 A D 34 " -0.021 2.00e-02 2.50e+03 pdb=" C8 A D 34 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A D 34 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A D 34 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A D 34 " 0.003 2.00e-02 2.50e+03 pdb=" N6 A D 34 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A D 34 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A D 34 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A D 34 " -0.003 2.00e-02 2.50e+03 pdb=" C4 A D 34 " -0.002 2.00e-02 2.50e+03 ... (remaining 1562 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 4 2.02 - 2.74: 885 2.74 - 3.46: 15375 3.46 - 4.18: 28452 4.18 - 4.90: 45448 Nonbonded interactions: 90164 Sorted by model distance: nonbonded pdb=" NZ LYS A 44 " pdb=" O6 G D 92 " model vdw 1.297 3.120 nonbonded pdb=" ND2 ASN A 77 " pdb=" O2 U D 59 " model vdw 1.297 3.120 nonbonded pdb=" NH2 ARG A1122 " pdb=" N3 A D 49 " model vdw 1.353 3.200 nonbonded pdb=" NH1 ARG A 71 " pdb=" C5 C D 18 " model vdw 1.431 3.420 nonbonded pdb=" N2 DG B 7 " pdb=" O2 DC C 10 " model vdw 2.101 2.496 ... (remaining 90159 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.900 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.003 0.037 11756 Z= 0.265 Angle : 0.597 4.754 16509 Z= 0.482 Chirality : 0.046 0.147 1904 Planarity : 0.003 0.042 1565 Dihedral : 16.781 172.925 5213 Min Nonbonded Distance : 1.297 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.27), residues: 985 helix: 2.09 (0.24), residues: 480 sheet: 1.53 (0.58), residues: 83 loop : 0.18 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1122 TYR 0.008 0.001 TYR A 517 PHE 0.013 0.001 PHE A 432 TRP 0.011 0.001 TRP A1126 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.26 (11756) covalent geometry : angle 0.59660 / 0.48 (16509) hydrogen bonds : bond 0.15070 / 10.39 ( 503) hydrogen bonds : angle 5.09930 / 3.67 ( 1331) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 534 MET cc_start: 0.5461 (mtt) cc_final: 0.4392 (ttm) REVERT: A 562 LYS cc_start: 0.9266 (tttt) cc_final: 0.8936 (tppt) REVERT: A 585 ASP cc_start: 0.8275 (m-30) cc_final: 0.8003 (m-30) REVERT: A 969 ASP cc_start: 0.9101 (m-30) cc_final: 0.8362 (m-30) REVERT: A 1097 LYS cc_start: 0.8956 (tttm) cc_final: 0.8364 (tptt) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1009 time to fit residues: 28.4631 Evaluate side-chains 127 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 40.0000 chunk 49 optimal weight: 0.0030 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 20.0000 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 30.0000 chunk 106 optimal weight: 50.0000 overall best weight: 3.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A 698 HIS A 980 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.044888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.033403 restraints weight = 80174.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.034778 restraints weight = 38807.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.035743 restraints weight = 24594.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.036347 restraints weight = 18054.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2744 r_free = 0.2744 target = 0.036799 restraints weight = 14693.871| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11756 Z= 0.177 Angle : 0.605 8.888 16509 Z= 0.347 Chirality : 0.040 0.265 1904 Planarity : 0.005 0.062 1565 Dihedral : 19.183 172.655 3095 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.13 % Allowed : 8.18 % Favored : 89.69 % 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: 1.66 (0.27), residues: 985 helix: 1.85 (0.24), residues: 487 sheet: 1.89 (0.59), residues: 80 loop : 0.12 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 71 TYR 0.019 0.002 TYR A 656 PHE 0.013 0.001 PHE A1181 TRP 0.007 0.001 TRP A 18 HIS 0.013 0.001 HIS A 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.18 (11756) covalent geometry : angle 0.60549 / 0.35 (16509) hydrogen bonds : bond 0.06078 / 4.25 ( 503) hydrogen bonds : angle 4.55578 / 3.24 ( 1331) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.9493 (mtm180) cc_final: 0.9278 (mtp85) REVERT: A 90 MET cc_start: 0.9054 (tpp) cc_final: 0.8654 (tpt) REVERT: A 321 MET cc_start: 0.9241 (mmm) cc_final: 0.8596 (mmm) REVERT: A 335 LEU cc_start: 0.9888 (OUTLIER) cc_final: 0.9635 (pp) REVERT: A 448 ILE cc_start: 0.9691 (mt) cc_final: 0.9462 (tp) REVERT: A 534 MET cc_start: 0.6528 (mtt) cc_final: 0.5232 (ttm) REVERT: A 558 LYS cc_start: 0.9518 (mttt) cc_final: 0.9125 (ttpp) REVERT: A 562 LYS cc_start: 0.9399 (tttt) cc_final: 0.9097 (tppt) REVERT: A 586 ARG cc_start: 0.9573 (ptp-170) cc_final: 0.9328 (ptm-80) REVERT: A 746 GLU cc_start: 0.9381 (tt0) cc_final: 0.9093 (tt0) REVERT: A 1089 MET cc_start: 0.9121 (tpp) cc_final: 0.8716 (tpp) REVERT: A 1213 MET cc_start: 0.9436 (ttm) cc_final: 0.9234 (tpp) REVERT: A 1228 LEU cc_start: 0.9104 (tp) cc_final: 0.8759 (tp) outliers start: 19 outliers final: 13 residues processed: 127 average time/residue: 0.0875 time to fit residues: 15.8081 Evaluate side-chains 105 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1153 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 51 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 95 optimal weight: 10.0000 chunk 108 optimal weight: 30.0000 chunk 99 optimal weight: 40.0000 chunk 62 optimal weight: 5.9990 chunk 98 optimal weight: 20.0000 chunk 34 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.043108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.031791 restraints weight = 85249.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.033069 restraints weight = 42359.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.033967 restraints weight = 27353.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.034549 restraints weight = 20371.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.034929 restraints weight = 16707.630| |-----------------------------------------------------------------------------| r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11756 Z= 0.223 Angle : 0.599 8.661 16509 Z= 0.343 Chirality : 0.041 0.269 1904 Planarity : 0.004 0.063 1565 Dihedral : 19.273 172.892 3095 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.58 % Allowed : 9.64 % Favored : 87.78 % 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: 1.36 (0.26), residues: 985 helix: 1.48 (0.23), residues: 488 sheet: 2.18 (0.62), residues: 70 loop : 0.08 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG A 655 TYR 0.014 0.002 TYR A 656 PHE 0.015 0.002 PHE A 98 TRP 0.009 0.002 TRP A 464 HIS 0.006 0.001 HIS A 511 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.22 (11756) covalent geometry : angle 0.59931 / 0.34 (16509) hydrogen bonds : bond 0.05876 / 4.11 ( 503) hydrogen bonds : angle 4.59689 / 3.26 ( 1331) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.9533 (mtm180) cc_final: 0.9263 (mtp180) REVERT: A 335 LEU cc_start: 0.9907 (OUTLIER) cc_final: 0.9671 (pp) REVERT: A 534 MET cc_start: 0.6693 (mtt) cc_final: 0.5389 (ttm) REVERT: A 739 GLN cc_start: 0.9723 (mm-40) cc_final: 0.9374 (mm-40) REVERT: A 746 GLU cc_start: 0.9423 (tt0) cc_final: 0.8996 (tt0) REVERT: A 939 MET cc_start: 0.9701 (mmm) cc_final: 0.9442 (mmm) REVERT: A 1089 MET cc_start: 0.9179 (tpp) cc_final: 0.8734 (mmm) outliers start: 23 outliers final: 16 residues processed: 110 average time/residue: 0.0826 time to fit residues: 13.2575 Evaluate side-chains 101 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1153 LYS Chi-restraints excluded: chain A residue 1238 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 30.0000 chunk 39 optimal weight: 5.9990 chunk 106 optimal weight: 50.0000 chunk 52 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.043187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2604 r_free = 0.2604 target = 0.031879 restraints weight = 82950.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.033151 restraints weight = 40229.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.034066 restraints weight = 25923.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.034687 restraints weight = 19105.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.035132 restraints weight = 15552.180| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11756 Z= 0.156 Angle : 0.554 10.110 16509 Z= 0.317 Chirality : 0.039 0.277 1904 Planarity : 0.004 0.058 1565 Dihedral : 19.360 173.677 3095 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.02 % Allowed : 11.77 % Favored : 86.21 % 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: 1.34 (0.26), residues: 985 helix: 1.43 (0.24), residues: 487 sheet: 1.86 (0.58), residues: 80 loop : 0.15 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 71 TYR 0.010 0.001 TYR A1326 PHE 0.013 0.001 PHE A 970 TRP 0.008 0.001 TRP A 464 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (11756) covalent geometry : angle 0.55424 / 0.32 (16509) hydrogen bonds : bond 0.05236 / 3.65 ( 503) hydrogen bonds : angle 4.45233 / 3.16 ( 1331) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.9555 (mtm180) cc_final: 0.8984 (mtp85) REVERT: A 90 MET cc_start: 0.9065 (tpp) cc_final: 0.8795 (tpp) REVERT: A 161 MET cc_start: 0.9568 (mmm) cc_final: 0.9368 (mmm) REVERT: A 335 LEU cc_start: 0.9898 (OUTLIER) cc_final: 0.9642 (pp) REVERT: A 461 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8913 (tmm-80) REVERT: A 534 MET cc_start: 0.6808 (mtt) cc_final: 0.5503 (ttm) REVERT: A 585 ASP cc_start: 0.8571 (m-30) cc_final: 0.8286 (p0) REVERT: A 739 GLN cc_start: 0.9722 (mm-40) cc_final: 0.9360 (mm-40) REVERT: A 746 GLU cc_start: 0.9433 (tt0) cc_final: 0.9095 (tt0) REVERT: A 1089 MET cc_start: 0.9133 (tpp) cc_final: 0.8740 (tpp) REVERT: A 1213 MET cc_start: 0.9488 (ttp) cc_final: 0.9203 (tpp) outliers start: 18 outliers final: 11 residues processed: 96 average time/residue: 0.0908 time to fit residues: 12.3678 Evaluate side-chains 96 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 633 GLU Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1153 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 9.9990 chunk 31 optimal weight: 9.9990 chunk 79 optimal weight: 0.0970 chunk 102 optimal weight: 30.0000 chunk 20 optimal weight: 0.0040 chunk 82 optimal weight: 10.0000 chunk 69 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 110 optimal weight: 30.0000 chunk 65 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 overall best weight: 3.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.042826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.031564 restraints weight = 83407.849| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.032849 restraints weight = 41311.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.033716 restraints weight = 26454.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.034321 restraints weight = 19832.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.034743 restraints weight = 16217.010| |-----------------------------------------------------------------------------| r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11756 Z= 0.152 Angle : 0.532 9.606 16509 Z= 0.304 Chirality : 0.039 0.299 1904 Planarity : 0.003 0.055 1565 Dihedral : 19.395 175.176 3095 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.35 % Allowed : 11.88 % Favored : 85.76 % 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: 1.44 (0.27), residues: 985 helix: 1.56 (0.24), residues: 486 sheet: 1.82 (0.58), residues: 80 loop : 0.15 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 71 TYR 0.010 0.001 TYR A 639 PHE 0.013 0.001 PHE A 970 TRP 0.005 0.001 TRP A 464 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.15 (11756) covalent geometry : angle 0.53192 / 0.30 (16509) hydrogen bonds : bond 0.05092 / 3.56 ( 503) hydrogen bonds : angle 4.34294 / 3.08 ( 1331) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.9553 (mtm180) cc_final: 0.8992 (mtp85) REVERT: A 161 MET cc_start: 0.9561 (mmm) cc_final: 0.9354 (mmm) REVERT: A 335 LEU cc_start: 0.9897 (OUTLIER) cc_final: 0.9655 (pp) REVERT: A 461 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8607 (tmm-80) REVERT: A 534 MET cc_start: 0.6941 (mtt) cc_final: 0.5652 (ttm) REVERT: A 585 ASP cc_start: 0.8609 (m-30) cc_final: 0.8337 (p0) REVERT: A 671 ARG cc_start: 0.9353 (OUTLIER) cc_final: 0.8887 (tmt170) REVERT: A 722 GLU cc_start: 0.9258 (mt-10) cc_final: 0.8876 (mp0) REVERT: A 739 GLN cc_start: 0.9726 (mm-40) cc_final: 0.9383 (mm-40) REVERT: A 746 GLU cc_start: 0.9432 (tt0) cc_final: 0.9053 (tt0) REVERT: A 1089 MET cc_start: 0.9155 (tpp) cc_final: 0.8678 (tpp) REVERT: A 1213 MET cc_start: 0.9502 (ttp) cc_final: 0.9213 (tpp) outliers start: 21 outliers final: 12 residues processed: 101 average time/residue: 0.0823 time to fit residues: 12.3130 Evaluate side-chains 93 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1153 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 24 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 87 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 23 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 595 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 612 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.041924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2573 r_free = 0.2573 target = 0.030893 restraints weight = 84919.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2611 r_free = 0.2611 target = 0.032144 restraints weight = 41800.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2638 r_free = 0.2638 target = 0.033005 restraints weight = 26919.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.033588 restraints weight = 19975.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.033995 restraints weight = 16311.084| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 11756 Z= 0.193 Angle : 0.563 12.190 16509 Z= 0.321 Chirality : 0.039 0.311 1904 Planarity : 0.004 0.054 1565 Dihedral : 19.469 175.616 3095 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.58 % Allowed : 12.56 % Favored : 84.87 % 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: 1.34 (0.27), residues: 985 helix: 1.44 (0.24), residues: 485 sheet: 1.78 (0.58), residues: 80 loop : 0.17 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.012 0.001 TYR A1356 PHE 0.015 0.001 PHE A 970 TRP 0.013 0.002 TRP A 464 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.19 (11756) covalent geometry : angle 0.56329 / 0.32 (16509) hydrogen bonds : bond 0.05289 / 3.66 ( 503) hydrogen bonds : angle 4.46323 / 3.15 ( 1331) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ARG cc_start: 0.9550 (mtm180) cc_final: 0.9343 (ttm110) REVERT: A 90 MET cc_start: 0.9013 (tpp) cc_final: 0.8770 (tpp) REVERT: A 161 MET cc_start: 0.9591 (mmm) cc_final: 0.9348 (mmm) REVERT: A 335 LEU cc_start: 0.9900 (OUTLIER) cc_final: 0.9658 (pp) REVERT: A 461 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8620 (tmm-80) REVERT: A 534 MET cc_start: 0.7110 (mtt) cc_final: 0.5859 (ttm) REVERT: A 585 ASP cc_start: 0.8588 (m-30) cc_final: 0.8282 (p0) REVERT: A 722 GLU cc_start: 0.9301 (mt-10) cc_final: 0.8942 (mp0) REVERT: A 739 GLN cc_start: 0.9762 (mm-40) cc_final: 0.9400 (mm-40) REVERT: A 746 GLU cc_start: 0.9448 (tt0) cc_final: 0.9156 (tt0) REVERT: A 1089 MET cc_start: 0.9188 (tpp) cc_final: 0.8729 (tpp) REVERT: A 1213 MET cc_start: 0.9513 (ttp) cc_final: 0.9209 (tpp) outliers start: 23 outliers final: 17 residues processed: 95 average time/residue: 0.0915 time to fit residues: 12.6918 Evaluate side-chains 99 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 80 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1153 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 96 optimal weight: 8.9990 chunk 30 optimal weight: 0.0870 chunk 26 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 37 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 overall best weight: 3.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.042329 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.031117 restraints weight = 85689.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.032401 restraints weight = 42064.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.033273 restraints weight = 26978.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.033864 restraints weight = 20113.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.034252 restraints weight = 16439.723| |-----------------------------------------------------------------------------| r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11756 Z= 0.148 Angle : 0.537 11.156 16509 Z= 0.305 Chirality : 0.038 0.338 1904 Planarity : 0.003 0.054 1565 Dihedral : 19.473 176.705 3095 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.13 % Allowed : 13.12 % Favored : 84.75 % 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: 1.44 (0.27), residues: 985 helix: 1.53 (0.24), residues: 485 sheet: 1.88 (0.59), residues: 80 loop : 0.18 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 71 TYR 0.011 0.001 TYR A1326 PHE 0.012 0.001 PHE A 970 TRP 0.008 0.001 TRP A 464 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (11756) covalent geometry : angle 0.53674 / 0.30 (16509) hydrogen bonds : bond 0.04998 / 3.47 ( 503) hydrogen bonds : angle 4.41566 / 3.11 ( 1331) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9610 (mmm) cc_final: 0.9353 (mmm) REVERT: A 335 LEU cc_start: 0.9896 (OUTLIER) cc_final: 0.9653 (pp) REVERT: A 461 ARG cc_start: 0.9046 (OUTLIER) cc_final: 0.8586 (tmm-80) REVERT: A 534 MET cc_start: 0.7154 (mtt) cc_final: 0.5925 (ttm) REVERT: A 585 ASP cc_start: 0.8586 (m-30) cc_final: 0.8285 (p0) REVERT: A 671 ARG cc_start: 0.9374 (OUTLIER) cc_final: 0.8931 (tmt170) REVERT: A 722 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8941 (mp0) REVERT: A 746 GLU cc_start: 0.9439 (tt0) cc_final: 0.9080 (tt0) REVERT: A 930 HIS cc_start: 0.9373 (m-70) cc_final: 0.8727 (m90) REVERT: A 1089 MET cc_start: 0.9197 (tpp) cc_final: 0.8756 (tpp) REVERT: A 1213 MET cc_start: 0.9518 (ttp) cc_final: 0.9218 (tpp) outliers start: 19 outliers final: 13 residues processed: 98 average time/residue: 0.0870 time to fit residues: 12.3817 Evaluate side-chains 95 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 671 ARG Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1139 VAL Chi-restraints excluded: chain A residue 1153 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 10.0000 chunk 102 optimal weight: 30.0000 chunk 24 optimal weight: 7.9990 chunk 111 optimal weight: 40.0000 chunk 64 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 89 optimal weight: 9.9990 chunk 93 optimal weight: 8.9990 chunk 81 optimal weight: 0.7980 overall best weight: 6.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.040870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2551 r_free = 0.2551 target = 0.029893 restraints weight = 87333.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.031132 restraints weight = 43477.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2615 r_free = 0.2615 target = 0.031954 restraints weight = 27971.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.032526 restraints weight = 21025.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.032875 restraints weight = 17220.190| |-----------------------------------------------------------------------------| r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.4053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11756 Z= 0.224 Angle : 0.617 12.124 16509 Z= 0.343 Chirality : 0.040 0.321 1904 Planarity : 0.004 0.053 1565 Dihedral : 19.543 177.023 3095 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.02 % Allowed : 13.79 % Favored : 84.19 % 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: 1.08 (0.27), residues: 985 helix: 1.17 (0.23), residues: 484 sheet: 1.67 (0.59), residues: 80 loop : 0.10 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 71 TYR 0.015 0.002 TYR A1356 PHE 0.017 0.002 PHE A 970 TRP 0.011 0.002 TRP A 464 HIS 0.005 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.22 (11756) covalent geometry : angle 0.61725 / 0.34 (16509) hydrogen bonds : bond 0.05677 / 3.91 ( 503) hydrogen bonds : angle 4.66436 / 3.30 ( 1331) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 MET cc_start: 0.9593 (mmm) cc_final: 0.9308 (mmm) REVERT: A 335 LEU cc_start: 0.9908 (OUTLIER) cc_final: 0.9669 (pp) REVERT: A 461 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8656 (tmm-80) REVERT: A 534 MET cc_start: 0.7333 (mtt) cc_final: 0.6076 (ttm) REVERT: A 585 ASP cc_start: 0.8561 (m-30) cc_final: 0.8283 (p0) REVERT: A 722 GLU cc_start: 0.9339 (mt-10) cc_final: 0.8974 (mp0) REVERT: A 746 GLU cc_start: 0.9430 (tt0) cc_final: 0.9162 (tt0) REVERT: A 1089 MET cc_start: 0.9235 (tpp) cc_final: 0.8793 (tpp) REVERT: A 1135 ASP cc_start: 0.9550 (p0) cc_final: 0.9233 (m-30) REVERT: A 1213 MET cc_start: 0.9541 (ttp) cc_final: 0.9217 (tpp) outliers start: 18 outliers final: 14 residues processed: 89 average time/residue: 0.0813 time to fit residues: 10.7791 Evaluate side-chains 91 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 540 LEU Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1095 VAL Chi-restraints excluded: chain A residue 1153 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 38 optimal weight: 8.9990 chunk 44 optimal weight: 30.0000 chunk 55 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 47 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 overall best weight: 8.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.039139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2512 r_free = 0.2512 target = 0.028607 restraints weight = 89709.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.2546 r_free = 0.2546 target = 0.029687 restraints weight = 44456.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2575 r_free = 0.2575 target = 0.030523 restraints weight = 29521.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2593 r_free = 0.2593 target = 0.031034 restraints weight = 21980.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.031424 restraints weight = 18137.894| |-----------------------------------------------------------------------------| r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 11756 Z= 0.308 Angle : 0.711 10.392 16509 Z= 0.394 Chirality : 0.043 0.254 1904 Planarity : 0.005 0.054 1565 Dihedral : 19.755 177.871 3095 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 19.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.47 % Allowed : 13.68 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.26), residues: 985 helix: 0.40 (0.22), residues: 486 sheet: 1.47 (0.58), residues: 72 loop : -0.13 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 69 TYR 0.026 0.002 TYR A1356 PHE 0.034 0.002 PHE A 693 TRP 0.012 0.002 TRP A 464 HIS 0.007 0.002 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.31 (11756) covalent geometry : angle 0.71055 / 0.39 (16509) hydrogen bonds : bond 0.06408 / 4.38 ( 503) hydrogen bonds : angle 5.03380 / 3.55 ( 1331) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.212 Fit side-chains revert: symmetry clash REVERT: A 125 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8150 (mm-30) REVERT: A 161 MET cc_start: 0.9562 (mmm) cc_final: 0.9259 (mmm) REVERT: A 335 LEU cc_start: 0.9912 (OUTLIER) cc_final: 0.9695 (pp) REVERT: A 461 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8684 (tmm-80) REVERT: A 534 MET cc_start: 0.7808 (mtt) cc_final: 0.6777 (ttm) REVERT: A 558 LYS cc_start: 0.9631 (mttt) cc_final: 0.9208 (mtpp) REVERT: A 585 ASP cc_start: 0.8552 (m-30) cc_final: 0.8265 (p0) REVERT: A 631 MET cc_start: 0.9150 (mmm) cc_final: 0.8469 (mmm) REVERT: A 722 GLU cc_start: 0.9427 (mt-10) cc_final: 0.9057 (mp0) REVERT: A 739 GLN cc_start: 0.9816 (mm-40) cc_final: 0.9483 (mm-40) REVERT: A 746 GLU cc_start: 0.9482 (tt0) cc_final: 0.9119 (tt0) REVERT: A 747 LEU cc_start: 0.9731 (mm) cc_final: 0.9513 (mt) REVERT: A 1089 MET cc_start: 0.9271 (tpp) cc_final: 0.8838 (tpp) REVERT: A 1213 MET cc_start: 0.9565 (ttp) cc_final: 0.9244 (tpp) outliers start: 22 outliers final: 14 residues processed: 90 average time/residue: 0.0854 time to fit residues: 11.4264 Evaluate side-chains 88 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 680 LEU Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1153 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 0 optimal weight: 20.0000 chunk 72 optimal weight: 20.0000 chunk 101 optimal weight: 30.0000 chunk 102 optimal weight: 30.0000 chunk 99 optimal weight: 40.0000 chunk 36 optimal weight: 7.9990 chunk 90 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 980 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.039845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2526 r_free = 0.2526 target = 0.029131 restraints weight = 87378.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.030350 restraints weight = 42869.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.031134 restraints weight = 27613.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.031712 restraints weight = 20790.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.032098 restraints weight = 17107.421| |-----------------------------------------------------------------------------| r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11756 Z= 0.189 Angle : 0.620 11.193 16509 Z= 0.341 Chirality : 0.042 0.335 1904 Planarity : 0.004 0.051 1565 Dihedral : 19.735 179.832 3095 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.91 % Allowed : 14.35 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.26), residues: 985 helix: 0.59 (0.23), residues: 493 sheet: 1.88 (0.59), residues: 70 loop : -0.04 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 71 TYR 0.015 0.002 TYR A 594 PHE 0.032 0.002 PHE A 693 TRP 0.015 0.001 TRP A 464 HIS 0.006 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.19 (11756) covalent geometry : angle 0.61971 / 0.34 (16509) hydrogen bonds : bond 0.05470 / 3.77 ( 503) hydrogen bonds : angle 4.81060 / 3.40 ( 1331) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1970 Ramachandran restraints generated. 985 Oldfield, 0 Emsley, 985 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 125 GLU cc_start: 0.9240 (OUTLIER) cc_final: 0.8109 (mm-30) REVERT: A 161 MET cc_start: 0.9573 (mmm) cc_final: 0.9241 (mmm) REVERT: A 335 LEU cc_start: 0.9909 (OUTLIER) cc_final: 0.9692 (pp) REVERT: A 461 ARG cc_start: 0.9019 (OUTLIER) cc_final: 0.8543 (tmm-80) REVERT: A 534 MET cc_start: 0.7950 (mtt) cc_final: 0.6770 (ttm) REVERT: A 558 LYS cc_start: 0.9628 (mttt) cc_final: 0.9250 (mtpp) REVERT: A 585 ASP cc_start: 0.8471 (m-30) cc_final: 0.8193 (p0) REVERT: A 631 MET cc_start: 0.9177 (mmm) cc_final: 0.8491 (mmm) REVERT: A 722 GLU cc_start: 0.9433 (mt-10) cc_final: 0.9083 (mp0) REVERT: A 739 GLN cc_start: 0.9726 (mm-40) cc_final: 0.9450 (mm-40) REVERT: A 746 GLU cc_start: 0.9496 (tt0) cc_final: 0.9156 (tt0) REVERT: A 1089 MET cc_start: 0.9249 (tpp) cc_final: 0.8803 (tpp) REVERT: A 1213 MET cc_start: 0.9590 (ttp) cc_final: 0.9326 (tpp) outliers start: 17 outliers final: 13 residues processed: 85 average time/residue: 0.0829 time to fit residues: 10.6341 Evaluate side-chains 87 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 125 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 448 ILE Chi-restraints excluded: chain A residue 461 ARG Chi-restraints excluded: chain A residue 465 MET Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 562 LYS Chi-restraints excluded: chain A residue 713 VAL Chi-restraints excluded: chain A residue 744 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 957 THR Chi-restraints excluded: chain A residue 1153 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 105 optimal weight: 30.0000 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 78 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.040548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2547 r_free = 0.2547 target = 0.029679 restraints weight = 86613.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.030923 restraints weight = 42281.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.031743 restraints weight = 27257.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.032328 restraints weight = 20445.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.032689 restraints weight = 16749.193| |-----------------------------------------------------------------------------| r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11756 Z= 0.146 Angle : 0.590 10.416 16509 Z= 0.322 Chirality : 0.040 0.302 1904 Planarity : 0.003 0.052 1565 Dihedral : 19.669 178.122 3095 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.91 % Allowed : 14.46 % Favored : 83.63 % 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: 0.83 (0.27), residues: 985 helix: 0.91 (0.23), residues: 493 sheet: 1.49 (0.56), residues: 85 loop : 0.03 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 71 TYR 0.011 0.001 TYR A 594 PHE 0.035 0.001 PHE A 693 TRP 0.014 0.001 TRP A 464 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 (11756) covalent geometry : angle 0.59019 / 0.32 (16509) hydrogen bonds : bond 0.05021 / 3.49 ( 503) hydrogen bonds : angle 4.58170 / 3.23 ( 1331) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1256.95 seconds wall clock time: 22 minutes 40.09 seconds (1360.09 seconds total)