Starting phenix.real_space_refine on Fri Jul 3 01:32:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w7t_65732/07_2026/9w7t_65732.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w7t_65732/07_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_65732/07_2026/9w7t_65732.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w7t_65732/07_2026/9w7t_65732.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w7t_65732/07_2026/9w7t_65732.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w7t_65732/07_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): 0.01s 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: 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: 2.86, per 1000 atoms: 0.25 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: 1.01 Conformation dependent library (CDL) restraints added in 440.5 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: 1.38 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: 2.47 Time building geometry restraints manager: 1.35 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: 15402 0.95 - 1.90: 887 1.90 - 2.85: 197 2.85 - 3.80: 20 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: 1320 0.029 - 0.059: 374 0.059 - 0.088: 133 0.088 - 0.118: 69 0.118 - 0.147: 8 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=" 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 2.46 2.33 0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" C1' A D 34 " pdb=" O4' A D 34 " pdb=" C2' A D 34 " pdb=" N9 A D 34 " both_signs ideal model delta sigma weight residual False 2.46 2.33 0.13 2.00e-01 2.50e+01 4.18e-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: 0.610 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: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 13.250 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.420 ------------------------------------------------------------------------------- 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= 0.260 Angle : 0.510 4.754 16509 Z= 0.417 Chirality : 0.036 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 0.00295 / 0.26 (11756) covalent geometry : angle 0.51007 / 0.42 (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 : 0.379 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: symmetry clash REVERT: A 473 ILE cc_start: 0.9129 (mt) cc_final: 0.8926 (tp) REVERT: A 534 MET cc_start: 0.5461 (mtt) cc_final: 0.4391 (ttm) REVERT: A 562 LYS cc_start: 0.9266 (tttt) cc_final: 0.8937 (tppt) REVERT: A 585 ASP cc_start: 0.8275 (m-30) cc_final: 0.7950 (m-30) REVERT: A 586 ARG cc_start: 0.9323 (ptp-170) cc_final: 0.9041 (ppt170) REVERT: A 969 ASP cc_start: 0.9101 (m-30) cc_final: 0.8363 (m-30) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.1318 time to fit residues: 36.9162 Evaluate side-chains 126 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.381 ------------------------------------------------------------------------------- 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: 30.0000 chunk 49 optimal weight: 0.0030 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 0.0570 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: 30.0000 overall best weight: 3.0114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 341 GLN 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 = 0.3025 r_free = 0.3025 target = 0.045394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2653 r_free = 0.2653 target = 0.033771 restraints weight = 80976.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.035135 restraints weight = 39571.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.036124 restraints weight = 25228.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.036716 restraints weight = 18558.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.036999 restraints weight = 15183.300| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11756 Z= 0.163 Angle : 0.613 9.610 16509 Z= 0.347 Chirality : 0.040 0.247 1904 Planarity : 0.005 0.065 1565 Dihedral : 19.211 173.127 3095 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.02 % Allowed : 8.18 % Favored : 89.80 % 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: 1.65 (0.27), residues: 985 helix: 1.84 (0.24), residues: 487 sheet: 1.86 (0.60), residues: 80 loop : 0.13 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 71 TYR 0.020 0.002 TYR A 656 PHE 0.013 0.001 PHE A1181 TRP 0.007 0.001 TRP A 18 HIS 0.014 0.001 HIS A 698 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (11756) covalent geometry : angle 0.61281 / 0.35 (16509) hydrogen bonds : bond 0.05920 / 4.13 ( 503) hydrogen bonds : angle 4.53021 / 3.22 ( 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 137 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.349 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: A 90 MET cc_start: 0.9054 (tpp) cc_final: 0.8638 (tpt) REVERT: A 335 LEU cc_start: 0.9884 (OUTLIER) cc_final: 0.9636 (pp) REVERT: A 448 ILE cc_start: 0.9688 (mt) cc_final: 0.9423 (tp) REVERT: A 455 LEU cc_start: 0.9498 (mp) cc_final: 0.8722 (tp) REVERT: A 473 ILE cc_start: 0.9751 (mt) cc_final: 0.9420 (mt) REVERT: A 534 MET cc_start: 0.6542 (mtt) cc_final: 0.5210 (ttp) REVERT: A 558 LYS cc_start: 0.9513 (mttt) cc_final: 0.9140 (ttpp) REVERT: A 562 LYS cc_start: 0.9407 (tttt) cc_final: 0.9111 (tppt) REVERT: A 586 ARG cc_start: 0.9587 (ptp-170) cc_final: 0.9353 (ppt170) REVERT: A 671 ARG cc_start: 0.9295 (OUTLIER) cc_final: 0.8919 (tmt170) REVERT: A 739 GLN cc_start: 0.9667 (mm-40) cc_final: 0.9192 (mm-40) REVERT: A 746 GLU cc_start: 0.9374 (tt0) cc_final: 0.9079 (tt0) REVERT: A 1089 MET cc_start: 0.9118 (tpp) cc_final: 0.8706 (tpp) REVERT: A 1097 LYS cc_start: 0.9621 (tttm) cc_final: 0.8564 (tptm) REVERT: A 1101 GLN cc_start: 0.9398 (mm-40) cc_final: 0.9061 (mm110) REVERT: A 1213 MET cc_start: 0.9446 (ttm) cc_final: 0.9228 (tpp) REVERT: A 1228 LEU cc_start: 0.9101 (tp) cc_final: 0.8827 (tp) outliers start: 18 outliers final: 12 residues processed: 131 average time/residue: 0.1136 time to fit residues: 20.9374 Evaluate side-chains 101 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 524 LEU 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 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: 10.0000 chunk 50 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 108 optimal weight: 30.0000 chunk 99 optimal weight: 40.0000 chunk 62 optimal weight: 6.9990 chunk 98 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 84 optimal weight: 20.0000 chunk 82 optimal weight: 3.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 990 ASN ** 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 = 0.2976 r_free = 0.2976 target = 0.043333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.032068 restraints weight = 83387.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.033377 restraints weight = 40535.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.034285 restraints weight = 25868.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.034911 restraints weight = 19105.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.035379 restraints weight = 15484.715| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 11756 Z= 0.204 Angle : 0.577 9.711 16509 Z= 0.334 Chirality : 0.040 0.280 1904 Planarity : 0.004 0.071 1565 Dihedral : 19.270 173.327 3095 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.35 % Allowed : 8.74 % Favored : 88.90 % 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: 1.47 (0.26), residues: 985 helix: 1.61 (0.23), residues: 488 sheet: 1.87 (0.59), residues: 80 loop : 0.11 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 655 TYR 0.013 0.002 TYR A 656 PHE 0.015 0.002 PHE A 553 TRP 0.009 0.001 TRP A 464 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.20 (11756) covalent geometry : angle 0.57679 / 0.33 (16509) hydrogen bonds : bond 0.05714 / 4.01 ( 503) hydrogen bonds : angle 4.48445 / 3.19 ( 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 113 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.9541 (ttp-170) cc_final: 0.8956 (ptp-110) REVERT: A 90 MET cc_start: 0.9215 (tpp) cc_final: 0.8962 (tpp) REVERT: A 335 LEU cc_start: 0.9907 (OUTLIER) cc_final: 0.9671 (pp) REVERT: A 448 ILE cc_start: 0.9669 (mt) cc_final: 0.9407 (tp) REVERT: A 473 ILE cc_start: 0.9748 (mt) cc_final: 0.9213 (tp) REVERT: A 534 MET cc_start: 0.6651 (mtt) cc_final: 0.5362 (ttm) REVERT: A 739 GLN cc_start: 0.9660 (mm-40) cc_final: 0.9229 (mm-40) REVERT: A 746 GLU cc_start: 0.9412 (tt0) cc_final: 0.8968 (tt0) REVERT: A 939 MET cc_start: 0.9679 (mmm) cc_final: 0.9425 (mmm) REVERT: A 1089 MET cc_start: 0.9142 (tpp) cc_final: 0.8678 (mmm) REVERT: A 1228 LEU cc_start: 0.9179 (tp) cc_final: 0.8897 (tp) outliers start: 21 outliers final: 13 residues processed: 106 average time/residue: 0.1096 time to fit residues: 16.8966 Evaluate side-chains 94 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 518 PHE 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: 8.9990 chunk 68 optimal weight: 0.6980 chunk 1 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 29 optimal weight: 5.9990 chunk 45 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 106 optimal weight: 30.0000 chunk 52 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 51 optimal weight: 10.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 990 ASN ** 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 = 0.2964 r_free = 0.2964 target = 0.042656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2590 r_free = 0.2590 target = 0.031407 restraints weight = 85615.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.032701 restraints weight = 42347.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.033583 restraints weight = 27200.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.034121 restraints weight = 20309.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.034534 restraints weight = 16765.732| |-----------------------------------------------------------------------------| r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.3183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 11756 Z= 0.200 Angle : 0.577 10.705 16509 Z= 0.332 Chirality : 0.039 0.250 1904 Planarity : 0.004 0.068 1565 Dihedral : 19.373 173.921 3095 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.13 % Allowed : 10.99 % Favored : 86.88 % 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: 1.22 (0.26), residues: 985 helix: 1.38 (0.23), residues: 486 sheet: 1.62 (0.58), residues: 80 loop : 0.07 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 395 TYR 0.011 0.001 TYR A1356 PHE 0.014 0.001 PHE A 970 TRP 0.008 0.001 TRP A 464 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.20 (11756) covalent geometry : angle 0.57738 / 0.33 (16509) hydrogen bonds : bond 0.05446 / 3.78 ( 503) hydrogen bonds : angle 4.54826 / 3.22 ( 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: 19 poor density : 83 time to evaluate : 0.392 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: A 63 ARG cc_start: 0.9538 (ttp-170) cc_final: 0.8965 (ptp-110) REVERT: A 90 MET cc_start: 0.9270 (tpp) cc_final: 0.9030 (tpp) REVERT: A 335 LEU cc_start: 0.9902 (OUTLIER) cc_final: 0.9652 (pp) REVERT: A 448 ILE cc_start: 0.9663 (mt) cc_final: 0.9394 (tp) REVERT: A 461 ARG cc_start: 0.9097 (OUTLIER) cc_final: 0.8637 (tmm-80) REVERT: A 534 MET cc_start: 0.6912 (mtt) cc_final: 0.5604 (ttm) REVERT: A 585 ASP cc_start: 0.8597 (m-30) cc_final: 0.8314 (p0) REVERT: A 671 ARG cc_start: 0.9314 (OUTLIER) cc_final: 0.8996 (tmt170) REVERT: A 722 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8892 (mp0) REVERT: A 746 GLU cc_start: 0.9430 (tt0) cc_final: 0.9069 (tt0) REVERT: A 1089 MET cc_start: 0.9165 (tpp) cc_final: 0.8338 (tmm) REVERT: A 1214 LEU cc_start: 0.9865 (tp) cc_final: 0.9623 (tp) REVERT: A 1228 LEU cc_start: 0.9124 (tp) cc_final: 0.8900 (tp) outliers start: 19 outliers final: 13 residues processed: 94 average time/residue: 0.1197 time to fit residues: 16.1121 Evaluate side-chains 96 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain A residue 1238 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 80 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 79 optimal weight: 7.9990 chunk 102 optimal weight: 30.0000 chunk 20 optimal weight: 0.2980 chunk 82 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 110 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- 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 = 0.2959 r_free = 0.2959 target = 0.042387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.031182 restraints weight = 84367.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.032488 restraints weight = 41386.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.033375 restraints weight = 26420.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.033922 restraints weight = 19654.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2682 r_free = 0.2682 target = 0.034325 restraints weight = 16161.792| |-----------------------------------------------------------------------------| r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11756 Z= 0.165 Angle : 0.546 10.449 16509 Z= 0.311 Chirality : 0.039 0.351 1904 Planarity : 0.004 0.065 1565 Dihedral : 19.420 175.651 3095 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.35 % Allowed : 11.66 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.27), residues: 985 helix: 1.47 (0.23), residues: 486 sheet: 1.71 (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 671 TYR 0.011 0.001 TYR A1356 PHE 0.014 0.001 PHE A 970 TRP 0.006 0.001 TRP A 464 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.17 (11756) covalent geometry : angle 0.54591 / 0.31 (16509) hydrogen bonds : bond 0.05143 / 3.58 ( 503) hydrogen bonds : angle 4.39802 / 3.12 ( 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 : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.9512 (ttp-170) cc_final: 0.8976 (ptp-110) REVERT: A 90 MET cc_start: 0.9330 (tpp) cc_final: 0.9096 (tpp) REVERT: A 161 MET cc_start: 0.9567 (mmm) cc_final: 0.9278 (mmm) REVERT: A 335 LEU cc_start: 0.9898 (OUTLIER) cc_final: 0.9656 (pp) REVERT: A 448 ILE cc_start: 0.9636 (mt) cc_final: 0.9380 (tp) REVERT: A 461 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8579 (tmm-80) REVERT: A 534 MET cc_start: 0.6945 (mtt) cc_final: 0.5638 (ttm) REVERT: A 558 LYS cc_start: 0.9540 (mttt) cc_final: 0.9111 (mtpp) REVERT: A 585 ASP cc_start: 0.8620 (m-30) cc_final: 0.8320 (p0) REVERT: A 722 GLU cc_start: 0.9283 (mt-10) cc_final: 0.8917 (mp0) REVERT: A 746 GLU cc_start: 0.9444 (tt0) cc_final: 0.9057 (tt0) REVERT: A 1089 MET cc_start: 0.9153 (tpp) cc_final: 0.8693 (tpp) REVERT: A 1097 LYS cc_start: 0.9153 (tttm) cc_final: 0.8853 (tptt) REVERT: A 1099 GLU cc_start: 0.7403 (mp0) cc_final: 0.7095 (mp0) REVERT: A 1204 PHE cc_start: 0.9675 (m-80) cc_final: 0.9439 (m-10) outliers start: 21 outliers final: 12 residues processed: 102 average time/residue: 0.1219 time to fit residues: 17.7495 Evaluate side-chains 94 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 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 646 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 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: 9.9990 chunk 47 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 95 optimal weight: 6.9990 chunk 45 optimal weight: 30.0000 chunk 6 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 80 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 612 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.041271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2559 r_free = 0.2559 target = 0.030298 restraints weight = 86124.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2598 r_free = 0.2598 target = 0.031540 restraints weight = 42470.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.032388 restraints weight = 27371.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.032965 restraints weight = 20342.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.033373 restraints weight = 16559.487| |-----------------------------------------------------------------------------| r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 11756 Z= 0.225 Angle : 0.589 12.333 16509 Z= 0.335 Chirality : 0.040 0.420 1904 Planarity : 0.004 0.063 1565 Dihedral : 19.523 176.029 3095 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 15.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.58 % Allowed : 12.67 % 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: 1.17 (0.27), residues: 985 helix: 1.29 (0.23), residues: 485 sheet: 2.05 (0.60), residues: 70 loop : 0.07 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 671 TYR 0.013 0.002 TYR A1356 PHE 0.016 0.002 PHE A 970 TRP 0.011 0.001 TRP A 464 HIS 0.004 0.001 HIS A 595 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.22 (11756) covalent geometry : angle 0.58914 / 0.34 (16509) hydrogen bonds : bond 0.05618 / 3.87 ( 503) hydrogen bonds : angle 4.58646 / 3.25 ( 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 101 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 78 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.9501 (ttp-170) cc_final: 0.9013 (ptp-170) REVERT: A 90 MET cc_start: 0.9358 (tpp) cc_final: 0.9076 (tpp) REVERT: A 161 MET cc_start: 0.9555 (mmm) cc_final: 0.9267 (mmm) REVERT: A 335 LEU cc_start: 0.9905 (OUTLIER) cc_final: 0.9670 (pp) REVERT: A 380 LEU cc_start: 0.9789 (OUTLIER) cc_final: 0.9587 (tp) REVERT: A 448 ILE cc_start: 0.9624 (mt) cc_final: 0.9382 (tp) REVERT: A 461 ARG cc_start: 0.9057 (OUTLIER) cc_final: 0.8632 (tmm-80) REVERT: A 534 MET cc_start: 0.7148 (mtt) cc_final: 0.5848 (ttm) REVERT: A 558 LYS cc_start: 0.9565 (mttt) cc_final: 0.8871 (mtpp) REVERT: A 586 ARG cc_start: 0.9291 (ttp-110) cc_final: 0.8997 (mtt-85) REVERT: A 633 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.9035 (mp0) REVERT: A 671 ARG cc_start: 0.9346 (OUTLIER) cc_final: 0.8920 (tmt170) REVERT: A 722 GLU cc_start: 0.9329 (mt-10) cc_final: 0.8966 (mp0) REVERT: A 746 GLU cc_start: 0.9465 (tt0) cc_final: 0.9094 (tt0) REVERT: A 1089 MET cc_start: 0.9212 (tpp) cc_final: 0.8769 (tpp) REVERT: A 1135 ASP cc_start: 0.9492 (p0) cc_final: 0.9272 (m-30) REVERT: A 1213 MET cc_start: 0.9365 (tpp) cc_final: 0.9094 (tpp) outliers start: 23 outliers final: 15 residues processed: 92 average time/residue: 0.1251 time to fit residues: 16.1849 Evaluate side-chains 97 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS 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 380 LEU 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 633 GLU Chi-restraints excluded: chain A residue 646 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: 9.9990 chunk 30 optimal weight: 9.9990 chunk 26 optimal weight: 0.5980 chunk 11 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 15 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 36 optimal weight: 4.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- 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 = 0.2957 r_free = 0.2957 target = 0.042038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.030927 restraints weight = 83947.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.032225 restraints weight = 40796.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.033097 restraints weight = 25941.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.033703 restraints weight = 19225.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.034095 restraints weight = 15591.121| |-----------------------------------------------------------------------------| r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11756 Z= 0.139 Angle : 0.547 13.837 16509 Z= 0.306 Chirality : 0.039 0.314 1904 Planarity : 0.003 0.059 1565 Dihedral : 19.517 177.703 3095 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.35 % Allowed : 12.78 % 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: 1.40 (0.27), residues: 985 helix: 1.50 (0.24), residues: 484 sheet: 1.89 (0.59), residues: 80 loop : 0.16 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 671 TYR 0.009 0.001 TYR A1356 PHE 0.012 0.001 PHE A 970 TRP 0.009 0.001 TRP A 464 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.14 (11756) covalent geometry : angle 0.54699 / 0.31 (16509) hydrogen bonds : bond 0.04963 / 3.45 ( 503) hydrogen bonds : angle 4.40100 / 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 107 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.9465 (ttp-170) cc_final: 0.8935 (ptp-170) REVERT: A 90 MET cc_start: 0.9360 (tpp) cc_final: 0.9052 (tpp) REVERT: A 161 MET cc_start: 0.9585 (mmm) cc_final: 0.9256 (mmm) REVERT: A 335 LEU cc_start: 0.9896 (OUTLIER) cc_final: 0.9652 (pp) REVERT: A 448 ILE cc_start: 0.9601 (mt) cc_final: 0.9371 (tp) REVERT: A 461 ARG cc_start: 0.9037 (OUTLIER) cc_final: 0.8545 (tmm-80) REVERT: A 534 MET cc_start: 0.7343 (mtt) cc_final: 0.6154 (ttm) REVERT: A 633 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.8984 (mp0) REVERT: A 722 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8927 (mp0) REVERT: A 746 GLU cc_start: 0.9448 (tt0) cc_final: 0.9101 (tt0) REVERT: A 930 HIS cc_start: 0.9375 (m-70) cc_final: 0.8728 (m90) REVERT: A 1089 MET cc_start: 0.9167 (tpp) cc_final: 0.8725 (tpp) REVERT: A 1097 LYS cc_start: 0.9212 (tttm) cc_final: 0.9007 (tptt) REVERT: A 1135 ASP cc_start: 0.9555 (p0) cc_final: 0.9242 (m-30) REVERT: A 1213 MET cc_start: 0.9350 (tpp) cc_final: 0.9103 (tpp) outliers start: 21 outliers final: 10 residues processed: 100 average time/residue: 0.1182 time to fit residues: 16.9145 Evaluate side-chains 94 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.379 ------------------------------------------------------------------------------- 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 461 ARG 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 633 GLU Chi-restraints excluded: chain A residue 646 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 1153 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 28 optimal weight: 2.9990 chunk 102 optimal weight: 30.0000 chunk 24 optimal weight: 7.9990 chunk 111 optimal weight: 30.0000 chunk 64 optimal weight: 0.2980 chunk 2 optimal weight: 0.0470 chunk 95 optimal weight: 7.9990 chunk 23 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 93 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.2684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 HIS ** 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 = 0.2977 r_free = 0.2977 target = 0.042785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2603 r_free = 0.2603 target = 0.031539 restraints weight = 83694.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.032854 restraints weight = 40807.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.033766 restraints weight = 26034.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.034328 restraints weight = 19267.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.034757 restraints weight = 15800.860| |-----------------------------------------------------------------------------| r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11756 Z= 0.115 Angle : 0.574 15.117 16509 Z= 0.308 Chirality : 0.039 0.314 1904 Planarity : 0.003 0.056 1565 Dihedral : 19.489 179.048 3095 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.46 % Allowed : 13.68 % 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: 1.42 (0.27), residues: 985 helix: 1.48 (0.24), residues: 486 sheet: 2.01 (0.59), residues: 80 loop : 0.18 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 671 TYR 0.008 0.001 TYR A 639 PHE 0.016 0.001 PHE A1204 TRP 0.010 0.001 TRP A 464 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.11 (11756) covalent geometry : angle 0.57382 / 0.31 (16509) hydrogen bonds : bond 0.04762 / 3.33 ( 503) hydrogen bonds : angle 4.31684 / 3.04 ( 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 103 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 ARG cc_start: 0.9443 (ttp-170) cc_final: 0.9151 (ptm160) REVERT: A 90 MET cc_start: 0.9358 (tpp) cc_final: 0.9030 (tpp) REVERT: A 161 MET cc_start: 0.9608 (mmm) cc_final: 0.9275 (mmm) REVERT: A 335 LEU cc_start: 0.9893 (tt) cc_final: 0.9650 (pp) REVERT: A 448 ILE cc_start: 0.9596 (mt) cc_final: 0.9362 (tp) REVERT: A 461 ARG cc_start: 0.9024 (OUTLIER) cc_final: 0.8518 (tmm-80) REVERT: A 534 MET cc_start: 0.7351 (mtt) cc_final: 0.6170 (ttm) REVERT: A 558 LYS cc_start: 0.9572 (mttt) cc_final: 0.8818 (mtpp) REVERT: A 671 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.8978 (tmt170) REVERT: A 722 GLU cc_start: 0.9279 (mt-10) cc_final: 0.8926 (mp0) REVERT: A 746 GLU cc_start: 0.9449 (tt0) cc_final: 0.9078 (tt0) REVERT: A 930 HIS cc_start: 0.9370 (m-70) cc_final: 0.8731 (m90) REVERT: A 1089 MET cc_start: 0.9167 (tpp) cc_final: 0.8738 (tpp) REVERT: A 1097 LYS cc_start: 0.9242 (tttm) cc_final: 0.9017 (tptt) REVERT: A 1135 ASP cc_start: 0.9573 (p0) cc_final: 0.9260 (m-30) REVERT: A 1213 MET cc_start: 0.9379 (tpp) cc_final: 0.9131 (tpp) outliers start: 13 outliers final: 8 residues processed: 101 average time/residue: 0.1200 time to fit residues: 17.2780 Evaluate side-chains 92 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.422 ------------------------------------------------------------------------------- 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 461 ARG Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 646 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 1153 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 6.9990 chunk 48 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 44 optimal weight: 40.0000 chunk 55 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 73 optimal weight: 7.9990 chunk 3 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 68 optimal weight: 7.9990 overall best weight: 8.3990 ------------------------------------------------------------------------------- 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 = 0.2914 r_free = 0.2914 target = 0.040393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2544 r_free = 0.2544 target = 0.029711 restraints weight = 87464.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2583 r_free = 0.2583 target = 0.030928 restraints weight = 43049.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.031745 restraints weight = 27580.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.032311 restraints weight = 20591.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2641 r_free = 0.2641 target = 0.032661 restraints weight = 16800.262| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 11756 Z= 0.300 Angle : 0.695 15.738 16509 Z= 0.380 Chirality : 0.041 0.256 1904 Planarity : 0.005 0.058 1565 Dihedral : 19.577 177.658 3095 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 1.46 % Allowed : 14.13 % Favored : 84.42 % 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: 0.79 (0.26), residues: 985 helix: 0.88 (0.23), residues: 487 sheet: 1.86 (0.59), residues: 70 loop : 0.01 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 629 TYR 0.017 0.002 TYR A1356 PHE 0.044 0.002 PHE A 693 TRP 0.010 0.002 TRP A 464 HIS 0.006 0.002 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00558 / 0.30 (11756) covalent geometry : angle 0.69514 / 0.38 (16509) hydrogen bonds : bond 0.05953 / 4.09 ( 503) hydrogen bonds : angle 4.90238 / 3.46 ( 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 92 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9409 (tpp) cc_final: 0.9072 (tpp) REVERT: A 125 GLU cc_start: 0.9233 (OUTLIER) cc_final: 0.8116 (mm-30) REVERT: A 161 MET cc_start: 0.9579 (mmm) cc_final: 0.9266 (mmm) REVERT: A 335 LEU cc_start: 0.9907 (tt) cc_final: 0.9677 (pp) REVERT: A 461 ARG cc_start: 0.9070 (OUTLIER) cc_final: 0.8655 (tmm-80) REVERT: A 534 MET cc_start: 0.7479 (mtt) cc_final: 0.6241 (ttm) REVERT: A 558 LYS cc_start: 0.9394 (mttt) cc_final: 0.9011 (tttm) REVERT: A 722 GLU cc_start: 0.9390 (mt-10) cc_final: 0.9023 (mp0) REVERT: A 746 GLU cc_start: 0.9453 (tt0) cc_final: 0.9094 (tt0) REVERT: A 1089 MET cc_start: 0.9261 (tpp) cc_final: 0.8826 (tpp) REVERT: A 1213 MET cc_start: 0.9307 (tpp) cc_final: 0.9103 (tpp) REVERT: A 1228 LEU cc_start: 0.9275 (tp) cc_final: 0.8944 (tp) outliers start: 13 outliers final: 10 residues processed: 90 average time/residue: 0.1220 time to fit residues: 15.5465 Evaluate side-chains 85 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 LYS 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 461 ARG Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 646 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 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: 8.9990 chunk 90 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 45 optimal weight: 0.7980 chunk 54 optimal weight: 7.9990 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 = 0.2915 r_free = 0.2915 target = 0.040464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2545 r_free = 0.2545 target = 0.029704 restraints weight = 86762.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.030935 restraints weight = 42524.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2612 r_free = 0.2612 target = 0.031786 restraints weight = 27181.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2629 r_free = 0.2629 target = 0.032317 restraints weight = 20174.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.032713 restraints weight = 16578.013| |-----------------------------------------------------------------------------| r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.4452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11756 Z= 0.221 Angle : 0.640 14.206 16509 Z= 0.350 Chirality : 0.041 0.290 1904 Planarity : 0.004 0.057 1565 Dihedral : 19.640 179.311 3095 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.57 % Allowed : 14.24 % 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: 0.71 (0.26), residues: 985 helix: 0.84 (0.23), residues: 486 sheet: 1.30 (0.55), residues: 85 loop : -0.03 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 671 TYR 0.015 0.002 TYR A 594 PHE 0.036 0.002 PHE A 693 TRP 0.013 0.001 TRP A 464 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.22 (11756) covalent geometry : angle 0.64004 / 0.35 (16509) hydrogen bonds : bond 0.05357 / 3.69 ( 503) hydrogen bonds : angle 4.79928 / 3.38 ( 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: 14 poor density : 77 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.9403 (tpp) cc_final: 0.9046 (tpp) REVERT: A 125 GLU cc_start: 0.9234 (OUTLIER) cc_final: 0.8079 (mm-30) REVERT: A 161 MET cc_start: 0.9565 (mmm) cc_final: 0.9211 (mmm) REVERT: A 335 LEU cc_start: 0.9909 (tt) cc_final: 0.9678 (pp) REVERT: A 461 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8571 (tmm-80) REVERT: A 534 MET cc_start: 0.7684 (mtt) cc_final: 0.6599 (ttm) REVERT: A 558 LYS cc_start: 0.9410 (mttt) cc_final: 0.9063 (tttm) REVERT: A 722 GLU cc_start: 0.9391 (mt-10) cc_final: 0.9032 (mp0) REVERT: A 746 GLU cc_start: 0.9483 (tt0) cc_final: 0.9128 (tt0) REVERT: A 1089 MET cc_start: 0.9200 (tpp) cc_final: 0.8758 (tpp) REVERT: A 1213 MET cc_start: 0.9387 (tpp) cc_final: 0.9164 (tpp) outliers start: 14 outliers final: 10 residues processed: 88 average time/residue: 0.1178 time to fit residues: 14.9910 Evaluate side-chains 86 residues out of total 892 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.350 ------------------------------------------------------------------------------- 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 461 ARG Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 646 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 1153 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 49 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 3 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 40 optimal weight: 20.0000 chunk 105 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 78 optimal weight: 30.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.2887 r_free = 0.2887 target = 0.039560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2519 r_free = 0.2519 target = 0.028976 restraints weight = 88623.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.030155 restraints weight = 43215.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.030945 restraints weight = 27804.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.031505 restraints weight = 20772.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2614 r_free = 0.2614 target = 0.031862 restraints weight = 17040.669| |-----------------------------------------------------------------------------| r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11756 Z= 0.259 Angle : 0.669 13.391 16509 Z= 0.368 Chirality : 0.041 0.282 1904 Planarity : 0.004 0.057 1565 Dihedral : 19.755 179.442 3095 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 18.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.57 % Allowed : 14.35 % Favored : 84.08 % 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: 0.45 (0.26), residues: 985 helix: 0.55 (0.23), residues: 487 sheet: 1.47 (0.58), residues: 72 loop : -0.05 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 403 TYR 0.017 0.002 TYR A1356 PHE 0.037 0.002 PHE A 693 TRP 0.012 0.002 TRP A 464 HIS 0.006 0.002 HIS A1262 Details of bonding type rmsd/Z covalent geometry : bond 0.00487 / 0.26 (11756) covalent geometry : angle 0.66890 / 0.37 (16509) hydrogen bonds : bond 0.05869 / 4.03 ( 503) hydrogen bonds : angle 4.97428 / 3.50 ( 1331) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1687.02 seconds wall clock time: 30 minutes 19.21 seconds (1819.21 seconds total)