Starting phenix.real_space_refine on Wed Aug 5 23:10:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k4h_62059/08_2026/9k4h_62059.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k4h_62059/08_2026/9k4h_62059.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k4h_62059/08_2026/9k4h_62059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k4h_62059/08_2026/9k4h_62059.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k4h_62059/08_2026/9k4h_62059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k4h_62059/08_2026/9k4h_62059.map" } resolution = 3.36 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= 0.006 sd= 0.124 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 133 5.49 5 S 19 5.16 5 C 7162 2.51 5 N 2115 2.21 5 O 2609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12038 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1126, 9173 Classifications: {'peptide': 1126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 30, 'TRANS': 1095} Chain breaks: 2 Chain: "B" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 581 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "C" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 325 Classifications: {'DNA': 16} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 15} Chain: "D" Number of atoms: 1959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1959 Classifications: {'RNA': 92} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 44, 'rna3p_pyr': 37} Link IDs: {'rna2p': 11, 'rna3p': 80} Time building chain proxies: 2.90, per 1000 atoms: 0.24 Number of scatterers: 12038 At special positions: 0 Unit cell: (132.495, 101.835, 142.35, 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 133 15.00 O 2609 8.00 N 2115 7.00 C 7162 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: 1.16 Conformation dependent library (CDL) restraints added in 515.1 milliseconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 5 sheets defined 54.9% alpha, 7.4% beta 38 base pairs and 82 stacking pairs defined. Time for finding SS restraints: 1.50 Creating SS restraints... Processing helix chain 'A' and resid 58 through 94 removed outlier: 4.552A pdb=" N THR A 62 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.604A 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 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.815A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.502A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 228 Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 286 through 304 Processing helix chain 'A' and resid 317 through 343 Processing helix chain 'A' and resid 346 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 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: 3.664A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 426 removed outlier: 3.869A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.663A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 474 through 476 No H-bonds generated for 'chain 'A' and resid 474 through 476' Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.923A pdb=" N MET A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.140A 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 602 Processing helix chain 'A' and resid 603 through 609 Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.545A pdb=" N PHE A 626 " --> pdb=" O THR A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.747A pdb=" N ILE A 632 " --> pdb=" O ASP A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 663 through 669 Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 699 Processing helix chain 'A' and resid 703 through 712 Processing helix chain 'A' and resid 723 through 727 Processing helix chain 'A' and resid 730 through 751 Processing helix chain 'A' and resid 928 through 940 removed outlier: 3.789A pdb=" N ARG A 938 " --> pdb=" O ILE A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 959 through 970 removed outlier: 3.593A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 998 Processing helix chain 'A' and resid 1081 through 1089 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 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 removed outlier: 3.725A pdb=" N PHE A1235 " --> pdb=" O LYS A1231 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A1237 " --> pdb=" O VAL A1233 " (cutoff:3.500A) Processing helix chain 'A' and resid 1248 through 1262 removed outlier: 3.644A pdb=" N HIS A1262 " --> pdb=" O PHE A1258 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1280 removed outlier: 4.024A pdb=" N ILE A1270 " --> pdb=" O LEU A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1313 removed outlier: 3.728A pdb=" N ASN A1308 " --> pdb=" O GLU A1304 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1343 removed outlier: 3.564A pdb=" N VAL A1342 " --> pdb=" O THR A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957 removed outlier: 5.953A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TRP A 18 " --> pdb=" O GLY A 49 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY A 49 " --> pdb=" O TRP A 18 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN A1093 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA A 50 " --> pdb=" O ASN A1093 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 4.718A pdb=" N GLU A1357 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE A1204 " --> pdb=" O ARG A1212 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A1212 " --> pdb=" O PHE A1204 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA4, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.527A pdb=" N LYS A1156 " --> pdb=" O LYS A1151 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1324 through 1326 removed outlier: 3.792A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 424 hydrogen bonds defined for protein. 1236 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 94 hydrogen bonds 176 hydrogen bond angles 0 basepair planarities 38 basepair parallelities 82 stacking parallelities Total time for adding SS restraints: 2.98 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2337 1.33 - 1.45: 3525 1.45 - 1.57: 6384 1.57 - 1.69: 266 1.69 - 1.81: 36 Bond restraints: 12548 Sorted by residual: bond pdb=" C3' DC B 3 " pdb=" C2' DC B 3 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.65e+00 bond pdb=" C3' DC B 13 " pdb=" C2' DC B 13 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.24e+00 bond pdb=" C3' DC C 15 " pdb=" C2' DC C 15 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.18e+00 bond pdb=" C3' DG B 12 " pdb=" C2' DG B 12 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.25e+00 bond pdb=" N9 G D 45 " pdb=" C4 G D 45 " ideal model delta sigma weight residual 1.375 1.396 -0.021 8.00e-03 1.56e+04 7.05e+00 ... (remaining 12543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 16443 1.29 - 2.57: 887 2.57 - 3.86: 182 3.86 - 5.15: 20 5.15 - 6.44: 5 Bond angle restraints: 17537 Sorted by residual: angle pdb=" C6 G D 45 " pdb=" N1 G D 45 " pdb=" C2 G D 45 " ideal model delta sigma weight residual 125.10 120.82 4.28 6.00e-01 2.78e+00 5.09e+01 angle pdb=" N9 G D 45 " pdb=" C4 G D 45 " pdb=" N3 G D 45 " ideal model delta sigma weight residual 126.00 129.67 -3.67 6.00e-01 2.78e+00 3.74e+01 angle pdb=" C5 G D 45 " pdb=" C4 G D 45 " pdb=" N3 G D 45 " ideal model delta sigma weight residual 128.60 125.74 2.86 5.00e-01 4.00e+00 3.28e+01 angle pdb=" C5 G D 45 " pdb=" C6 G D 45 " pdb=" O6 G D 45 " ideal model delta sigma weight residual 128.60 125.49 3.11 6.00e-01 2.78e+00 2.69e+01 angle pdb=" O4' DG B 23 " pdb=" C4' DG B 23 " pdb=" C3' DG B 23 " ideal model delta sigma weight residual 106.00 103.06 2.94 6.00e-01 2.78e+00 2.40e+01 ... (remaining 17532 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.11: 7124 30.11 - 60.22: 406 60.22 - 90.34: 74 90.34 - 120.45: 0 120.45 - 150.56: 1 Dihedral angle restraints: 7605 sinusoidal: 4297 harmonic: 3308 Sorted by residual: dihedral pdb=" CA LEU A 625 " pdb=" C LEU A 625 " pdb=" N PHE A 626 " pdb=" CA PHE A 626 " ideal model delta harmonic sigma weight residual 180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" CA LEU A 720 " pdb=" C LEU A 720 " pdb=" N HIS A 721 " pdb=" CA HIS A 721 " ideal model delta harmonic sigma weight residual 180.00 160.76 19.24 0 5.00e+00 4.00e-02 1.48e+01 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 69.44 150.56 1 3.50e+01 8.16e-04 1.47e+01 ... (remaining 7602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1332 0.034 - 0.067: 419 0.067 - 0.101: 137 0.101 - 0.135: 114 0.135 - 0.169: 21 Chirality restraints: 2023 Sorted by residual: chirality pdb=" C1' U D 12 " pdb=" O4' U D 12 " pdb=" C2' U D 12 " pdb=" N1 U D 12 " both_signs ideal model delta sigma weight residual False 2.47 2.30 0.17 2.00e-01 2.50e+01 7.11e-01 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 -2.57 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" C2' U D 12 " pdb=" C3' U D 12 " pdb=" O2' U D 12 " pdb=" C1' U D 12 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.79e-01 ... (remaining 2020 not shown) Planarity restraints: 1743 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U D 12 " -0.029 2.00e-02 2.50e+03 1.49e-02 4.98e+00 pdb=" N1 U D 12 " 0.032 2.00e-02 2.50e+03 pdb=" C2 U D 12 " 0.000 2.00e-02 2.50e+03 pdb=" O2 U D 12 " 0.004 2.00e-02 2.50e+03 pdb=" N3 U D 12 " -0.002 2.00e-02 2.50e+03 pdb=" C4 U D 12 " -0.006 2.00e-02 2.50e+03 pdb=" O4 U D 12 " -0.008 2.00e-02 2.50e+03 pdb=" C5 U D 12 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U D 12 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G D 45 " -0.017 2.00e-02 2.50e+03 9.53e-03 2.72e+00 pdb=" N9 G D 45 " 0.021 2.00e-02 2.50e+03 pdb=" C8 G D 45 " 0.001 2.00e-02 2.50e+03 pdb=" N7 G D 45 " 0.000 2.00e-02 2.50e+03 pdb=" C5 G D 45 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G D 45 " 0.003 2.00e-02 2.50e+03 pdb=" O6 G D 45 " -0.013 2.00e-02 2.50e+03 pdb=" N1 G D 45 " 0.011 2.00e-02 2.50e+03 pdb=" C2 G D 45 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G D 45 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G D 45 " 0.002 2.00e-02 2.50e+03 pdb=" C4 G D 45 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 44 " -0.019 2.00e-02 2.50e+03 8.69e-03 2.08e+00 pdb=" N9 A D 44 " 0.020 2.00e-02 2.50e+03 pdb=" C8 A D 44 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A D 44 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A D 44 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A D 44 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A D 44 " -0.004 2.00e-02 2.50e+03 pdb=" N1 A D 44 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A D 44 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A D 44 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A D 44 " 0.003 2.00e-02 2.50e+03 ... (remaining 1740 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 11 2.02 - 2.74: 1066 2.74 - 3.46: 16825 3.46 - 4.18: 31124 4.18 - 4.90: 50864 Nonbonded interactions: 99890 Sorted by model distance: nonbonded pdb=" NZ LYS A 742 " pdb=" OP1 C D 69 " model vdw 1.297 3.120 nonbonded pdb=" NH2 ARG A 340 " pdb=" OP1 A D 43 " model vdw 1.297 3.120 nonbonded pdb=" NZ LYS A1340 " pdb=" OP2 DA B 8 " model vdw 1.298 3.120 nonbonded pdb=" OD2 ASP A 364 " pdb=" N3 G D 45 " model vdw 1.299 3.120 nonbonded pdb=" N LYS A1113 " pdb=" OP1 U D 26 " model vdw 1.306 3.120 ... (remaining 99885 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.430 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: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.310 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 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 : 0.004 0.041 12548 Z= 0.280 Angle : 0.671 6.436 17537 Z= 0.519 Chirality : 0.047 0.169 2023 Planarity : 0.003 0.046 1743 Dihedral : 16.911 150.559 5463 Min Nonbonded Distance : 1.297 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 0.00 % Allowed : 0.10 % Favored : 99.90 % 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: 0.58 (0.25), residues: 1120 helix: 1.22 (0.22), residues: 555 sheet: -0.66 (0.60), residues: 82 loop : -0.33 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 74 TYR 0.022 0.002 TYR A1265 PHE 0.017 0.002 PHE A1276 TRP 0.014 0.002 TRP A 464 HIS 0.005 0.001 HIS A 983 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.28 (12548) covalent geometry : angle 0.67103 / 0.52 (17537) hydrogen bonds : bond 0.16632 / 10.51 ( 518) hydrogen bonds : angle 6.20671 / 4.51 ( 1412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.335 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 199 ASN cc_start: 0.5703 (t0) cc_final: 0.4350 (p0) REVERT: A 238 PHE cc_start: 0.5451 (t80) cc_final: 0.5185 (t80) REVERT: A 334 LEU cc_start: 0.8220 (tp) cc_final: 0.7622 (mp) REVERT: A 466 THR cc_start: 0.8192 (m) cc_final: 0.7890 (p) REVERT: A 534 MET cc_start: 0.1284 (mtp) cc_final: -0.1893 (ttp) REVERT: A 645 ASP cc_start: 0.7792 (m-30) cc_final: 0.7171 (p0) REVERT: A 648 MET cc_start: 0.8121 (mmm) cc_final: 0.7846 (ppp) REVERT: A 682 PHE cc_start: 0.7719 (m-80) cc_final: 0.7415 (m-10) REVERT: A 1131 TYR cc_start: 0.7895 (m-80) cc_final: 0.7675 (m-80) REVERT: A 1332 ASP cc_start: 0.7090 (m-30) cc_final: 0.6496 (t0) outliers start: 0 outliers final: 0 residues processed: 203 average time/residue: 0.1353 time to fit residues: 37.4121 Evaluate side-chains 117 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 123 optimal weight: 30.0000 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 369 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 595 HIS A 698 HIS A 980 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.182939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.129687 restraints weight = 20324.656| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.99 r_work: 0.3794 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12548 Z= 0.158 Angle : 0.604 10.663 17537 Z= 0.338 Chirality : 0.041 0.324 2023 Planarity : 0.004 0.045 1743 Dihedral : 19.331 150.859 3096 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.29 % Allowed : 5.77 % Favored : 92.94 % 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: 0.56 (0.25), residues: 1120 helix: 1.13 (0.22), residues: 567 sheet: -0.57 (0.59), residues: 77 loop : -0.29 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 71 TYR 0.020 0.002 TYR A 973 PHE 0.023 0.002 PHE A 372 TRP 0.010 0.002 TRP A 464 HIS 0.004 0.001 HIS A1349 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (12548) covalent geometry : angle 0.60398 / 0.34 (17537) hydrogen bonds : bond 0.06348 / 3.99 ( 518) hydrogen bonds : angle 5.08990 / 3.66 ( 1412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASN cc_start: 0.5703 (t0) cc_final: 0.4362 (p0) REVERT: A 334 LEU cc_start: 0.8230 (tp) cc_final: 0.7542 (mp) REVERT: A 466 THR cc_start: 0.8180 (m) cc_final: 0.7916 (p) REVERT: A 534 MET cc_start: 0.1227 (mtp) cc_final: -0.1777 (ttp) REVERT: A 633 GLU cc_start: 0.5828 (pt0) cc_final: 0.5432 (pp20) REVERT: A 645 ASP cc_start: 0.8031 (m-30) cc_final: 0.6856 (p0) REVERT: A 682 PHE cc_start: 0.7696 (m-80) cc_final: 0.7382 (m-10) REVERT: A 1131 TYR cc_start: 0.8107 (m-80) cc_final: 0.7905 (m-80) REVERT: A 1332 ASP cc_start: 0.6974 (m-30) cc_final: 0.6393 (t0) outliers start: 13 outliers final: 7 residues processed: 141 average time/residue: 0.1189 time to fit residues: 23.6431 Evaluate side-chains 112 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1290 VAL Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 8.9990 chunk 71 optimal weight: 0.0870 chunk 39 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 93 optimal weight: 0.9980 chunk 95 optimal weight: 0.0870 chunk 86 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 62 optimal weight: 4.9990 chunk 122 optimal weight: 40.0000 chunk 27 optimal weight: 10.0000 overall best weight: 1.8340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.180214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.126421 restraints weight = 20577.932| |-----------------------------------------------------------------------------| r_work (start): 0.3833 rms_B_bonded: 2.99 r_work: 0.3673 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12548 Z= 0.162 Angle : 0.600 8.307 17537 Z= 0.329 Chirality : 0.042 0.363 2023 Planarity : 0.004 0.035 1743 Dihedral : 19.380 149.916 3096 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.99 % Allowed : 6.96 % Favored : 91.05 % 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 (0.25), residues: 1120 helix: 1.05 (0.22), residues: 568 sheet: -0.72 (0.56), residues: 85 loop : -0.33 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 71 TYR 0.023 0.002 TYR A 973 PHE 0.019 0.002 PHE A 119 TRP 0.011 0.002 TRP A 464 HIS 0.004 0.001 HIS A1349 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.16 (12548) covalent geometry : angle 0.60002 / 0.33 (17537) hydrogen bonds : bond 0.05985 / 3.76 ( 518) hydrogen bonds : angle 4.86644 / 3.51 ( 1412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.6416 (tmm) cc_final: 0.5044 (tpp) REVERT: A 112 LYS cc_start: 0.7451 (mmtm) cc_final: 0.6988 (mmtm) REVERT: A 199 ASN cc_start: 0.5605 (t0) cc_final: 0.4198 (p0) REVERT: A 225 LEU cc_start: 0.5649 (OUTLIER) cc_final: 0.5436 (tt) REVERT: A 334 LEU cc_start: 0.8074 (tp) cc_final: 0.7420 (mp) REVERT: A 403 ARG cc_start: 0.8651 (mmm160) cc_final: 0.7629 (mmm160) REVERT: A 466 THR cc_start: 0.8429 (m) cc_final: 0.8004 (p) REVERT: A 534 MET cc_start: 0.1052 (mtp) cc_final: -0.1977 (ttp) REVERT: A 633 GLU cc_start: 0.5855 (pt0) cc_final: 0.5476 (pp20) REVERT: A 645 ASP cc_start: 0.7660 (m-30) cc_final: 0.7053 (p0) REVERT: A 682 PHE cc_start: 0.7716 (m-80) cc_final: 0.7374 (m-10) REVERT: A 694 MET cc_start: 0.6762 (tmm) cc_final: 0.6537 (tmm) REVERT: A 939 MET cc_start: 0.6084 (OUTLIER) cc_final: 0.5296 (ptm) REVERT: A 1332 ASP cc_start: 0.6953 (m-30) cc_final: 0.6237 (t0) outliers start: 20 outliers final: 8 residues processed: 130 average time/residue: 0.1116 time to fit residues: 21.0540 Evaluate side-chains 112 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 102 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1312 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 123 optimal weight: 30.0000 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 106 optimal weight: 10.0000 overall best weight: 4.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 369 GLN A1101 GLN A1350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.174390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.119718 restraints weight = 20508.286| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.96 r_work: 0.3551 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7263 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 12548 Z= 0.301 Angle : 0.762 9.955 17537 Z= 0.407 Chirality : 0.049 0.304 2023 Planarity : 0.005 0.047 1743 Dihedral : 19.663 145.987 3096 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.68 % Allowed : 8.05 % Favored : 89.26 % 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: -0.30 (0.24), residues: 1120 helix: 0.57 (0.21), residues: 565 sheet: -1.34 (0.58), residues: 76 loop : -0.85 (0.26), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1114 TYR 0.032 0.003 TYR A1237 PHE 0.033 0.003 PHE A 98 TRP 0.015 0.003 TRP A 464 HIS 0.008 0.002 HIS A1349 Details of bonding type rmsd/Z covalent geometry : bond 0.00637 / 0.30 (12548) covalent geometry : angle 0.76227 / 0.41 (17537) hydrogen bonds : bond 0.07555 / 4.82 ( 518) hydrogen bonds : angle 5.15173 / 3.70 ( 1412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3456 (ppp) cc_final: 0.3159 (ppp) REVERT: A 48 ILE cc_start: 0.8336 (OUTLIER) cc_final: 0.7545 (mt) REVERT: A 112 LYS cc_start: 0.7464 (mmtm) cc_final: 0.6546 (pttt) REVERT: A 225 LEU cc_start: 0.5747 (OUTLIER) cc_final: 0.5538 (tt) REVERT: A 238 PHE cc_start: 0.5980 (t80) cc_final: 0.5655 (t80) REVERT: A 334 LEU cc_start: 0.8054 (tp) cc_final: 0.7465 (mp) REVERT: A 466 THR cc_start: 0.8638 (m) cc_final: 0.8231 (p) REVERT: A 534 MET cc_start: 0.0505 (mtp) cc_final: -0.2280 (ttp) REVERT: A 633 GLU cc_start: 0.6134 (pt0) cc_final: 0.5745 (pp20) REVERT: A 645 ASP cc_start: 0.7709 (m-30) cc_final: 0.7278 (p0) REVERT: A 939 MET cc_start: 0.6319 (OUTLIER) cc_final: 0.5128 (ptm) REVERT: A 1166 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7613 (mm) REVERT: A 1191 LYS cc_start: 0.8403 (mppt) cc_final: 0.7778 (mmmt) REVERT: A 1332 ASP cc_start: 0.7173 (m-30) cc_final: 0.6444 (t0) outliers start: 27 outliers final: 14 residues processed: 132 average time/residue: 0.0917 time to fit residues: 17.8569 Evaluate side-chains 117 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1098 THR Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 96 optimal weight: 0.6980 chunk 72 optimal weight: 8.9990 chunk 123 optimal weight: 30.0000 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 99 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 120 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 = 0.4438 r_free = 0.4438 target = 0.176804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.122490 restraints weight = 20418.422| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 2.95 r_work: 0.3589 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 12548 Z= 0.183 Angle : 0.607 7.727 17537 Z= 0.334 Chirality : 0.042 0.316 2023 Planarity : 0.004 0.037 1743 Dihedral : 19.656 146.113 3096 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.68 % Allowed : 9.15 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.25), residues: 1120 helix: 0.89 (0.22), residues: 560 sheet: -1.05 (0.58), residues: 79 loop : -0.72 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1114 TYR 0.020 0.002 TYR A 973 PHE 0.018 0.002 PHE A 478 TRP 0.016 0.002 TRP A 18 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.18 (12548) covalent geometry : angle 0.60746 / 0.33 (17537) hydrogen bonds : bond 0.06134 / 3.85 ( 518) hydrogen bonds : angle 4.83596 / 3.49 ( 1412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 108 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.7642 (mmtm) cc_final: 0.7283 (mmtm) REVERT: A 238 PHE cc_start: 0.6064 (t80) cc_final: 0.5791 (t80) REVERT: A 274 ASP cc_start: 0.6615 (m-30) cc_final: 0.5651 (t0) REVERT: A 334 LEU cc_start: 0.8053 (tp) cc_final: 0.7473 (mp) REVERT: A 400 ARG cc_start: 0.6443 (OUTLIER) cc_final: 0.6224 (ttp-170) REVERT: A 466 THR cc_start: 0.8563 (m) cc_final: 0.8237 (p) REVERT: A 534 MET cc_start: 0.0340 (mtp) cc_final: -0.2119 (ptt) REVERT: A 633 GLU cc_start: 0.6137 (pt0) cc_final: 0.5813 (pp20) REVERT: A 663 SER cc_start: 0.8194 (t) cc_final: 0.7803 (p) REVERT: A 939 MET cc_start: 0.6263 (OUTLIER) cc_final: 0.5096 (ptm) REVERT: A 973 TYR cc_start: 0.7432 (m-10) cc_final: 0.6833 (m-10) REVERT: A 1166 ILE cc_start: 0.7822 (OUTLIER) cc_final: 0.7578 (mm) REVERT: A 1237 TYR cc_start: 0.4955 (OUTLIER) cc_final: 0.3295 (t80) REVERT: A 1332 ASP cc_start: 0.7108 (m-30) cc_final: 0.6329 (t0) outliers start: 27 outliers final: 14 residues processed: 125 average time/residue: 0.0966 time to fit residues: 18.0827 Evaluate side-chains 115 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 400 ARG Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1237 TYR Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 7.9990 chunk 45 optimal weight: 0.0670 chunk 111 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 51 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 933 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.173808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.119299 restraints weight = 20199.705| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 2.96 r_work: 0.3561 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 12548 Z= 0.236 Angle : 0.665 7.660 17537 Z= 0.360 Chirality : 0.045 0.302 2023 Planarity : 0.004 0.036 1743 Dihedral : 19.684 145.210 3096 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 2.78 % Allowed : 9.54 % Favored : 87.67 % 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: -0.10 (0.24), residues: 1120 helix: 0.81 (0.22), residues: 561 sheet: -1.35 (0.60), residues: 74 loop : -0.82 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1114 TYR 0.021 0.002 TYR A1237 PHE 0.022 0.002 PHE A 98 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 0.00502 / 0.24 (12548) covalent geometry : angle 0.66525 / 0.36 (17537) hydrogen bonds : bond 0.06627 / 4.22 ( 518) hydrogen bonds : angle 4.92873 / 3.55 ( 1412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 107 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7540 (mt) REVERT: A 90 MET cc_start: 0.7212 (tmm) cc_final: 0.5787 (tpt) REVERT: A 100 ARG cc_start: 0.7699 (mtm-85) cc_final: 0.7492 (mtm180) REVERT: A 112 LYS cc_start: 0.7721 (mmtm) cc_final: 0.7385 (mmtm) REVERT: A 238 PHE cc_start: 0.6109 (t80) cc_final: 0.5856 (t80) REVERT: A 274 ASP cc_start: 0.6674 (m-30) cc_final: 0.5694 (t0) REVERT: A 334 LEU cc_start: 0.7896 (tp) cc_final: 0.7336 (mp) REVERT: A 466 THR cc_start: 0.8697 (m) cc_final: 0.8266 (p) REVERT: A 534 MET cc_start: 0.0370 (mtp) cc_final: -0.2137 (ptt) REVERT: A 633 GLU cc_start: 0.6155 (pt0) cc_final: 0.5870 (pp20) REVERT: A 649 LYS cc_start: 0.6988 (tttt) cc_final: 0.6654 (ttpp) REVERT: A 663 SER cc_start: 0.8121 (t) cc_final: 0.7713 (p) REVERT: A 939 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.5248 (ptm) REVERT: A 973 TYR cc_start: 0.7405 (m-10) cc_final: 0.6640 (m-10) REVERT: A 1166 ILE cc_start: 0.7883 (OUTLIER) cc_final: 0.7618 (mm) REVERT: A 1237 TYR cc_start: 0.4999 (OUTLIER) cc_final: 0.3187 (t80) REVERT: A 1332 ASP cc_start: 0.7254 (m-30) cc_final: 0.6431 (t0) outliers start: 28 outliers final: 17 residues processed: 125 average time/residue: 0.1029 time to fit residues: 18.7534 Evaluate side-chains 118 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1237 TYR Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 1.9990 chunk 90 optimal weight: 5.9990 chunk 52 optimal weight: 20.0000 chunk 93 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 91 optimal weight: 0.0980 chunk 37 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 120 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 111 optimal weight: 2.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.176330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.121993 restraints weight = 20227.786| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.99 r_work: 0.3599 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12548 Z= 0.153 Angle : 0.589 11.820 17537 Z= 0.321 Chirality : 0.042 0.401 2023 Planarity : 0.004 0.036 1743 Dihedral : 19.663 146.327 3096 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.39 % Allowed : 10.24 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.25), residues: 1120 helix: 1.00 (0.22), residues: 562 sheet: -1.10 (0.57), residues: 79 loop : -0.70 (0.27), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 664 TYR 0.015 0.002 TYR A1237 PHE 0.021 0.002 PHE A 491 TRP 0.016 0.002 TRP A 464 HIS 0.006 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.15 (12548) covalent geometry : angle 0.58864 / 0.32 (17537) hydrogen bonds : bond 0.05732 / 3.60 ( 518) hydrogen bonds : angle 4.74227 / 3.40 ( 1412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7067 (tmm) cc_final: 0.5736 (tpt) REVERT: A 100 ARG cc_start: 0.7530 (mtm-85) cc_final: 0.7297 (mtm180) REVERT: A 112 LYS cc_start: 0.7659 (mmtm) cc_final: 0.7254 (mmtm) REVERT: A 220 ARG cc_start: 0.6510 (mmm160) cc_final: 0.6305 (mmm160) REVERT: A 238 PHE cc_start: 0.6056 (t80) cc_final: 0.5828 (t80) REVERT: A 274 ASP cc_start: 0.6636 (m-30) cc_final: 0.5638 (t0) REVERT: A 334 LEU cc_start: 0.7929 (tp) cc_final: 0.7383 (mp) REVERT: A 466 THR cc_start: 0.8536 (m) cc_final: 0.8120 (p) REVERT: A 534 MET cc_start: 0.0365 (mtp) cc_final: -0.2080 (ptt) REVERT: A 633 GLU cc_start: 0.6180 (pt0) cc_final: 0.5867 (pp20) REVERT: A 649 LYS cc_start: 0.6909 (tttt) cc_final: 0.6659 (tmmt) REVERT: A 663 SER cc_start: 0.8125 (t) cc_final: 0.7723 (p) REVERT: A 939 MET cc_start: 0.6386 (OUTLIER) cc_final: 0.5269 (ptm) REVERT: A 973 TYR cc_start: 0.7443 (m-10) cc_final: 0.6746 (m-10) REVERT: A 1089 MET cc_start: 0.3724 (OUTLIER) cc_final: 0.3408 (mmt) REVERT: A 1108 GLU cc_start: 0.7971 (tp30) cc_final: 0.7459 (tm-30) REVERT: A 1166 ILE cc_start: 0.7849 (OUTLIER) cc_final: 0.7587 (mm) REVERT: A 1237 TYR cc_start: 0.4921 (OUTLIER) cc_final: 0.3302 (t80) REVERT: A 1332 ASP cc_start: 0.7184 (m-30) cc_final: 0.6352 (t0) outliers start: 24 outliers final: 17 residues processed: 119 average time/residue: 0.1117 time to fit residues: 19.2288 Evaluate side-chains 120 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1237 TYR Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 38 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 116 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 121 optimal weight: 20.0000 overall best weight: 2.8986 ------------------------------------------------------------------------------- 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 = 0.4406 r_free = 0.4406 target = 0.174304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.119706 restraints weight = 20359.333| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.97 r_work: 0.3565 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 12548 Z= 0.199 Angle : 0.623 8.752 17537 Z= 0.337 Chirality : 0.044 0.299 2023 Planarity : 0.004 0.034 1743 Dihedral : 19.633 146.502 3096 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.19 % Allowed : 10.64 % Favored : 87.18 % 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: 0.08 (0.25), residues: 1120 helix: 0.96 (0.22), residues: 561 sheet: -0.89 (0.63), residues: 69 loop : -0.82 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 400 TYR 0.015 0.002 TYR A1237 PHE 0.038 0.002 PHE A 372 TRP 0.012 0.002 TRP A 464 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.20 (12548) covalent geometry : angle 0.62278 / 0.34 (17537) hydrogen bonds : bond 0.06201 / 3.94 ( 518) hydrogen bonds : angle 4.80129 / 3.46 ( 1412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 105 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7166 (tmm) cc_final: 0.5830 (tpt) REVERT: A 100 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7461 (mtm180) REVERT: A 112 LYS cc_start: 0.7732 (mmtm) cc_final: 0.7287 (mmtm) REVERT: A 220 ARG cc_start: 0.6519 (mmm160) cc_final: 0.6311 (mmm160) REVERT: A 238 PHE cc_start: 0.6000 (t80) cc_final: 0.5790 (t80) REVERT: A 274 ASP cc_start: 0.6687 (m-30) cc_final: 0.5719 (t0) REVERT: A 334 LEU cc_start: 0.7835 (tp) cc_final: 0.7292 (mp) REVERT: A 466 THR cc_start: 0.8572 (m) cc_final: 0.8213 (p) REVERT: A 534 MET cc_start: 0.0376 (mtp) cc_final: -0.2160 (ptt) REVERT: A 633 GLU cc_start: 0.6132 (pt0) cc_final: 0.5853 (pp20) REVERT: A 649 LYS cc_start: 0.6986 (tttt) cc_final: 0.6752 (tmmt) REVERT: A 663 SER cc_start: 0.8103 (t) cc_final: 0.7744 (p) REVERT: A 939 MET cc_start: 0.6574 (OUTLIER) cc_final: 0.5538 (ptm) REVERT: A 973 TYR cc_start: 0.7777 (m-10) cc_final: 0.7129 (m-10) REVERT: A 1089 MET cc_start: 0.3788 (OUTLIER) cc_final: 0.3478 (mmt) REVERT: A 1108 GLU cc_start: 0.7973 (tp30) cc_final: 0.7490 (tm-30) REVERT: A 1166 ILE cc_start: 0.7856 (OUTLIER) cc_final: 0.7605 (mm) REVERT: A 1237 TYR cc_start: 0.4974 (OUTLIER) cc_final: 0.3306 (t80) REVERT: A 1332 ASP cc_start: 0.7248 (m-30) cc_final: 0.6410 (t0) outliers start: 22 outliers final: 15 residues processed: 116 average time/residue: 0.1081 time to fit residues: 18.6054 Evaluate side-chains 120 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1237 TYR Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 34 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 123 optimal weight: 30.0000 chunk 33 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 112 optimal weight: 50.0000 chunk 113 optimal weight: 20.0000 chunk 75 optimal weight: 0.9980 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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 = 0.4412 r_free = 0.4412 target = 0.174790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.129191 restraints weight = 20256.657| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 3.55 r_work: 0.3532 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12548 Z= 0.179 Angle : 0.605 12.053 17537 Z= 0.328 Chirality : 0.042 0.344 2023 Planarity : 0.004 0.035 1743 Dihedral : 19.622 147.807 3096 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.99 % Allowed : 11.03 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.25), residues: 1120 helix: 0.94 (0.22), residues: 560 sheet: -1.28 (0.57), residues: 84 loop : -0.72 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 400 TYR 0.015 0.002 TYR A1237 PHE 0.029 0.002 PHE A 372 TRP 0.014 0.002 TRP A 18 HIS 0.004 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.18 (12548) covalent geometry : angle 0.60514 / 0.33 (17537) hydrogen bonds : bond 0.05853 / 3.69 ( 518) hydrogen bonds : angle 4.77635 / 3.44 ( 1412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 105 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7141 (tmm) cc_final: 0.5832 (tpt) REVERT: A 100 ARG cc_start: 0.7780 (mtm-85) cc_final: 0.7555 (mtm180) REVERT: A 112 LYS cc_start: 0.7795 (mmtm) cc_final: 0.7377 (mmtm) REVERT: A 220 ARG cc_start: 0.6448 (mmm160) cc_final: 0.6231 (mmm160) REVERT: A 238 PHE cc_start: 0.6123 (t80) cc_final: 0.5799 (t80) REVERT: A 274 ASP cc_start: 0.6642 (m-30) cc_final: 0.5736 (t0) REVERT: A 334 LEU cc_start: 0.7822 (tp) cc_final: 0.7281 (mp) REVERT: A 466 THR cc_start: 0.8582 (m) cc_final: 0.8154 (p) REVERT: A 491 PHE cc_start: 0.7268 (t80) cc_final: 0.6625 (t80) REVERT: A 534 MET cc_start: 0.0462 (mtp) cc_final: -0.2063 (ptt) REVERT: A 633 GLU cc_start: 0.6204 (pt0) cc_final: 0.5892 (pp20) REVERT: A 649 LYS cc_start: 0.6931 (tttt) cc_final: 0.6644 (tmmt) REVERT: A 663 SER cc_start: 0.8132 (t) cc_final: 0.7785 (p) REVERT: A 939 MET cc_start: 0.6445 (OUTLIER) cc_final: 0.5374 (ptm) REVERT: A 973 TYR cc_start: 0.7815 (m-10) cc_final: 0.7112 (m-10) REVERT: A 1089 MET cc_start: 0.3750 (OUTLIER) cc_final: 0.3437 (mmt) REVERT: A 1108 GLU cc_start: 0.8000 (tp30) cc_final: 0.7522 (tm-30) REVERT: A 1166 ILE cc_start: 0.7829 (OUTLIER) cc_final: 0.7582 (mm) REVERT: A 1237 TYR cc_start: 0.5046 (OUTLIER) cc_final: 0.3209 (t80) REVERT: A 1332 ASP cc_start: 0.7176 (m-30) cc_final: 0.6290 (t0) outliers start: 20 outliers final: 15 residues processed: 115 average time/residue: 0.0953 time to fit residues: 16.4384 Evaluate side-chains 121 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 102 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1237 TYR Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1353 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 41 optimal weight: 1.9990 chunk 22 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- 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 = 0.4415 r_free = 0.4415 target = 0.175086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.129551 restraints weight = 20225.553| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 3.53 r_work: 0.3536 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 moved from start: 0.3949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12548 Z= 0.164 Angle : 0.590 11.184 17537 Z= 0.321 Chirality : 0.042 0.344 2023 Planarity : 0.004 0.035 1743 Dihedral : 19.566 149.287 3096 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.09 % Allowed : 10.54 % Favored : 87.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.25), residues: 1120 helix: 0.96 (0.22), residues: 559 sheet: -1.15 (0.58), residues: 81 loop : -0.76 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1114 TYR 0.014 0.001 TYR A1237 PHE 0.027 0.002 PHE A 372 TRP 0.014 0.002 TRP A 464 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.16 (12548) covalent geometry : angle 0.58975 / 0.32 (17537) hydrogen bonds : bond 0.05737 / 3.61 ( 518) hydrogen bonds : angle 4.74432 / 3.42 ( 1412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 90 MET cc_start: 0.7164 (tmm) cc_final: 0.5881 (tpt) REVERT: A 100 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.7540 (mtm180) REVERT: A 112 LYS cc_start: 0.7823 (mmtm) cc_final: 0.7415 (mmtm) REVERT: A 220 ARG cc_start: 0.6440 (mmm160) cc_final: 0.6224 (mmm160) REVERT: A 238 PHE cc_start: 0.6120 (t80) cc_final: 0.5799 (t80) REVERT: A 274 ASP cc_start: 0.6646 (m-30) cc_final: 0.5735 (t0) REVERT: A 334 LEU cc_start: 0.7831 (tp) cc_final: 0.7304 (mp) REVERT: A 466 THR cc_start: 0.8530 (m) cc_final: 0.8136 (p) REVERT: A 491 PHE cc_start: 0.7164 (t80) cc_final: 0.6418 (t80) REVERT: A 534 MET cc_start: 0.0043 (mtp) cc_final: -0.2248 (ptt) REVERT: A 633 GLU cc_start: 0.6150 (pt0) cc_final: 0.5861 (pp20) REVERT: A 649 LYS cc_start: 0.6928 (tttt) cc_final: 0.6643 (tmmt) REVERT: A 663 SER cc_start: 0.8307 (t) cc_final: 0.7981 (p) REVERT: A 939 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.5396 (ptm) REVERT: A 973 TYR cc_start: 0.7893 (m-10) cc_final: 0.7226 (m-10) REVERT: A 1089 MET cc_start: 0.3711 (OUTLIER) cc_final: 0.3417 (mmt) REVERT: A 1108 GLU cc_start: 0.7962 (tp30) cc_final: 0.7481 (tm-30) REVERT: A 1166 ILE cc_start: 0.7839 (OUTLIER) cc_final: 0.7603 (mm) REVERT: A 1169 MET cc_start: 0.8028 (ttm) cc_final: 0.7810 (ttm) REVERT: A 1237 TYR cc_start: 0.4954 (OUTLIER) cc_final: 0.3225 (t80) REVERT: A 1332 ASP cc_start: 0.7209 (m-30) cc_final: 0.6328 (t0) outliers start: 21 outliers final: 15 residues processed: 117 average time/residue: 0.0933 time to fit residues: 16.0916 Evaluate side-chains 122 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 173 ASP Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 443 ILE Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 628 ASP Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1237 TYR Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 57 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 5 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** 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 = 0.4378 r_free = 0.4378 target = 0.171467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.116753 restraints weight = 20479.732| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 2.92 r_work: 0.3503 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.103 12548 Z= 0.307 Angle : 0.764 9.672 17537 Z= 0.403 Chirality : 0.049 0.324 2023 Planarity : 0.005 0.037 1743 Dihedral : 19.719 148.212 3096 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.09 % Allowed : 10.74 % Favored : 87.18 % 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: -0.41 (0.24), residues: 1120 helix: 0.61 (0.22), residues: 559 sheet: -1.60 (0.57), residues: 74 loop : -1.03 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 967 TYR 0.023 0.002 TYR A 430 PHE 0.024 0.003 PHE A 478 TRP 0.013 0.003 TRP A 476 HIS 0.008 0.002 HIS A1311 Details of bonding type rmsd/Z covalent geometry : bond 0.00664 / 0.31 (12548) covalent geometry : angle 0.76380 / 0.40 (17537) hydrogen bonds : bond 0.07391 / 4.73 ( 518) hydrogen bonds : angle 5.10109 / 3.63 ( 1412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2895.05 seconds wall clock time: 50 minutes 19.13 seconds (3019.13 seconds total)