Starting phenix.real_space_refine on Fri Jul 3 05:04:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k4h_62059/07_2026/9k4h_62059.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k4h_62059/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9k4h_62059/07_2026/9k4h_62059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k4h_62059/07_2026/9k4h_62059.map" model { file = "/net/cci-nas-00/data/ceres_data/9k4h_62059/07_2026/9k4h_62059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k4h_62059/07_2026/9k4h_62059.cif" } 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-dev-6108/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: 2.54, per 1000 atoms: 0.21 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: 0.96 Conformation dependent library (CDL) restraints added in 494.4 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: 1.46 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: 2.74 Time building geometry restraints manager: 1.34 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: 16704 1.29 - 2.57: 709 2.57 - 3.86: 99 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 - 0.033: 1408 0.033 - 0.066: 426 0.066 - 0.099: 130 0.099 - 0.132: 54 0.132 - 0.165: 5 Chirality restraints: 2023 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 -2.57 -0.16 2.00e-01 2.50e+01 6.80e-01 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 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" P DA B 8 " pdb=" OP1 DA B 8 " pdb=" OP2 DA B 8 " pdb=" O5' DA B 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.47 -0.14 2.00e-01 2.50e+01 4.78e-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: 0.470 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.960 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.940 ------------------------------------------------------------------------------- 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= 0.274 Angle : 0.604 6.436 17537 Z= 0.465 Chirality : 0.038 0.165 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 0.00352 / 0.27 (12548) covalent geometry : angle 0.60413 / 0.46 (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 : 0.296 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: 0.4351 (p0) REVERT: A 238 PHE cc_start: 0.5451 (t80) cc_final: 0.5190 (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: 0.7889 (p) REVERT: A 534 MET cc_start: 0.1284 (mtp) cc_final: -0.1891 (ttp) REVERT: A 645 ASP cc_start: 0.7792 (m-30) cc_final: 0.7172 (p0) REVERT: A 648 MET cc_start: 0.8121 (mmm) cc_final: 0.7847 (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: 0.7673 (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: 0.1225 time to fit residues: 33.7019 Evaluate side-chains 118 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 118 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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: 20.0000 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 369 GLN A 595 HIS 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 = 0.4492 r_free = 0.4492 target = 0.181799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.128395 restraints weight = 20350.416| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 3.01 r_work: 0.3679 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12548 Z= 0.182 Angle : 0.615 10.373 17537 Z= 0.346 Chirality : 0.041 0.304 2023 Planarity : 0.005 0.054 1743 Dihedral : 19.442 151.808 3096 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.29 % Allowed : 5.96 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.25), residues: 1120 helix: 1.09 (0.22), residues: 567 sheet: -0.72 (0.57), residues: 80 loop : -0.33 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 71 TYR 0.019 0.002 TYR A 973 PHE 0.022 0.002 PHE A 372 TRP 0.011 0.002 TRP A 464 HIS 0.005 0.001 HIS A1349 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (12548) covalent geometry : angle 0.61499 / 0.35 (17537) hydrogen bonds : bond 0.06419 / 4.04 ( 518) hydrogen bonds : angle 5.10810 / 3.68 ( 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 145 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.293 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: 0.5686 (t0) cc_final: 0.4356 (p0) REVERT: A 334 LEU cc_start: 0.8133 (tp) cc_final: 0.7464 (mp) REVERT: A 466 THR cc_start: 0.8332 (m) cc_final: 0.7993 (p) REVERT: A 534 MET cc_start: 0.1373 (mtp) cc_final: -0.1676 (ttp) REVERT: A 633 GLU cc_start: 0.5810 (pt0) cc_final: 0.5441 (pp20) REVERT: A 645 ASP cc_start: 0.8062 (m-30) cc_final: 0.6871 (p0) REVERT: A 682 PHE cc_start: 0.7719 (m-80) cc_final: 0.7391 (m-10) REVERT: A 1131 TYR cc_start: 0.8169 (m-80) cc_final: 0.7944 (m-80) REVERT: A 1332 ASP cc_start: 0.7133 (m-30) cc_final: 0.6451 (t0) outliers start: 13 outliers final: 7 residues processed: 140 average time/residue: 0.1197 time to fit residues: 23.3585 Evaluate side-chains 114 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 107 time to evaluate : 0.606 ------------------------------------------------------------------------------- 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: 9.9990 chunk 71 optimal weight: 20.0000 chunk 39 optimal weight: 1.9990 chunk 109 optimal weight: 8.9990 chunk 93 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 122 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 415 HIS A1101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.178948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.124870 restraints weight = 20591.467| |-----------------------------------------------------------------------------| r_work (start): 0.3811 rms_B_bonded: 2.99 r_work: 0.3651 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2347 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= 0.178 Angle : 0.607 8.279 17537 Z= 0.336 Chirality : 0.042 0.367 2023 Planarity : 0.004 0.035 1743 Dihedral : 19.540 150.717 3096 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.19 % Allowed : 7.06 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.32 (0.25), residues: 1120 helix: 0.95 (0.22), residues: 568 sheet: -0.80 (0.56), residues: 85 loop : -0.39 (0.27), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 71 TYR 0.023 0.002 TYR A 973 PHE 0.019 0.002 PHE A 119 TRP 0.012 0.002 TRP A 464 HIS 0.004 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.18 (12548) covalent geometry : angle 0.60697 / 0.34 (17537) hydrogen bonds : bond 0.06065 / 3.81 ( 518) hydrogen bonds : angle 4.89785 / 3.54 ( 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 143 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.403 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: 0.5921 (tmm) cc_final: 0.4836 (tpp) REVERT: A 112 LYS cc_start: 0.7431 (mmtm) cc_final: 0.6435 (pttt) REVERT: A 199 ASN cc_start: 0.5614 (t0) cc_final: 0.4196 (p0) REVERT: A 225 LEU cc_start: 0.5511 (OUTLIER) cc_final: 0.5289 (tt) REVERT: A 334 LEU cc_start: 0.8091 (tp) cc_final: 0.7436 (mp) REVERT: A 466 THR cc_start: 0.8459 (m) cc_final: 0.8017 (p) REVERT: A 534 MET cc_start: 0.1068 (mtp) cc_final: -0.2006 (ttp) REVERT: A 633 GLU cc_start: 0.5944 (pt0) cc_final: 0.5558 (pp20) REVERT: A 645 ASP cc_start: 0.7678 (m-30) cc_final: 0.7020 (p0) REVERT: A 682 PHE cc_start: 0.7720 (m-80) cc_final: 0.7375 (m-10) REVERT: A 694 MET cc_start: 0.6745 (tmm) cc_final: 0.6533 (tmm) REVERT: A 939 MET cc_start: 0.6050 (OUTLIER) cc_final: 0.5259 (ptm) REVERT: A 1332 ASP cc_start: 0.7050 (m-30) cc_final: 0.6315 (t0) outliers start: 22 outliers final: 11 residues processed: 138 average time/residue: 0.1143 time to fit residues: 22.4620 Evaluate side-chains 118 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 225 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 306 LEU 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 1138 THR Chi-restraints excluded: chain A residue 1307 GLU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 123 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4437 r_free = 0.4437 target = 0.176676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.122504 restraints weight = 20306.915| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.95 r_work: 0.3615 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12548 Z= 0.202 Angle : 0.609 8.475 17537 Z= 0.338 Chirality : 0.042 0.342 2023 Planarity : 0.004 0.049 1743 Dihedral : 19.634 148.624 3096 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.19 % Allowed : 8.15 % Favored : 89.66 % 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: 0.16 (0.25), residues: 1120 helix: 0.87 (0.22), residues: 569 sheet: -0.73 (0.60), residues: 73 loop : -0.60 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1114 TYR 0.020 0.002 TYR A1237 PHE 0.018 0.002 PHE A 478 TRP 0.011 0.002 TRP A 464 HIS 0.005 0.001 HIS A1349 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (12548) covalent geometry : angle 0.60913 / 0.34 (17537) hydrogen bonds : bond 0.06122 / 3.83 ( 518) hydrogen bonds : angle 4.84095 / 3.49 ( 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 135 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.7450 (mmtm) cc_final: 0.6526 (pttt) REVERT: A 114 GLU cc_start: 0.4510 (tm-30) cc_final: 0.4119 (pm20) REVERT: A 225 LEU cc_start: 0.5702 (OUTLIER) cc_final: 0.5480 (tt) REVERT: A 334 LEU cc_start: 0.8088 (tp) cc_final: 0.7440 (mp) REVERT: A 370 GLU cc_start: 0.7523 (tt0) cc_final: 0.7269 (tm-30) REVERT: A 466 THR cc_start: 0.8555 (m) cc_final: 0.8048 (p) REVERT: A 534 MET cc_start: 0.0792 (mtp) cc_final: -0.2093 (ttp) REVERT: A 633 GLU cc_start: 0.6060 (pt0) cc_final: 0.5688 (pp20) REVERT: A 645 ASP cc_start: 0.7589 (m-30) cc_final: 0.7289 (p0) REVERT: A 939 MET cc_start: 0.6196 (OUTLIER) cc_final: 0.5413 (ptm) REVERT: A 1166 ILE cc_start: 0.7842 (OUTLIER) cc_final: 0.7585 (mm) REVERT: A 1191 LYS cc_start: 0.8389 (mppt) cc_final: 0.7688 (mmmt) REVERT: A 1332 ASP cc_start: 0.7036 (m-30) cc_final: 0.6297 (t0) outliers start: 22 outliers final: 14 residues processed: 124 average time/residue: 0.1022 time to fit residues: 18.7788 Evaluate side-chains 112 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 306 LEU Chi-restraints excluded: chain A residue 404 THR 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 1312 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 96 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 99 optimal weight: 9.9990 chunk 101 optimal weight: 0.0470 chunk 40 optimal weight: 1.9990 chunk 69 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 52 optimal weight: 30.0000 overall best weight: 2.0086 ------------------------------------------------------------------------------- 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 = 0.4447 r_free = 0.4447 target = 0.177644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.123372 restraints weight = 20307.414| |-----------------------------------------------------------------------------| r_work (start): 0.3792 rms_B_bonded: 2.97 r_work: 0.3624 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.2926 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= 0.160 Angle : 0.563 8.292 17537 Z= 0.315 Chirality : 0.041 0.303 2023 Planarity : 0.004 0.041 1743 Dihedral : 19.665 148.043 3096 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.99 % Allowed : 9.24 % Favored : 88.77 % 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: 0.37 (0.25), residues: 1120 helix: 1.11 (0.22), residues: 559 sheet: -0.44 (0.56), residues: 83 loop : -0.60 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 220 TYR 0.018 0.002 TYR A 973 PHE 0.025 0.002 PHE A 97 TRP 0.010 0.002 TRP A 464 HIS 0.011 0.001 HIS A 420 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.16 (12548) covalent geometry : angle 0.56298 / 0.31 (17537) hydrogen bonds : bond 0.05700 / 3.56 ( 518) hydrogen bonds : angle 4.68158 / 3.39 ( 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 131 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 PHE cc_start: 0.7126 (t80) cc_final: 0.6871 (t80) REVERT: A 112 LYS cc_start: 0.7547 (mmtm) cc_final: 0.7157 (mmtm) REVERT: A 225 LEU cc_start: 0.5695 (OUTLIER) cc_final: 0.5477 (tt) REVERT: A 274 ASP cc_start: 0.6588 (m-30) cc_final: 0.5619 (t0) REVERT: A 334 LEU cc_start: 0.8117 (tp) cc_final: 0.7481 (mp) REVERT: A 370 GLU cc_start: 0.7543 (tt0) cc_final: 0.7290 (tm-30) REVERT: A 466 THR cc_start: 0.8505 (m) cc_final: 0.8100 (p) REVERT: A 534 MET cc_start: 0.0436 (mtp) cc_final: -0.2289 (ttp) REVERT: A 633 GLU cc_start: 0.6195 (pt0) cc_final: 0.5813 (pp20) REVERT: A 645 ASP cc_start: 0.7463 (m-30) cc_final: 0.7257 (p0) REVERT: A 663 SER cc_start: 0.7978 (t) cc_final: 0.7474 (p) REVERT: A 939 MET cc_start: 0.6243 (OUTLIER) cc_final: 0.5097 (ptm) REVERT: A 973 TYR cc_start: 0.7505 (m-10) cc_final: 0.6963 (m-10) REVERT: A 1166 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7545 (mm) REVERT: A 1237 TYR cc_start: 0.4731 (OUTLIER) cc_final: 0.3433 (t80) REVERT: A 1332 ASP cc_start: 0.6949 (m-30) cc_final: 0.6215 (t0) outliers start: 20 outliers final: 11 residues processed: 123 average time/residue: 0.0827 time to fit residues: 15.4545 Evaluate side-chains 112 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 97 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 306 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 443 ILE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 111 optimal weight: 8.9990 chunk 104 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 82 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- 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 = 0.4425 r_free = 0.4425 target = 0.175772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.121433 restraints weight = 20164.443| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 2.95 r_work: 0.3603 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7173 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12548 Z= 0.195 Angle : 0.596 7.660 17537 Z= 0.331 Chirality : 0.042 0.292 2023 Planarity : 0.004 0.040 1743 Dihedral : 19.686 147.075 3096 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.49 % Allowed : 9.44 % Favored : 88.07 % 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: 0.26 (0.25), residues: 1120 helix: 1.04 (0.22), residues: 560 sheet: -0.88 (0.57), residues: 79 loop : -0.61 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1114 TYR 0.018 0.002 TYR A1237 PHE 0.028 0.002 PHE A 372 TRP 0.010 0.002 TRP A 464 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00403 / 0.19 (12548) covalent geometry : angle 0.59593 / 0.33 (17537) hydrogen bonds : bond 0.05982 / 3.77 ( 518) hydrogen bonds : angle 4.71734 / 3.42 ( 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 130 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.7650 (mmtm) cc_final: 0.7294 (mmtm) REVERT: A 225 LEU cc_start: 0.5674 (OUTLIER) cc_final: 0.5443 (tt) REVERT: A 274 ASP cc_start: 0.6617 (m-30) cc_final: 0.5609 (t0) REVERT: A 334 LEU cc_start: 0.8077 (tp) cc_final: 0.7443 (mp) REVERT: A 370 GLU cc_start: 0.7538 (tt0) cc_final: 0.7270 (tm-30) REVERT: A 466 THR cc_start: 0.8462 (m) cc_final: 0.8042 (p) REVERT: A 534 MET cc_start: 0.0249 (mtp) cc_final: -0.2204 (ptt) REVERT: A 626 PHE cc_start: 0.7357 (m-10) cc_final: 0.6857 (m-80) REVERT: A 633 GLU cc_start: 0.6203 (pt0) cc_final: 0.5806 (pp20) REVERT: A 649 LYS cc_start: 0.6980 (tttt) cc_final: 0.6670 (ttpp) REVERT: A 663 SER cc_start: 0.8088 (t) cc_final: 0.7662 (p) REVERT: A 939 MET cc_start: 0.6276 (OUTLIER) cc_final: 0.5134 (ptm) REVERT: A 973 TYR cc_start: 0.7542 (m-10) cc_final: 0.7040 (m-10) REVERT: A 1166 ILE cc_start: 0.7784 (OUTLIER) cc_final: 0.7537 (mm) REVERT: A 1237 TYR cc_start: 0.4797 (OUTLIER) cc_final: 0.3294 (t80) REVERT: A 1332 ASP cc_start: 0.7054 (m-30) cc_final: 0.6275 (t0) outliers start: 25 outliers final: 15 residues processed: 121 average time/residue: 0.0812 time to fit residues: 15.2927 Evaluate side-chains 115 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 306 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 418 GLU 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 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: 2.9990 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 99 optimal weight: 9.9990 chunk 91 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.4444 r_free = 0.4444 target = 0.177325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.123308 restraints weight = 20183.059| |-----------------------------------------------------------------------------| r_work (start): 0.3788 rms_B_bonded: 2.93 r_work: 0.3621 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.3271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12548 Z= 0.140 Angle : 0.558 12.510 17537 Z= 0.309 Chirality : 0.041 0.332 2023 Planarity : 0.004 0.036 1743 Dihedral : 19.681 147.809 3096 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.79 % Allowed : 9.94 % Favored : 88.27 % 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: 0.49 (0.25), residues: 1120 helix: 1.25 (0.22), residues: 554 sheet: -0.78 (0.58), residues: 81 loop : -0.49 (0.27), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1114 TYR 0.015 0.001 TYR A1237 PHE 0.022 0.002 PHE A 491 TRP 0.012 0.002 TRP A 464 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (12548) covalent geometry : angle 0.55842 / 0.31 (17537) hydrogen bonds : bond 0.05401 / 3.37 ( 518) hydrogen bonds : angle 4.61963 / 3.35 ( 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 120 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.7590 (mmtm) cc_final: 0.7227 (mmtm) REVERT: A 225 LEU cc_start: 0.5559 (OUTLIER) cc_final: 0.5310 (tt) REVERT: A 274 ASP cc_start: 0.6606 (m-30) cc_final: 0.5608 (t0) REVERT: A 334 LEU cc_start: 0.8109 (tp) cc_final: 0.7474 (mp) REVERT: A 370 GLU cc_start: 0.7526 (tt0) cc_final: 0.7253 (tm-30) REVERT: A 466 THR cc_start: 0.8338 (m) cc_final: 0.7965 (p) REVERT: A 534 MET cc_start: 0.0252 (mtp) cc_final: -0.2144 (ptt) REVERT: A 633 GLU cc_start: 0.6253 (pt0) cc_final: 0.5868 (pp20) REVERT: A 649 LYS cc_start: 0.6915 (tttt) cc_final: 0.6686 (tmmt) REVERT: A 939 MET cc_start: 0.6251 (OUTLIER) cc_final: 0.5145 (ptm) REVERT: A 973 TYR cc_start: 0.7530 (m-10) cc_final: 0.7074 (m-10) REVERT: A 1166 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7512 (mm) REVERT: A 1237 TYR cc_start: 0.4680 (OUTLIER) cc_final: 0.3324 (t80) REVERT: A 1332 ASP cc_start: 0.6949 (m-30) cc_final: 0.6229 (t0) outliers start: 18 outliers final: 11 residues processed: 111 average time/residue: 0.0857 time to fit residues: 14.4074 Evaluate side-chains 109 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 225 LEU Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 495 MET 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 116 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 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 = 0.4367 r_free = 0.4367 target = 0.170633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.115703 restraints weight = 20653.056| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.99 r_work: 0.3487 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.073 12548 Z= 0.409 Angle : 0.850 10.069 17537 Z= 0.456 Chirality : 0.051 0.298 2023 Planarity : 0.006 0.065 1743 Dihedral : 19.946 144.734 3096 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.78 % Allowed : 9.74 % Favored : 87.48 % 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: -0.53 (0.24), residues: 1120 helix: 0.42 (0.21), residues: 564 sheet: -1.63 (0.57), residues: 75 loop : -0.97 (0.27), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 70 TYR 0.027 0.003 TYR A1237 PHE 0.044 0.004 PHE A 98 TRP 0.014 0.004 TRP A 464 HIS 0.010 0.002 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00873 / 0.41 (12548) covalent geometry : angle 0.84980 / 0.46 (17537) hydrogen bonds : bond 0.08429 / 5.46 ( 518) hydrogen bonds : angle 5.32646 / 3.83 ( 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 132 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 104 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7924 (mtm-85) cc_final: 0.7355 (mtm180) REVERT: A 112 LYS cc_start: 0.7778 (mmtm) cc_final: 0.7362 (mmtm) REVERT: A 225 LEU cc_start: 0.5479 (OUTLIER) cc_final: 0.5264 (tt) REVERT: A 274 ASP cc_start: 0.6651 (m-30) cc_final: 0.5715 (t0) REVERT: A 334 LEU cc_start: 0.7815 (tp) cc_final: 0.7278 (mp) REVERT: A 370 GLU cc_start: 0.7672 (tt0) cc_final: 0.7301 (tm-30) REVERT: A 466 THR cc_start: 0.8815 (m) cc_final: 0.8302 (p) REVERT: A 633 GLU cc_start: 0.6161 (pt0) cc_final: 0.5858 (pp20) REVERT: A 649 LYS cc_start: 0.6942 (tttt) cc_final: 0.6613 (ttpp) REVERT: A 663 SER cc_start: 0.8018 (t) cc_final: 0.7654 (p) REVERT: A 939 MET cc_start: 0.6478 (OUTLIER) cc_final: 0.5400 (ptm) REVERT: A 973 TYR cc_start: 0.7914 (m-10) cc_final: 0.7339 (m-10) REVERT: A 1166 ILE cc_start: 0.7819 (OUTLIER) cc_final: 0.7550 (mm) REVERT: A 1237 TYR cc_start: 0.5331 (OUTLIER) cc_final: 0.3531 (t80) REVERT: A 1332 ASP cc_start: 0.7440 (m-30) cc_final: 0.6609 (t0) outliers start: 28 outliers final: 16 residues processed: 122 average time/residue: 0.0928 time to fit residues: 17.1516 Evaluate side-chains 118 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.280 ------------------------------------------------------------------------------- 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 225 LEU 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 508 LEU 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 1098 THR 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: 1.9990 chunk 43 optimal weight: 1.9990 chunk 123 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 112 optimal weight: 50.0000 chunk 113 optimal weight: 9.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 GLN A 721 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.175148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.120715 restraints weight = 20171.447| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 3.00 r_work: 0.3578 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 12548 Z= 0.151 Angle : 0.611 9.461 17537 Z= 0.335 Chirality : 0.042 0.312 2023 Planarity : 0.004 0.066 1743 Dihedral : 19.814 147.695 3096 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.49 % Allowed : 12.03 % Favored : 86.48 % 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: 0.02 (0.25), residues: 1120 helix: 0.92 (0.22), residues: 554 sheet: -1.05 (0.59), residues: 69 loop : -0.82 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 220 TYR 0.018 0.002 TYR A1237 PHE 0.026 0.002 PHE A 491 TRP 0.019 0.002 TRP A 464 HIS 0.005 0.001 HIS A 721 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (12548) covalent geometry : angle 0.61130 / 0.34 (17537) hydrogen bonds : bond 0.05906 / 3.70 ( 518) hydrogen bonds : angle 4.81541 / 3.49 ( 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 121 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 106 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7635 (mtm-85) cc_final: 0.7396 (mtm180) REVERT: A 112 LYS cc_start: 0.7717 (mmtm) cc_final: 0.7288 (mmtm) REVERT: A 225 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5517 (tt) REVERT: A 238 PHE cc_start: 0.6016 (t80) cc_final: 0.5633 (t80) REVERT: A 274 ASP cc_start: 0.6607 (m-30) cc_final: 0.5712 (t0) REVERT: A 334 LEU cc_start: 0.7824 (tp) cc_final: 0.7276 (mp) REVERT: A 370 GLU cc_start: 0.7579 (tt0) cc_final: 0.7303 (tm-30) REVERT: A 466 THR cc_start: 0.8580 (m) cc_final: 0.8273 (p) REVERT: A 534 MET cc_start: -0.0241 (mtt) cc_final: -0.2854 (ptt) REVERT: A 633 GLU cc_start: 0.6215 (pt0) cc_final: 0.5931 (pp20) REVERT: A 649 LYS cc_start: 0.6893 (tttt) cc_final: 0.6640 (tmmt) REVERT: A 663 SER cc_start: 0.8087 (t) cc_final: 0.7710 (p) REVERT: A 939 MET cc_start: 0.6346 (OUTLIER) cc_final: 0.5212 (ptm) REVERT: A 973 TYR cc_start: 0.7962 (m-10) cc_final: 0.7451 (m-10) REVERT: A 1166 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7491 (mm) REVERT: A 1237 TYR cc_start: 0.4848 (OUTLIER) cc_final: 0.3271 (t80) REVERT: A 1332 ASP cc_start: 0.7140 (m-30) cc_final: 0.6369 (t0) outliers start: 15 outliers final: 11 residues processed: 115 average time/residue: 0.0820 time to fit residues: 14.6320 Evaluate side-chains 117 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.366 ------------------------------------------------------------------------------- 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 225 LEU Chi-restraints excluded: chain A residue 265 GLN Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 508 LEU 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 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 41 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 103 optimal weight: 6.9990 chunk 64 optimal weight: 0.3980 chunk 99 optimal weight: 9.9990 chunk 44 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.4414 r_free = 0.4414 target = 0.174918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.120520 restraints weight = 20162.162| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.00 r_work: 0.3578 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.264 12548 Z= 0.226 Angle : 0.828 59.176 17537 Z= 0.483 Chirality : 0.043 0.449 2023 Planarity : 0.004 0.067 1743 Dihedral : 19.810 147.724 3096 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.69 % Allowed : 11.83 % Favored : 86.48 % Cbeta Deviations : 0.09 % 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: 0.01 (0.25), residues: 1120 helix: 0.91 (0.22), residues: 554 sheet: -1.21 (0.56), residues: 79 loop : -0.78 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 220 TYR 0.018 0.002 TYR A1237 PHE 0.022 0.002 PHE A 491 TRP 0.017 0.002 TRP A 464 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.23 (12548) covalent geometry : angle 0.82775 / 0.48 (17537) hydrogen bonds : bond 0.05912 / 3.70 ( 518) hydrogen bonds : angle 4.81930 / 3.49 ( 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 120 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 100 ARG cc_start: 0.7652 (mtm-85) cc_final: 0.7411 (mtm180) REVERT: A 112 LYS cc_start: 0.7722 (mmtm) cc_final: 0.7296 (mmtm) REVERT: A 225 LEU cc_start: 0.5740 (OUTLIER) cc_final: 0.5518 (tt) REVERT: A 238 PHE cc_start: 0.6014 (t80) cc_final: 0.5629 (t80) REVERT: A 274 ASP cc_start: 0.6613 (m-30) cc_final: 0.5717 (t0) REVERT: A 334 LEU cc_start: 0.7821 (tp) cc_final: 0.7274 (mp) REVERT: A 370 GLU cc_start: 0.7589 (tt0) cc_final: 0.7308 (tm-30) REVERT: A 466 THR cc_start: 0.8683 (m) cc_final: 0.8271 (p) REVERT: A 534 MET cc_start: -0.0247 (mtt) cc_final: -0.2886 (ptt) REVERT: A 633 GLU cc_start: 0.6204 (pt0) cc_final: 0.5929 (pp20) REVERT: A 649 LYS cc_start: 0.6879 (tttt) cc_final: 0.6643 (tmmt) REVERT: A 663 SER cc_start: 0.8098 (t) cc_final: 0.7723 (p) REVERT: A 939 MET cc_start: 0.6352 (OUTLIER) cc_final: 0.5215 (ptm) REVERT: A 973 TYR cc_start: 0.7954 (m-10) cc_final: 0.7450 (m-10) REVERT: A 1166 ILE cc_start: 0.7725 (OUTLIER) cc_final: 0.7490 (mm) REVERT: A 1237 TYR cc_start: 0.4873 (OUTLIER) cc_final: 0.3280 (t80) REVERT: A 1332 ASP cc_start: 0.7140 (m-30) cc_final: 0.6377 (t0) outliers start: 17 outliers final: 11 residues processed: 113 average time/residue: 0.0849 time to fit residues: 14.5415 Evaluate side-chains 118 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 103 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 225 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 429 PHE Chi-restraints excluded: chain A residue 508 LEU 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 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: 40.0000 chunk 115 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 117 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 36 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 114 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 721 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.174878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.120462 restraints weight = 20207.405| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 3.01 r_work: 0.3576 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.264 12548 Z= 0.226 Angle : 0.828 59.200 17537 Z= 0.483 Chirality : 0.043 0.448 2023 Planarity : 0.004 0.067 1743 Dihedral : 19.810 147.724 3096 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 14.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 1.49 % Allowed : 12.03 % Favored : 86.48 % Cbeta Deviations : 0.09 % 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: 0.01 (0.25), residues: 1120 helix: 0.91 (0.22), residues: 554 sheet: -1.21 (0.56), residues: 79 loop : -0.78 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 220 TYR 0.018 0.002 TYR A1237 PHE 0.022 0.002 PHE A 491 TRP 0.017 0.002 TRP A 464 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.23 (12548) covalent geometry : angle 0.82777 / 0.48 (17537) hydrogen bonds : bond 0.05912 / 3.71 ( 518) hydrogen bonds : angle 4.81930 / 3.49 ( 1412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2882.53 seconds wall clock time: 50 minutes 7.79 seconds (3007.79 seconds total)