Starting phenix.real_space_refine on Wed Feb 4 17:55:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k4h_62059/02_2026/9k4h_62059.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k4h_62059/02_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_62059/02_2026/9k4h_62059.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k4h_62059/02_2026/9k4h_62059.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k4h_62059/02_2026/9k4h_62059.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k4h_62059/02_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-2.0-5952/lib/python3.9/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: 3.02, per 1000 atoms: 0.25 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: 1.09 Conformation dependent library (CDL) restraints added in 483.0 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: 1.68 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: 2.92 Time building geometry restraints manager: 1.44 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=" P U D 26 " pdb=" OP1 U D 26 " ideal model delta sigma weight residual 1.485 1.514 -0.029 2.00e-02 2.50e+03 2.15e+00 bond pdb=" C ALA A 315 " pdb=" N PRO A 316 " ideal model delta sigma weight residual 1.334 1.323 0.011 8.40e-03 1.42e+04 1.64e+00 bond pdb=" CB ILE A 363 " pdb=" CG2 ILE A 363 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.54e+00 bond pdb=" CA ALA A 50 " pdb=" C ALA A 50 " ideal model delta sigma weight residual 1.529 1.516 0.013 1.04e-02 9.25e+03 1.44e+00 bond pdb=" C PHE A 351 " pdb=" O PHE A 351 " ideal model delta sigma weight residual 1.236 1.251 -0.015 1.32e-02 5.74e+03 1.33e+00 ... (remaining 12543 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.29: 16821 1.29 - 2.57: 599 2.57 - 3.86: 92 3.86 - 5.15: 20 5.15 - 6.44: 5 Bond angle restraints: 17537 Sorted by residual: angle pdb=" N GLU A1307 " pdb=" CA GLU A1307 " pdb=" CB GLU A1307 " ideal model delta sigma weight residual 110.12 114.70 -4.58 1.47e+00 4.63e-01 9.69e+00 angle pdb=" C GLN A1091 " pdb=" N VAL A1092 " pdb=" CA VAL A1092 " ideal model delta sigma weight residual 120.49 124.22 -3.73 1.38e+00 5.25e-01 7.30e+00 angle pdb=" C2' U D 12 " pdb=" C1' U D 12 " pdb=" N1 U D 12 " ideal model delta sigma weight residual 112.00 115.86 -3.86 1.50e+00 4.44e-01 6.63e+00 angle pdb=" N VAL A 308 " pdb=" CA VAL A 308 " pdb=" C VAL A 308 " ideal model delta sigma weight residual 106.55 110.28 -3.73 1.45e+00 4.76e-01 6.62e+00 angle pdb=" C ALA A1306 " pdb=" N GLU A1307 " pdb=" CA GLU A1307 " ideal model delta sigma weight residual 120.28 117.02 3.26 1.34e+00 5.57e-01 5.93e+00 ... (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: 1451 0.033 - 0.065: 419 0.065 - 0.098: 108 0.098 - 0.131: 43 0.131 - 0.164: 2 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 0.16 2.00e-01 2.50e+01 6.70e-01 chirality pdb=" C1' U D 25 " pdb=" O4' U D 25 " pdb=" C2' U D 25 " pdb=" N1 U D 25 " both_signs ideal model delta sigma weight residual False 2.47 2.33 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA VAL A 20 " pdb=" N VAL A 20 " pdb=" C VAL A 20 " pdb=" CB VAL A 20 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.23e-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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.580 Find NCS groups from input model: 0.040 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:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12548 Z= 0.155 Angle : 0.577 6.436 17537 Z= 0.324 Chirality : 0.036 0.164 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 covalent geometry : bond 0.00309 (12548) covalent geometry : angle 0.57716 (17537) hydrogen bonds : bond 0.16632 ( 518) hydrogen bonds : angle 6.20671 ( 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 : 0.475 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: 0.1454 time to fit residues: 39.9177 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 : 0.378 ------------------------------------------------------------------------------- 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: 0.7980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 123 optimal weight: 9.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 GLN A 369 GLN A 415 HIS A 595 HIS A 698 HIS A 933 GLN A 980 ASN A1101 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.179465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.125359 restraints weight = 20303.285| |-----------------------------------------------------------------------------| r_work (start): 0.3818 rms_B_bonded: 2.97 r_work: 0.3657 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6986 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12548 Z= 0.173 Angle : 0.590 7.788 17537 Z= 0.314 Chirality : 0.038 0.187 2023 Planarity : 0.004 0.051 1743 Dihedral : 19.452 147.635 3096 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.69 % Allowed : 5.77 % Favored : 92.54 % 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: 0.62 (0.25), residues: 1120 helix: 1.22 (0.22), residues: 565 sheet: -0.36 (0.63), residues: 72 loop : -0.35 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 71 TYR 0.020 0.002 TYR A 973 PHE 0.019 0.002 PHE A 97 TRP 0.015 0.002 TRP A 464 HIS 0.004 0.001 HIS A 983 Details of bonding type rmsd covalent geometry : bond 0.00364 (12548) covalent geometry : angle 0.58956 (17537) hydrogen bonds : bond 0.05636 ( 518) hydrogen bonds : angle 4.82682 ( 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 156 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 LEU cc_start: 0.5230 (OUTLIER) cc_final: 0.4968 (tt) REVERT: A 238 PHE cc_start: 0.5422 (t80) cc_final: 0.5108 (t80) REVERT: A 334 LEU cc_start: 0.8041 (tp) cc_final: 0.7464 (mp) REVERT: A 370 GLU cc_start: 0.7551 (tt0) cc_final: 0.7260 (tm-30) REVERT: A 466 THR cc_start: 0.8364 (m) cc_final: 0.7974 (p) REVERT: A 534 MET cc_start: 0.0740 (mtp) cc_final: -0.1909 (ptt) REVERT: A 633 GLU cc_start: 0.6014 (pt0) cc_final: 0.5577 (pp20) REVERT: A 645 ASP cc_start: 0.8082 (m-30) cc_final: 0.6924 (p0) REVERT: A 648 MET cc_start: 0.7979 (mmm) cc_final: 0.7751 (ppp) REVERT: A 663 SER cc_start: 0.7853 (t) cc_final: 0.7374 (p) REVERT: A 939 MET cc_start: 0.6159 (OUTLIER) cc_final: 0.5405 (ptm) REVERT: A 1332 ASP cc_start: 0.6876 (m-30) cc_final: 0.6154 (t0) outliers start: 17 outliers final: 7 residues processed: 150 average time/residue: 0.1332 time to fit residues: 27.6953 Evaluate side-chains 116 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 107 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR 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 685 SER Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 1138 THR 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: 10.0000 chunk 71 optimal weight: 30.0000 chunk 39 optimal weight: 1.9990 chunk 109 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 95 optimal weight: 0.9980 chunk 86 optimal weight: 0.0870 chunk 83 optimal weight: 10.0000 chunk 62 optimal weight: 0.7980 chunk 122 optimal weight: 10.0000 chunk 27 optimal weight: 20.0000 overall best weight: 1.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 933 GLN A1350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.177931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.123754 restraints weight = 20403.288| |-----------------------------------------------------------------------------| r_work (start): 0.3796 rms_B_bonded: 2.95 r_work: 0.3632 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.2983 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= 0.166 Angle : 0.574 9.040 17537 Z= 0.303 Chirality : 0.038 0.216 2023 Planarity : 0.004 0.047 1743 Dihedral : 19.474 145.644 3096 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.69 % Allowed : 8.85 % Favored : 89.46 % 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: 0.60 (0.25), residues: 1120 helix: 1.28 (0.22), residues: 556 sheet: -0.67 (0.58), residues: 82 loop : -0.37 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 71 TYR 0.024 0.002 TYR A1237 PHE 0.015 0.002 PHE A 97 TRP 0.010 0.002 TRP A 464 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00355 (12548) covalent geometry : angle 0.57364 (17537) hydrogen bonds : bond 0.05331 ( 518) hydrogen bonds : angle 4.60978 ( 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 133 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.3417 (ppp) cc_final: 0.3186 (ppp) REVERT: A 112 LYS cc_start: 0.7616 (mmtm) cc_final: 0.7147 (mmtm) REVERT: A 225 LEU cc_start: 0.5670 (OUTLIER) cc_final: 0.5426 (tt) REVERT: A 238 PHE cc_start: 0.5621 (t80) cc_final: 0.4916 (t80) REVERT: A 274 ASP cc_start: 0.6595 (m-30) cc_final: 0.5621 (t0) REVERT: A 334 LEU cc_start: 0.8031 (tp) cc_final: 0.7466 (mp) REVERT: A 370 GLU cc_start: 0.7586 (tt0) cc_final: 0.7247 (tm-30) REVERT: A 466 THR cc_start: 0.8383 (m) cc_final: 0.7919 (p) REVERT: A 491 PHE cc_start: 0.7063 (t80) cc_final: 0.6062 (t80) REVERT: A 534 MET cc_start: 0.0095 (mtp) cc_final: -0.2259 (ptt) REVERT: A 633 GLU cc_start: 0.6227 (pt0) cc_final: 0.5840 (pp20) REVERT: A 645 ASP cc_start: 0.8001 (m-30) cc_final: 0.6657 (p0) REVERT: A 648 MET cc_start: 0.8033 (mmm) cc_final: 0.7720 (ppp) REVERT: A 663 SER cc_start: 0.7893 (t) cc_final: 0.7438 (p) REVERT: A 939 MET cc_start: 0.6219 (OUTLIER) cc_final: 0.5050 (ptm) REVERT: A 1332 ASP cc_start: 0.6894 (m-30) cc_final: 0.6140 (t0) outliers start: 17 outliers final: 8 residues processed: 128 average time/residue: 0.1174 time to fit residues: 21.7002 Evaluate side-chains 108 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 225 LEU 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 1138 THR 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: 10.0000 chunk 55 optimal weight: 30.0000 chunk 45 optimal weight: 2.9990 chunk 31 optimal weight: 0.0070 chunk 98 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 10 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.179622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.126542 restraints weight = 20049.966| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 2.92 r_work: 0.3674 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12548 Z= 0.122 Angle : 0.523 8.423 17537 Z= 0.275 Chirality : 0.036 0.243 2023 Planarity : 0.003 0.046 1743 Dihedral : 19.267 145.276 3096 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.89 % Allowed : 9.64 % Favored : 88.47 % 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: 0.76 (0.25), residues: 1120 helix: 1.40 (0.22), residues: 559 sheet: -0.55 (0.59), residues: 82 loop : -0.30 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 403 TYR 0.012 0.001 TYR A1237 PHE 0.022 0.001 PHE A 372 TRP 0.011 0.002 TRP A 464 HIS 0.003 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00255 (12548) covalent geometry : angle 0.52310 (17537) hydrogen bonds : bond 0.04656 ( 518) hydrogen bonds : angle 4.33899 ( 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 140 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 121 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 ILE cc_start: 0.8094 (OUTLIER) cc_final: 0.7489 (mt) REVERT: A 112 LYS cc_start: 0.7621 (mmtm) cc_final: 0.7139 (mmtm) REVERT: A 238 PHE cc_start: 0.5294 (t80) cc_final: 0.4476 (t80) REVERT: A 274 ASP cc_start: 0.6615 (m-30) cc_final: 0.5633 (t0) REVERT: A 334 LEU cc_start: 0.8135 (tp) cc_final: 0.7511 (mp) REVERT: A 370 GLU cc_start: 0.7435 (tt0) cc_final: 0.6954 (pp20) REVERT: A 466 THR cc_start: 0.8382 (m) cc_final: 0.7993 (p) REVERT: A 491 PHE cc_start: 0.6823 (t80) cc_final: 0.5987 (t80) REVERT: A 534 MET cc_start: 0.0059 (mtp) cc_final: -0.2275 (ptt) REVERT: A 633 GLU cc_start: 0.6135 (pt0) cc_final: 0.5849 (pp20) REVERT: A 645 ASP cc_start: 0.7961 (m-30) cc_final: 0.6611 (p0) REVERT: A 648 MET cc_start: 0.7983 (mmm) cc_final: 0.7708 (ppp) REVERT: A 663 SER cc_start: 0.7920 (t) cc_final: 0.7488 (p) REVERT: A 664 ARG cc_start: 0.7340 (tmm160) cc_final: 0.7089 (tmt-80) REVERT: A 939 MET cc_start: 0.6297 (OUTLIER) cc_final: 0.5175 (ptm) REVERT: A 973 TYR cc_start: 0.7766 (m-10) cc_final: 0.7471 (m-10) REVERT: A 1237 TYR cc_start: 0.4630 (OUTLIER) cc_final: 0.3478 (t80) REVERT: A 1267 ASP cc_start: 0.7648 (p0) cc_final: 0.7413 (p0) REVERT: A 1268 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7179 (mm-30) REVERT: A 1332 ASP cc_start: 0.6888 (m-30) cc_final: 0.6133 (t0) outliers start: 19 outliers final: 8 residues processed: 133 average time/residue: 0.1178 time to fit residues: 22.6918 Evaluate side-chains 114 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.408 ------------------------------------------------------------------------------- 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 244 LEU Chi-restraints excluded: chain A residue 306 LEU 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 939 MET Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1237 TYR 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: 5.9990 chunk 72 optimal weight: 4.9990 chunk 123 optimal weight: 9.9990 chunk 6 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 99 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 40 optimal weight: 5.9990 chunk 69 optimal weight: 20.0000 chunk 120 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.172253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.117628 restraints weight = 20532.778| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 2.99 r_work: 0.3517 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 12548 Z= 0.320 Angle : 0.740 8.723 17537 Z= 0.383 Chirality : 0.044 0.238 2023 Planarity : 0.005 0.061 1743 Dihedral : 19.718 140.701 3096 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.29 % Allowed : 9.24 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.24), residues: 1120 helix: 0.70 (0.22), residues: 556 sheet: -0.80 (0.61), residues: 76 loop : -0.67 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 324 TYR 0.029 0.002 TYR A1237 PHE 0.029 0.003 PHE A 372 TRP 0.015 0.003 TRP A 476 HIS 0.007 0.002 HIS A1349 Details of bonding type rmsd covalent geometry : bond 0.00697 (12548) covalent geometry : angle 0.73962 (17537) hydrogen bonds : bond 0.06819 ( 518) hydrogen bonds : angle 4.93573 ( 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 138 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 115 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.7773 (mmtm) cc_final: 0.7393 (mmtm) REVERT: A 274 ASP cc_start: 0.6699 (m-30) cc_final: 0.5803 (t0) REVERT: A 334 LEU cc_start: 0.7755 (tp) cc_final: 0.7231 (mp) REVERT: A 370 GLU cc_start: 0.7646 (tt0) cc_final: 0.7389 (tm-30) REVERT: A 466 THR cc_start: 0.8766 (m) cc_final: 0.8324 (p) REVERT: A 633 GLU cc_start: 0.6351 (pt0) cc_final: 0.6086 (pp20) REVERT: A 645 ASP cc_start: 0.7771 (m-30) cc_final: 0.7301 (p0) REVERT: A 648 MET cc_start: 0.7937 (mmm) cc_final: 0.7571 (mmm) REVERT: A 939 MET cc_start: 0.6598 (OUTLIER) cc_final: 0.5487 (ptm) REVERT: A 976 ARG cc_start: 0.8673 (ttt-90) cc_final: 0.8378 (tmt170) REVERT: A 1089 MET cc_start: 0.3513 (OUTLIER) cc_final: 0.2278 (mmm) REVERT: A 1237 TYR cc_start: 0.5262 (OUTLIER) cc_final: 0.3283 (t80) REVERT: A 1262 HIS cc_start: 0.5445 (m-70) cc_final: 0.5044 (m-70) REVERT: A 1267 ASP cc_start: 0.7624 (p0) cc_final: 0.7290 (p0) REVERT: A 1332 ASP cc_start: 0.7202 (m-30) cc_final: 0.6437 (t0) outliers start: 23 outliers final: 12 residues processed: 128 average time/residue: 0.1076 time to fit residues: 20.7154 Evaluate side-chains 119 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 418 GLU 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 1089 MET Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1237 TYR Chi-restraints excluded: chain A residue 1352 ILE Chi-restraints excluded: chain A residue 1353 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 111 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 27 optimal weight: 30.0000 chunk 91 optimal weight: 9.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS A1221 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.177724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.123689 restraints weight = 19958.854| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.94 r_work: 0.3616 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12548 Z= 0.129 Angle : 0.556 10.904 17537 Z= 0.286 Chirality : 0.037 0.347 2023 Planarity : 0.003 0.038 1743 Dihedral : 19.447 145.092 3096 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 1.79 % Allowed : 10.44 % Favored : 87.77 % 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: 0.43 (0.25), residues: 1120 helix: 1.14 (0.22), residues: 555 sheet: -0.23 (0.60), residues: 73 loop : -0.57 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 220 TYR 0.012 0.001 TYR A1141 PHE 0.013 0.001 PHE A 478 TRP 0.016 0.002 TRP A 464 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00273 (12548) covalent geometry : angle 0.55580 (17537) hydrogen bonds : bond 0.04831 ( 518) hydrogen bonds : angle 4.42746 ( 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 137 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.7759 (mmtm) cc_final: 0.7310 (mmtm) REVERT: A 274 ASP cc_start: 0.6661 (m-30) cc_final: 0.5752 (t0) REVERT: A 334 LEU cc_start: 0.7901 (tp) cc_final: 0.7359 (mp) REVERT: A 370 GLU cc_start: 0.7459 (tt0) cc_final: 0.7201 (tm-30) REVERT: A 466 THR cc_start: 0.8426 (m) cc_final: 0.8019 (p) REVERT: A 491 PHE cc_start: 0.6872 (t80) cc_final: 0.6039 (t80) REVERT: A 645 ASP cc_start: 0.7810 (m-30) cc_final: 0.6556 (p0) REVERT: A 648 MET cc_start: 0.8005 (mmm) cc_final: 0.7654 (ppp) REVERT: A 663 SER cc_start: 0.7825 (t) cc_final: 0.7474 (p) REVERT: A 664 ARG cc_start: 0.7435 (tmm160) cc_final: 0.7158 (tmt-80) REVERT: A 939 MET cc_start: 0.6511 (OUTLIER) cc_final: 0.6101 (ptm) REVERT: A 973 TYR cc_start: 0.8043 (m-10) cc_final: 0.7384 (m-10) REVERT: A 976 ARG cc_start: 0.8490 (ttt-90) cc_final: 0.8067 (tmt170) REVERT: A 1237 TYR cc_start: 0.4927 (OUTLIER) cc_final: 0.3385 (t80) REVERT: A 1262 HIS cc_start: 0.5232 (m-70) cc_final: 0.4813 (m-70) REVERT: A 1332 ASP cc_start: 0.7024 (m-30) cc_final: 0.6271 (t0) outliers start: 18 outliers final: 9 residues processed: 132 average time/residue: 0.1076 time to fit residues: 21.0603 Evaluate side-chains 116 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1237 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 89 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 99 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 chunk 120 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1221 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.177113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.123419 restraints weight = 20054.388| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.91 r_work: 0.3612 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.4445 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= 0.139 Angle : 0.578 13.501 17537 Z= 0.297 Chirality : 0.038 0.339 2023 Planarity : 0.003 0.033 1743 Dihedral : 19.345 145.293 3096 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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: 0.48 (0.25), residues: 1120 helix: 1.24 (0.22), residues: 554 sheet: -0.33 (0.59), residues: 73 loop : -0.59 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 220 TYR 0.013 0.001 TYR A1237 PHE 0.015 0.001 PHE A 478 TRP 0.014 0.002 TRP A 464 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00297 (12548) covalent geometry : angle 0.57830 (17537) hydrogen bonds : bond 0.04857 ( 518) hydrogen bonds : angle 4.34768 ( 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 135 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 112 LYS cc_start: 0.7825 (mmtm) cc_final: 0.7404 (mmtm) REVERT: A 274 ASP cc_start: 0.6685 (m-30) cc_final: 0.5773 (t0) REVERT: A 334 LEU cc_start: 0.7909 (tp) cc_final: 0.7375 (mp) REVERT: A 370 GLU cc_start: 0.7523 (tt0) cc_final: 0.7077 (pp20) REVERT: A 466 THR cc_start: 0.8465 (m) cc_final: 0.7856 (p) REVERT: A 491 PHE cc_start: 0.6808 (t80) cc_final: 0.6075 (t80) REVERT: A 645 ASP cc_start: 0.7722 (m-30) cc_final: 0.7214 (p0) REVERT: A 648 MET cc_start: 0.7989 (mmm) cc_final: 0.7643 (mmm) REVERT: A 664 ARG cc_start: 0.7422 (tmm160) cc_final: 0.7215 (tmt-80) REVERT: A 939 MET cc_start: 0.6572 (OUTLIER) cc_final: 0.5226 (ptm) REVERT: A 970 PHE cc_start: 0.5520 (OUTLIER) cc_final: 0.5169 (m-80) REVERT: A 976 ARG cc_start: 0.8447 (ttt-90) cc_final: 0.8085 (tmt170) REVERT: A 1237 TYR cc_start: 0.5036 (OUTLIER) cc_final: 0.3242 (t80) REVERT: A 1255 LYS cc_start: 0.5039 (OUTLIER) cc_final: 0.4824 (tmmt) REVERT: A 1332 ASP cc_start: 0.7052 (m-30) cc_final: 0.6318 (t0) outliers start: 22 outliers final: 13 residues processed: 130 average time/residue: 0.1032 time to fit residues: 20.2737 Evaluate side-chains 124 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 418 GLU 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 657 THR Chi-restraints excluded: chain A residue 939 MET Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1237 TYR Chi-restraints excluded: chain A residue 1255 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.9990 chunk 27 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 12 optimal weight: 0.1980 chunk 49 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 116 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 overall best weight: 1.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.178220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.125466 restraints weight = 20030.724| |-----------------------------------------------------------------------------| r_work (start): 0.3806 rms_B_bonded: 2.90 r_work: 0.3637 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12548 Z= 0.123 Angle : 0.549 15.017 17537 Z= 0.281 Chirality : 0.037 0.354 2023 Planarity : 0.003 0.045 1743 Dihedral : 19.215 149.227 3096 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.99 % Allowed : 11.23 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.25), residues: 1120 helix: 1.39 (0.23), residues: 557 sheet: -0.69 (0.57), residues: 85 loop : -0.46 (0.27), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 403 TYR 0.015 0.001 TYR A 973 PHE 0.016 0.001 PHE A 372 TRP 0.013 0.001 TRP A 464 HIS 0.004 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00264 (12548) covalent geometry : angle 0.54851 (17537) hydrogen bonds : bond 0.04575 ( 518) hydrogen bonds : angle 4.23802 ( 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 136 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 116 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASP cc_start: 0.6674 (m-30) cc_final: 0.5919 (t0) REVERT: A 334 LEU cc_start: 0.7923 (tp) cc_final: 0.7345 (mp) REVERT: A 370 GLU cc_start: 0.7486 (tt0) cc_final: 0.7060 (pp20) REVERT: A 491 PHE cc_start: 0.6846 (t80) cc_final: 0.6041 (t80) REVERT: A 534 MET cc_start: 0.0185 (mtt) cc_final: -0.2229 (ptt) REVERT: A 645 ASP cc_start: 0.7724 (m-30) cc_final: 0.7231 (p0) REVERT: A 648 MET cc_start: 0.8022 (mmm) cc_final: 0.7626 (mmm) REVERT: A 939 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.5338 (ptm) REVERT: A 954 LYS cc_start: 0.6587 (mttt) cc_final: 0.6341 (tptt) REVERT: A 970 PHE cc_start: 0.5449 (OUTLIER) cc_final: 0.5056 (m-80) REVERT: A 976 ARG cc_start: 0.8442 (ttt-90) cc_final: 0.7987 (tmt170) REVERT: A 1089 MET cc_start: 0.3274 (OUTLIER) cc_final: 0.2574 (mmt) REVERT: A 1332 ASP cc_start: 0.7022 (m-30) cc_final: 0.6291 (t0) outliers start: 20 outliers final: 13 residues processed: 129 average time/residue: 0.1018 time to fit residues: 19.9454 Evaluate side-chains 123 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 TYR Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 244 LEU Chi-restraints excluded: chain A residue 418 GLU 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 970 PHE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1237 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 34 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 chunk 123 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 112 optimal weight: 20.0000 chunk 113 optimal weight: 4.9990 chunk 75 optimal weight: 0.2980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.173655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.119350 restraints weight = 20136.551| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.90 r_work: 0.3551 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12548 Z= 0.203 Angle : 0.632 14.029 17537 Z= 0.324 Chirality : 0.040 0.335 2023 Planarity : 0.004 0.042 1743 Dihedral : 19.357 151.920 3096 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 1.89 % Allowed : 12.23 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1120 helix: 1.12 (0.22), residues: 560 sheet: -0.40 (0.62), residues: 73 loop : -0.68 (0.27), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 220 TYR 0.016 0.002 TYR A1237 PHE 0.024 0.002 PHE A 372 TRP 0.012 0.002 TRP A 464 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00444 (12548) covalent geometry : angle 0.63159 (17537) hydrogen bonds : bond 0.05566 ( 518) hydrogen bonds : angle 4.46289 ( 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: 19 poor density : 106 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.7895 (mm-30) cc_final: 0.7642 (tp30) REVERT: A 274 ASP cc_start: 0.6702 (m-30) cc_final: 0.5816 (t0) REVERT: A 334 LEU cc_start: 0.7858 (tp) cc_final: 0.7355 (mp) REVERT: A 370 GLU cc_start: 0.7619 (tt0) cc_final: 0.7303 (tm-30) REVERT: A 491 PHE cc_start: 0.7019 (t80) cc_final: 0.6090 (t80) REVERT: A 534 MET cc_start: 0.0190 (mtt) cc_final: -0.2258 (ptt) REVERT: A 645 ASP cc_start: 0.7761 (m-30) cc_final: 0.7312 (p0) REVERT: A 648 MET cc_start: 0.7975 (mmm) cc_final: 0.7587 (mmm) REVERT: A 976 ARG cc_start: 0.8483 (ttt-90) cc_final: 0.8048 (tmt170) REVERT: A 1089 MET cc_start: 0.3254 (OUTLIER) cc_final: 0.2153 (mmm) REVERT: A 1237 TYR cc_start: 0.5190 (OUTLIER) cc_final: 0.3201 (t80) REVERT: A 1332 ASP cc_start: 0.7232 (m-30) cc_final: 0.6399 (t0) outliers start: 19 outliers final: 14 residues processed: 118 average time/residue: 0.0880 time to fit residues: 16.3759 Evaluate side-chains 117 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.386 ------------------------------------------------------------------------------- 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 244 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1237 TYR 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: 20.0000 chunk 32 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.176497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.123137 restraints weight = 20002.236| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 2.90 r_work: 0.3608 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.5011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12548 Z= 0.137 Angle : 0.572 14.122 17537 Z= 0.293 Chirality : 0.038 0.354 2023 Planarity : 0.003 0.039 1743 Dihedral : 19.217 154.817 3096 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.79 % Allowed : 12.43 % Favored : 85.79 % 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 (0.25), residues: 1120 helix: 1.38 (0.23), residues: 552 sheet: -0.74 (0.57), residues: 85 loop : -0.60 (0.27), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 220 TYR 0.011 0.001 TYR A1242 PHE 0.016 0.001 PHE A 372 TRP 0.014 0.002 TRP A 464 HIS 0.005 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00298 (12548) covalent geometry : angle 0.57211 (17537) hydrogen bonds : bond 0.04761 ( 518) hydrogen bonds : angle 4.28085 ( 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 123 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 105 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASP cc_start: 0.6682 (m-30) cc_final: 0.5927 (t0) REVERT: A 334 LEU cc_start: 0.7890 (tp) cc_final: 0.7367 (mp) REVERT: A 370 GLU cc_start: 0.7540 (tt0) cc_final: 0.7088 (pp20) REVERT: A 491 PHE cc_start: 0.6862 (t80) cc_final: 0.6028 (t80) REVERT: A 534 MET cc_start: 0.0433 (mtt) cc_final: -0.2113 (ptt) REVERT: A 645 ASP cc_start: 0.7771 (m-30) cc_final: 0.7345 (p0) REVERT: A 648 MET cc_start: 0.8050 (mmm) cc_final: 0.7668 (mmm) REVERT: A 746 GLU cc_start: 0.8516 (mt-10) cc_final: 0.7992 (tt0) REVERT: A 1089 MET cc_start: 0.3085 (OUTLIER) cc_final: 0.2250 (mmt) REVERT: A 1237 TYR cc_start: 0.5144 (OUTLIER) cc_final: 0.2272 (t80) REVERT: A 1332 ASP cc_start: 0.7188 (m-30) cc_final: 0.6342 (t0) outliers start: 18 outliers final: 15 residues processed: 117 average time/residue: 0.0939 time to fit residues: 16.9725 Evaluate side-chains 117 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.375 ------------------------------------------------------------------------------- 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 244 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 418 GLU Chi-restraints excluded: chain A residue 495 MET Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 657 THR Chi-restraints excluded: chain A residue 685 SER Chi-restraints excluded: chain A residue 970 PHE Chi-restraints excluded: chain A residue 998 ILE Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1089 MET Chi-restraints excluded: chain A residue 1138 THR Chi-restraints excluded: chain A residue 1237 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 57 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 117 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 18 optimal weight: 0.0980 chunk 114 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 415 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.174074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.120203 restraints weight = 20161.889| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.89 r_work: 0.3561 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.5235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 12548 Z= 0.201 Angle : 0.634 13.438 17537 Z= 0.325 Chirality : 0.040 0.335 2023 Planarity : 0.004 0.039 1743 Dihedral : 19.351 154.144 3096 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.89 % Allowed : 12.43 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.25), residues: 1120 helix: 1.17 (0.22), residues: 554 sheet: -0.86 (0.58), residues: 78 loop : -0.67 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 220 TYR 0.015 0.002 TYR A1237 PHE 0.022 0.002 PHE A 372 TRP 0.012 0.002 TRP A 464 HIS 0.007 0.001 HIS A 328 Details of bonding type rmsd covalent geometry : bond 0.00438 (12548) covalent geometry : angle 0.63374 (17537) hydrogen bonds : bond 0.05532 ( 518) hydrogen bonds : angle 4.47204 ( 1412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3271.89 seconds wall clock time: 56 minutes 58.14 seconds (3418.14 seconds total)