Starting phenix.real_space_refine on Wed Aug 5 23:10:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k4f_62057/08_2026/9k4f_62057.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k4f_62057/08_2026/9k4f_62057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k4f_62057/08_2026/9k4f_62057.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k4f_62057/08_2026/9k4f_62057.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k4f_62057/08_2026/9k4f_62057.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k4f_62057/08_2026/9k4f_62057.map" } resolution = 3.27 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= 0.007 sd= 0.128 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 130 5.49 5 S 19 5.16 5 C 7192 2.51 5 N 2118 2.21 5 O 2607 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12066 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9268 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1136, 9268 Classifications: {'peptide': 1136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 31, 'TRANS': 1104} Chain breaks: 2 Chain: "B" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 560 Classifications: {'DNA': 27} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 305 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "D" Number of atoms: 1933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1933 Classifications: {'RNA': 91} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 42, 'rna3p_pyr': 38} Link IDs: {'rna2p': 11, 'rna3p': 79} Time building chain proxies: 3.18, per 1000 atoms: 0.26 Number of scatterers: 12066 At special positions: 0 Unit cell: (129.21, 106.215, 148.92, 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 130 15.00 O 2607 8.00 N 2118 7.00 C 7192 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: 1.07 Conformation dependent library (CDL) restraints added in 532.8 milliseconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 7 sheets defined 56.0% alpha, 10.1% beta 50 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.715A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.641A 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: 3.807A 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 306 removed outlier: 4.346A pdb=" N ASP A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ILE A 305 " --> pdb=" O LEU A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 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: 3.807A pdb=" N ASN A 407 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.108A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 Processing helix chain 'A' and resid 512 through 526 removed outlier: 4.066A pdb=" N LYS A 526 " --> pdb=" O ASN A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 541 through 553 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 Processing helix chain 'A' and resid 628 through 637 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 652 Processing helix chain 'A' and resid 663 through 668 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 720 through 726 removed outlier: 3.844A pdb=" N ILE A 724 " --> pdb=" O LEU A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 751 Processing helix chain 'A' and resid 926 through 940 Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.073A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1001 removed outlier: 4.530A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1075 through 1088 removed outlier: 3.580A pdb=" N ASP A1079 " --> pdb=" O ASP A1075 " (cutoff:3.500A) 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 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1264 through 1281 Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1317 removed outlier: 3.731A pdb=" N HIS A1311 " --> pdb=" O GLU A1307 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N PHE A1313 " --> pdb=" O ILE A1309 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR A1314 " --> pdb=" O ILE A1310 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N LEU A1315 " --> pdb=" O HIS A1311 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N THR A1316 " --> pdb=" O LEU A1312 " (cutoff:3.500A) Processing helix chain 'A' and resid 1340 through 1344 removed outlier: 3.695A pdb=" N ASP A1344 " --> pdb=" O GLU A1341 " (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: 5.913A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N TYR A 5 " --> pdb=" O ASN A 758 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N VAL A 760 " --> pdb=" O TYR A 5 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33 Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36 removed outlier: 6.274A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER A1202 " --> pdb=" O LEU A1214 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.508A pdb=" N ALA A 538 " --> pdb=" O TYR A 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.522A pdb=" N GLU A1162 " --> pdb=" O VAL A1145 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.522A pdb=" N GLU A1162 " --> pdb=" O VAL A1145 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE A1196 " --> pdb=" O LEU A1144 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1326 462 hydrogen bonds defined for protein. 1353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 127 hydrogen bonds 250 hydrogen bond angles 0 basepair planarities 50 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 3.41 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: 2773 1.33 - 1.45: 3140 1.45 - 1.57: 6362 1.57 - 1.69: 260 1.69 - 1.81: 36 Bond restraints: 12571 Sorted by residual: bond pdb=" C3' DA B 8 " pdb=" C2' DA B 8 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.76e+00 bond pdb=" C3' DT B 17 " pdb=" C2' DT B 17 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.26e+00 bond pdb=" C3' DC B 16 " pdb=" C2' DC B 16 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 7.07e+00 bond pdb=" C3' DC C 5 " pdb=" C2' DC C 5 " ideal model delta sigma weight residual 1.516 1.537 -0.021 8.00e-03 1.56e+04 6.96e+00 bond pdb=" C3' DA B 5 " pdb=" C2' DA B 5 " ideal model delta sigma weight residual 1.516 1.534 -0.018 8.00e-03 1.56e+04 5.25e+00 ... (remaining 12566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 16853 1.45 - 2.89: 646 2.89 - 4.34: 43 4.34 - 5.78: 7 5.78 - 7.23: 1 Bond angle restraints: 17550 Sorted by residual: angle pdb=" O4' DT B 19 " pdb=" C4' DT B 19 " pdb=" C3' DT B 19 " ideal model delta sigma weight residual 106.00 103.05 2.95 6.00e-01 2.78e+00 2.42e+01 angle pdb=" N3 DT B 4 " pdb=" C4 DT B 4 " pdb=" O4 DT B 4 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" O4' DG B 23 " pdb=" C4' DG B 23 " pdb=" C3' DG B 23 " ideal model delta sigma weight residual 106.00 103.41 2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT B 6 " pdb=" C4 DT B 6 " pdb=" O4 DT B 6 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 angle pdb=" N3 DT B 10 " pdb=" C4 DT B 10 " pdb=" O4 DT B 10 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 ... (remaining 17545 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.80: 7164 28.80 - 57.59: 352 57.59 - 86.39: 106 86.39 - 115.18: 0 115.18 - 143.98: 1 Dihedral angle restraints: 7623 sinusoidal: 4286 harmonic: 3337 Sorted by residual: dihedral pdb=" CA SER A 719 " pdb=" C SER A 719 " pdb=" N LEU A 720 " pdb=" CA LEU A 720 " ideal model delta harmonic sigma weight residual -180.00 -159.44 -20.56 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA ASN A 497 " pdb=" C ASN A 497 " pdb=" N PHE A 498 " pdb=" CA PHE A 498 " ideal model delta harmonic sigma weight residual 180.00 161.08 18.92 0 5.00e+00 4.00e-02 1.43e+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 76.02 143.98 1 3.50e+01 8.16e-04 1.42e+01 ... (remaining 7620 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1268 0.031 - 0.062: 458 0.062 - 0.092: 141 0.092 - 0.123: 74 0.123 - 0.154: 78 Chirality restraints: 2019 Sorted by residual: chirality pdb=" C2' C D 17 " pdb=" C3' C D 17 " pdb=" O2' C D 17 " pdb=" C1' C D 17 " both_signs ideal model delta sigma weight residual False -2.62 -2.77 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" C2' U D 16 " pdb=" C3' U D 16 " pdb=" O2' U D 16 " pdb=" C1' U D 16 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.15 2.00e-01 2.50e+01 5.28e-01 chirality pdb=" C2' A D 70 " pdb=" C3' A D 70 " pdb=" O2' A D 70 " pdb=" C1' A D 70 " both_signs ideal model delta sigma weight residual False -2.62 -2.76 0.14 2.00e-01 2.50e+01 5.20e-01 ... (remaining 2016 not shown) Planarity restraints: 1757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G D 56 " 0.018 2.00e-02 2.50e+03 8.20e-03 2.02e+00 pdb=" N9 G D 56 " -0.021 2.00e-02 2.50e+03 pdb=" C8 G D 56 " -0.001 2.00e-02 2.50e+03 pdb=" N7 G D 56 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G D 56 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G D 56 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G D 56 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G D 56 " 0.002 2.00e-02 2.50e+03 pdb=" C2 G D 56 " -0.003 2.00e-02 2.50e+03 pdb=" N2 G D 56 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G D 56 " -0.002 2.00e-02 2.50e+03 pdb=" C4 G D 56 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A D 44 " 0.018 2.00e-02 2.50e+03 7.92e-03 1.72e+00 pdb=" N9 A D 44 " -0.017 2.00e-02 2.50e+03 pdb=" C8 A D 44 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A D 44 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A D 44 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A D 44 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A D 44 " 0.005 2.00e-02 2.50e+03 pdb=" N1 A D 44 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A D 44 " -0.001 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 delta sigma weight rms_deltas residual plane pdb=" C SER A 730 " -0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO A 731 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 731 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 731 " -0.017 5.00e-02 4.00e+02 ... (remaining 1754 not shown) Histogram of nonbonded interaction distances: 1.30 - 2.02: 3 2.02 - 2.74: 1020 2.74 - 3.46: 16157 3.46 - 4.18: 30616 4.18 - 4.90: 50323 Nonbonded interactions: 98119 Sorted by model distance: nonbonded pdb=" NZ LYS A1340 " pdb=" OP2 DA B 8 " model vdw 1.297 3.120 nonbonded pdb=" NZ LYS A 44 " pdb=" O6 G D 94 " model vdw 1.297 3.120 nonbonded pdb=" NH1 ARG A 71 " pdb=" N4 C D 20 " model vdw 1.352 3.200 nonbonded pdb=" CE LYS A1340 " pdb=" OP2 DA B 8 " model vdw 2.067 3.440 nonbonded pdb=" NH1 ARG A 71 " pdb=" C4 C D 20 " model vdw 2.080 3.340 ... (remaining 98114 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: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 14.640 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 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 0.028 12571 Z= 0.267 Angle : 0.609 7.227 17550 Z= 0.459 Chirality : 0.046 0.154 2019 Planarity : 0.003 0.032 1757 Dihedral : 16.450 143.976 5463 Min Nonbonded Distance : 1.297 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.83 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.25), residues: 1130 helix: 1.69 (0.22), residues: 575 sheet: 0.79 (0.54), residues: 87 loop : 0.40 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 74 TYR 0.012 0.001 TYR A 155 PHE 0.012 0.001 PHE A1204 TRP 0.014 0.002 TRP A1074 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.27 (12571) covalent geometry : angle 0.60899 / 0.46 (17550) hydrogen bonds : bond 0.15131 / 9.92 ( 579) hydrogen bonds : angle 5.42549 / 3.84 ( 1603) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8173 (m-30) cc_final: 0.7784 (m-30) REVERT: A 327 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7358 (tt0) REVERT: A 498 PHE cc_start: 0.8167 (m-10) cc_final: 0.7754 (m-80) REVERT: A 534 MET cc_start: -0.0229 (mtp) cc_final: -0.1429 (mmt) REVERT: A 596 ASP cc_start: 0.7182 (m-30) cc_final: 0.6940 (m-30) REVERT: A 629 ARG cc_start: 0.7573 (mtt180) cc_final: 0.7199 (ppt170) REVERT: A 648 MET cc_start: 0.7113 (mmm) cc_final: 0.6851 (mmt) REVERT: A 751 MET cc_start: 0.8818 (mmm) cc_final: 0.8432 (mmt) REVERT: A 929 LYS cc_start: 0.7532 (mttt) cc_final: 0.7257 (mmtm) REVERT: A 1129 LYS cc_start: 0.8703 (mttt) cc_final: 0.8457 (mttm) REVERT: A 1157 LEU cc_start: 0.7644 (mt) cc_final: 0.7284 (mp) REVERT: A 1255 LYS cc_start: 0.6711 (mttt) cc_final: 0.6287 (mttm) REVERT: A 1325 LYS cc_start: 0.8828 (mttt) cc_final: 0.8402 (ttmm) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.1407 time to fit residues: 35.5602 Evaluate side-chains 97 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 113 optimal weight: 40.0000 chunk 53 optimal weight: 0.0980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 123 optimal weight: 30.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 10.0000 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 402 GLN A 426 GLN A 712 GLN A 723 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.169395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.122840 restraints weight = 19320.252| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 3.26 r_work: 0.3333 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12571 Z= 0.168 Angle : 0.557 10.225 17550 Z= 0.310 Chirality : 0.039 0.155 2019 Planarity : 0.004 0.059 1757 Dihedral : 18.673 147.168 3066 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.48 % Favored : 97.43 % Rotamer: Outliers : 1.28 % Allowed : 4.23 % Favored : 94.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.25), residues: 1130 helix: 1.52 (0.22), residues: 595 sheet: 0.47 (0.54), residues: 87 loop : 0.10 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 71 TYR 0.040 0.002 TYR A 136 PHE 0.012 0.001 PHE A1327 TRP 0.006 0.001 TRP A1074 HIS 0.006 0.001 HIS A 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.17 (12571) covalent geometry : angle 0.55657 / 0.31 (17550) hydrogen bonds : bond 0.05290 / 3.58 ( 579) hydrogen bonds : angle 4.49807 / 3.19 ( 1603) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 104 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8177 (m-30) cc_final: 0.7743 (m-30) REVERT: A 76 LYS cc_start: 0.8093 (tttt) cc_final: 0.7802 (tptt) REVERT: A 498 PHE cc_start: 0.8212 (m-10) cc_final: 0.7768 (m-80) REVERT: A 534 MET cc_start: -0.0237 (mtp) cc_final: -0.0942 (mmm) REVERT: A 596 ASP cc_start: 0.7226 (m-30) cc_final: 0.7000 (m-30) REVERT: A 648 MET cc_start: 0.6840 (mmm) cc_final: 0.6593 (mmt) REVERT: A 651 LEU cc_start: 0.8324 (mt) cc_final: 0.8095 (mp) REVERT: A 751 MET cc_start: 0.8867 (mmm) cc_final: 0.8560 (mmt) REVERT: A 929 LYS cc_start: 0.7547 (mttt) cc_final: 0.7303 (mmtm) REVERT: A 1325 LYS cc_start: 0.8880 (mttt) cc_final: 0.8442 (ttmm) outliers start: 13 outliers final: 7 residues processed: 110 average time/residue: 0.1283 time to fit residues: 19.6027 Evaluate side-chains 88 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1273 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 62 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 34 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 106 optimal weight: 9.9990 chunk 80 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 122 optimal weight: 20.0000 chunk 13 optimal weight: 4.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 723 HIS ** A 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.165733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.118313 restraints weight = 19600.326| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 3.37 r_work: 0.3265 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12571 Z= 0.226 Angle : 0.591 9.920 17550 Z= 0.322 Chirality : 0.042 0.214 2019 Planarity : 0.004 0.055 1757 Dihedral : 18.858 146.130 3066 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.10 % Favored : 96.81 % Rotamer: Outliers : 1.57 % Allowed : 5.51 % Favored : 92.91 % 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: 0.89 (0.25), residues: 1130 helix: 1.34 (0.21), residues: 596 sheet: -0.31 (0.50), residues: 105 loop : -0.12 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1279 TYR 0.029 0.002 TYR A 136 PHE 0.015 0.002 PHE A 372 TRP 0.008 0.002 TRP A1074 HIS 0.007 0.001 HIS A1349 Details of bonding type rmsd/Z covalent geometry : bond 0.00498 / 0.23 (12571) covalent geometry : angle 0.59061 / 0.32 (17550) hydrogen bonds : bond 0.05485 / 3.77 ( 579) hydrogen bonds : angle 4.39740 / 3.11 ( 1603) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.234 Fit side-chains REVERT: A 76 LYS cc_start: 0.8203 (tttt) cc_final: 0.7879 (tptt) REVERT: A 498 PHE cc_start: 0.8222 (m-10) cc_final: 0.7685 (m-80) REVERT: A 534 MET cc_start: -0.0513 (mtp) cc_final: -0.1575 (mmt) REVERT: A 596 ASP cc_start: 0.7184 (m-30) cc_final: 0.6975 (m-30) REVERT: A 926 GLN cc_start: 0.8155 (tp40) cc_final: 0.7850 (tp40) REVERT: A 929 LYS cc_start: 0.7710 (mttt) cc_final: 0.7458 (mmtm) REVERT: A 1256 GLN cc_start: 0.8250 (mt0) cc_final: 0.7871 (mp10) REVERT: A 1325 LYS cc_start: 0.8957 (mttt) cc_final: 0.8496 (ttmm) outliers start: 16 outliers final: 12 residues processed: 96 average time/residue: 0.1143 time to fit residues: 15.4069 Evaluate side-chains 94 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 112 optimal weight: 0.8980 chunk 71 optimal weight: 40.0000 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 100 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 82 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 723 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.167906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.120789 restraints weight = 19369.072| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 3.19 r_work: 0.3312 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12571 Z= 0.131 Angle : 0.495 8.247 17550 Z= 0.279 Chirality : 0.038 0.206 2019 Planarity : 0.004 0.053 1757 Dihedral : 18.910 147.329 3066 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer: Outliers : 1.67 % Allowed : 6.30 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.25), residues: 1130 helix: 1.55 (0.22), residues: 594 sheet: -0.33 (0.49), residues: 105 loop : -0.04 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 653 TYR 0.023 0.001 TYR A 136 PHE 0.015 0.001 PHE A1327 TRP 0.009 0.001 TRP A1074 HIS 0.007 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (12571) covalent geometry : angle 0.49531 / 0.28 (17550) hydrogen bonds : bond 0.04479 / 3.06 ( 579) hydrogen bonds : angle 4.22864 / 3.01 ( 1603) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8246 (m-30) cc_final: 0.7952 (m-30) REVERT: A 76 LYS cc_start: 0.8144 (tttt) cc_final: 0.7878 (tptt) REVERT: A 498 PHE cc_start: 0.8187 (m-10) cc_final: 0.7729 (m-80) REVERT: A 534 MET cc_start: -0.0437 (mtp) cc_final: -0.1497 (mmt) REVERT: A 596 ASP cc_start: 0.7194 (m-30) cc_final: 0.6983 (m-30) REVERT: A 929 LYS cc_start: 0.7698 (mttt) cc_final: 0.7379 (mmtm) REVERT: A 1145 VAL cc_start: 0.8977 (t) cc_final: 0.8708 (p) REVERT: A 1256 GLN cc_start: 0.8267 (mt0) cc_final: 0.7888 (mp10) REVERT: A 1325 LYS cc_start: 0.8890 (mttt) cc_final: 0.8437 (ttmm) REVERT: A 1346 THR cc_start: 0.8623 (p) cc_final: 0.8392 (t) outliers start: 17 outliers final: 12 residues processed: 96 average time/residue: 0.1110 time to fit residues: 15.2542 Evaluate side-chains 90 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 977 GLU Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1273 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 83 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 30.0000 chunk 98 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 20.0000 chunk 11 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 71 optimal weight: 30.0000 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 723 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.166115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.119234 restraints weight = 19552.772| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 3.20 r_work: 0.3277 rms_B_bonded: 4.28 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.2455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12571 Z= 0.182 Angle : 0.539 9.840 17550 Z= 0.297 Chirality : 0.040 0.217 2019 Planarity : 0.004 0.052 1757 Dihedral : 19.010 146.962 3066 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.10 % Favored : 96.81 % Rotamer: Outliers : 1.57 % Allowed : 7.09 % Favored : 91.34 % 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: 0.94 (0.25), residues: 1130 helix: 1.46 (0.22), residues: 596 sheet: -0.51 (0.49), residues: 105 loop : -0.16 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 165 TYR 0.020 0.001 TYR A 136 PHE 0.022 0.001 PHE A1327 TRP 0.009 0.001 TRP A1074 HIS 0.006 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (12571) covalent geometry : angle 0.53919 / 0.30 (17550) hydrogen bonds : bond 0.04807 / 3.32 ( 579) hydrogen bonds : angle 4.23635 / 3.02 ( 1603) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.386 Fit side-chains revert: symmetry clash REVERT: A 54 ASP cc_start: 0.8262 (m-30) cc_final: 0.7945 (m-30) REVERT: A 76 LYS cc_start: 0.8195 (tttt) cc_final: 0.7927 (tptt) REVERT: A 498 PHE cc_start: 0.8202 (m-10) cc_final: 0.7743 (m-80) REVERT: A 534 MET cc_start: -0.0311 (mtp) cc_final: -0.1438 (mmt) REVERT: A 596 ASP cc_start: 0.6879 (m-30) cc_final: 0.6652 (m-30) REVERT: A 652 LYS cc_start: 0.8331 (tmtt) cc_final: 0.8092 (tmtt) REVERT: A 1145 VAL cc_start: 0.9019 (t) cc_final: 0.8781 (p) REVERT: A 1256 GLN cc_start: 0.8343 (mt0) cc_final: 0.7989 (mp10) REVERT: A 1325 LYS cc_start: 0.8882 (mttt) cc_final: 0.8429 (ttmm) outliers start: 16 outliers final: 15 residues processed: 96 average time/residue: 0.1007 time to fit residues: 13.7717 Evaluate side-chains 94 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 ILE Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 97 optimal weight: 4.9990 chunk 24 optimal weight: 40.0000 chunk 17 optimal weight: 8.9990 chunk 116 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 51 optimal weight: 6.9990 chunk 67 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 64 optimal weight: 6.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 HIS A1272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.162344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.113633 restraints weight = 19411.600| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 3.35 r_work: 0.3170 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12571 Z= 0.243 Angle : 0.617 11.103 17550 Z= 0.330 Chirality : 0.043 0.223 2019 Planarity : 0.004 0.052 1757 Dihedral : 19.220 146.267 3066 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.27 % Favored : 96.64 % Rotamer: Outliers : 1.67 % Allowed : 7.78 % Favored : 90.55 % 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: 0.55 (0.25), residues: 1130 helix: 1.23 (0.21), residues: 596 sheet: -0.77 (0.49), residues: 105 loop : -0.46 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 653 TYR 0.022 0.002 TYR A 136 PHE 0.025 0.002 PHE A1327 TRP 0.010 0.002 TRP A1074 HIS 0.007 0.002 HIS A1349 Details of bonding type rmsd/Z covalent geometry : bond 0.00542 / 0.24 (12571) covalent geometry : angle 0.61653 / 0.33 (17550) hydrogen bonds : bond 0.05385 / 3.76 ( 579) hydrogen bonds : angle 4.35740 / 3.11 ( 1603) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8286 (tttt) cc_final: 0.7961 (tptt) REVERT: A 534 MET cc_start: -0.0159 (mtp) cc_final: -0.1346 (mmt) REVERT: A 596 ASP cc_start: 0.6923 (m-30) cc_final: 0.6669 (m-30) REVERT: A 651 LEU cc_start: 0.8408 (mp) cc_final: 0.8139 (mp) REVERT: A 656 TYR cc_start: 0.7019 (m-80) cc_final: 0.6739 (m-80) REVERT: A 1145 VAL cc_start: 0.8996 (t) cc_final: 0.8753 (p) REVERT: A 1256 GLN cc_start: 0.8389 (mt0) cc_final: 0.8067 (mp10) REVERT: A 1325 LYS cc_start: 0.8925 (mttt) cc_final: 0.8447 (ttmm) outliers start: 17 outliers final: 14 residues processed: 98 average time/residue: 0.1121 time to fit residues: 15.7335 Evaluate side-chains 96 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 112 LYS Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 42 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 122 optimal weight: 30.0000 chunk 65 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 402 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.166862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.119429 restraints weight = 19435.926| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 3.45 r_work: 0.3277 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12571 Z= 0.127 Angle : 0.508 10.657 17550 Z= 0.281 Chirality : 0.037 0.193 2019 Planarity : 0.004 0.056 1757 Dihedral : 19.182 149.797 3066 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.65 % Favored : 97.26 % Rotamer: Outliers : 1.28 % Allowed : 8.37 % Favored : 90.35 % 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: 0.86 (0.25), residues: 1130 helix: 1.55 (0.22), residues: 593 sheet: -0.76 (0.48), residues: 105 loop : -0.36 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 629 TYR 0.018 0.001 TYR A 136 PHE 0.018 0.001 PHE A1327 TRP 0.012 0.001 TRP A1074 HIS 0.007 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 (12571) covalent geometry : angle 0.50820 / 0.28 (17550) hydrogen bonds : bond 0.04328 / 2.96 ( 579) hydrogen bonds : angle 4.16698 / 2.98 ( 1603) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8214 (tttt) cc_final: 0.7950 (tptt) REVERT: A 498 PHE cc_start: 0.8025 (m-80) cc_final: 0.7002 (m-80) REVERT: A 534 MET cc_start: -0.0251 (mtp) cc_final: -0.1407 (mmt) REVERT: A 596 ASP cc_start: 0.6889 (m-30) cc_final: 0.6622 (m-30) REVERT: A 694 MET cc_start: 0.5331 (ptp) cc_final: 0.5115 (ptp) REVERT: A 1145 VAL cc_start: 0.9030 (t) cc_final: 0.8799 (p) REVERT: A 1177 ASN cc_start: 0.7744 (t0) cc_final: 0.6938 (t0) REVERT: A 1256 GLN cc_start: 0.8401 (mt0) cc_final: 0.8091 (mp10) REVERT: A 1325 LYS cc_start: 0.8895 (mttt) cc_final: 0.8637 (mtpp) outliers start: 13 outliers final: 13 residues processed: 94 average time/residue: 0.0986 time to fit residues: 13.3681 Evaluate side-chains 92 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 45 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 44 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 113 optimal weight: 50.0000 chunk 84 optimal weight: 5.9990 chunk 35 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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 = 0.4256 r_free = 0.4256 target = 0.164196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.116828 restraints weight = 19489.402| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.43 r_work: 0.3233 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12571 Z= 0.221 Angle : 0.594 13.549 17550 Z= 0.316 Chirality : 0.041 0.205 2019 Planarity : 0.004 0.052 1757 Dihedral : 19.248 149.072 3066 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.54 % Favored : 96.37 % Rotamer: Outliers : 1.77 % Allowed : 8.17 % Favored : 90.06 % 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: 1130 helix: 1.32 (0.21), residues: 595 sheet: -0.86 (0.49), residues: 105 loop : -0.53 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 653 TYR 0.018 0.002 TYR A 136 PHE 0.018 0.002 PHE A1327 TRP 0.012 0.002 TRP A1074 HIS 0.006 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.22 (12571) covalent geometry : angle 0.59356 / 0.32 (17550) hydrogen bonds : bond 0.05049 / 3.52 ( 579) hydrogen bonds : angle 4.28224 / 3.06 ( 1603) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8245 (tttt) cc_final: 0.7925 (tptt) REVERT: A 498 PHE cc_start: 0.7991 (m-80) cc_final: 0.6956 (m-80) REVERT: A 534 MET cc_start: -0.0222 (mtp) cc_final: -0.1315 (mmt) REVERT: A 596 ASP cc_start: 0.6905 (m-30) cc_final: 0.6654 (m-30) REVERT: A 1145 VAL cc_start: 0.8991 (t) cc_final: 0.8754 (p) REVERT: A 1325 LYS cc_start: 0.8944 (mttt) cc_final: 0.8655 (mtpp) outliers start: 18 outliers final: 15 residues processed: 93 average time/residue: 0.1215 time to fit residues: 16.4654 Evaluate side-chains 94 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 953 VAL Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1346 THR Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 78 optimal weight: 0.1980 chunk 111 optimal weight: 3.9990 chunk 61 optimal weight: 8.9990 chunk 38 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 2 optimal weight: 0.1980 chunk 91 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 = 0.4283 r_free = 0.4283 target = 0.166365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.119097 restraints weight = 19297.324| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 3.44 r_work: 0.3276 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12571 Z= 0.133 Angle : 0.523 15.280 17550 Z= 0.285 Chirality : 0.038 0.184 2019 Planarity : 0.004 0.053 1757 Dihedral : 19.241 150.972 3066 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.90 % Rotamer: Outliers : 1.38 % Allowed : 8.76 % Favored : 89.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.25), residues: 1130 helix: 1.50 (0.22), residues: 594 sheet: -0.81 (0.48), residues: 105 loop : -0.48 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 629 TYR 0.017 0.001 TYR A 136 PHE 0.018 0.001 PHE A1327 TRP 0.014 0.001 TRP A1074 HIS 0.007 0.001 HIS A 930 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (12571) covalent geometry : angle 0.52318 / 0.29 (17550) hydrogen bonds : bond 0.04289 / 2.94 ( 579) hydrogen bonds : angle 4.17336 / 3.00 ( 1603) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8233 (tttt) cc_final: 0.7961 (tptt) REVERT: A 498 PHE cc_start: 0.7990 (m-80) cc_final: 0.6925 (m-80) REVERT: A 534 MET cc_start: -0.0219 (mtp) cc_final: -0.1231 (mmt) REVERT: A 596 ASP cc_start: 0.6910 (m-30) cc_final: 0.6651 (m-30) REVERT: A 694 MET cc_start: 0.5323 (ptp) cc_final: 0.5102 (ptp) REVERT: A 1145 VAL cc_start: 0.8920 (t) cc_final: 0.8712 (p) REVERT: A 1256 GLN cc_start: 0.8409 (mt0) cc_final: 0.8105 (mp10) REVERT: A 1325 LYS cc_start: 0.8907 (mttt) cc_final: 0.8648 (mtpp) outliers start: 14 outliers final: 14 residues processed: 88 average time/residue: 0.1152 time to fit residues: 14.8908 Evaluate side-chains 93 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 9 optimal weight: 7.9990 chunk 106 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 54 optimal weight: 20.0000 chunk 39 optimal weight: 0.0270 chunk 119 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 3 optimal weight: 3.9990 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 982 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4255 r_free = 0.4255 target = 0.164036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.116546 restraints weight = 19547.818| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 3.46 r_work: 0.3232 rms_B_bonded: 4.45 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12571 Z= 0.217 Angle : 0.598 13.994 17550 Z= 0.318 Chirality : 0.042 0.202 2019 Planarity : 0.004 0.051 1757 Dihedral : 19.332 149.376 3066 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.11 % Rotamer: Outliers : 1.48 % Allowed : 8.76 % Favored : 89.76 % 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: 0.51 (0.25), residues: 1130 helix: 1.34 (0.22), residues: 589 sheet: -0.78 (0.50), residues: 100 loop : -0.71 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 165 TYR 0.019 0.002 TYR A 136 PHE 0.019 0.002 PHE A1327 TRP 0.013 0.002 TRP A1074 HIS 0.006 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (12571) covalent geometry : angle 0.59850 / 0.32 (17550) hydrogen bonds : bond 0.05164 / 3.61 ( 579) hydrogen bonds : angle 4.28470 / 3.07 ( 1603) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 LYS cc_start: 0.8297 (tttt) cc_final: 0.8006 (tptt) REVERT: A 498 PHE cc_start: 0.8009 (m-80) cc_final: 0.6969 (m-80) REVERT: A 534 MET cc_start: -0.0133 (mtp) cc_final: -0.1136 (mmp) REVERT: A 596 ASP cc_start: 0.6952 (m-30) cc_final: 0.6691 (m-30) REVERT: A 694 MET cc_start: 0.5262 (ptp) cc_final: 0.5020 (ptp) REVERT: A 1325 LYS cc_start: 0.8950 (mttt) cc_final: 0.8689 (mtpp) outliers start: 15 outliers final: 14 residues processed: 90 average time/residue: 0.1236 time to fit residues: 16.0614 Evaluate side-chains 92 residues out of total 1016 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 161 MET Chi-restraints excluded: chain A residue 296 LEU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 466 THR Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 748 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 927 ILE Chi-restraints excluded: chain A residue 950 ILE Chi-restraints excluded: chain A residue 969 ASP Chi-restraints excluded: chain A residue 1263 LYS Chi-restraints excluded: chain A residue 1273 ILE Chi-restraints excluded: chain A residue 1352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 54 optimal weight: 30.0000 chunk 35 optimal weight: 6.9990 chunk 52 optimal weight: 40.0000 chunk 39 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 79 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 20.0000 chunk 84 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 overall best weight: 4.1388 ------------------------------------------------------------------------------- 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 = 0.4247 r_free = 0.4247 target = 0.163325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.115949 restraints weight = 19497.504| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 3.41 r_work: 0.3226 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 12571 Z= 0.237 Angle : 0.623 13.537 17550 Z= 0.332 Chirality : 0.042 0.196 2019 Planarity : 0.004 0.052 1757 Dihedral : 19.499 149.108 3066 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.89 % Favored : 96.02 % Rotamer: Outliers : 1.67 % Allowed : 8.76 % Favored : 89.57 % 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: 0.35 (0.24), residues: 1130 helix: 1.25 (0.22), residues: 588 sheet: -0.92 (0.50), residues: 100 loop : -0.82 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 494 TYR 0.021 0.002 TYR A 136 PHE 0.019 0.002 PHE A1327 TRP 0.014 0.002 TRP A1074 HIS 0.011 0.001 HIS A 982 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 (12571) covalent geometry : angle 0.62325 / 0.33 (17550) hydrogen bonds : bond 0.05246 / 3.65 ( 579) hydrogen bonds : angle 4.37717 / 3.14 ( 1603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2744.84 seconds wall clock time: 47 minutes 45.79 seconds (2865.79 seconds total)