Starting phenix.real_space_refine on Wed Aug 5 21:50:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lkj_63180/08_2026/9lkj_63180.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lkj_63180/08_2026/9lkj_63180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lkj_63180/08_2026/9lkj_63180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lkj_63180/08_2026/9lkj_63180.map" model { file = "/net/cci-nas-00/data/ceres_data/9lkj_63180/08_2026/9lkj_63180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lkj_63180/08_2026/9lkj_63180.cif" } resolution = 2.68 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= -0.001 sd= 0.047 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 92 5.49 5 S 20 5.16 5 C 7008 2.51 5 N 2034 2.21 5 O 2491 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 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: 11645 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 653 Classifications: {'peptide': 77} Link IDs: {'TRANS': 76} Chain: "C" Number of atoms: 9019 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1211, 9019 Classifications: {'peptide': 1211} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PTRANS': 32, 'TRANS': 1178} Chain breaks: 1 Unresolved non-hydrogen bonds: 898 Unresolved non-hydrogen angles: 1048 Unresolved non-hydrogen dihedrals: 804 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLU:plan': 31, 'ASP:plan': 11, 'ASN:plan1': 7, 'PHE:plan': 15, 'TYR:plan': 8, 'ARG:plan': 19, 'GLN:plan1': 8} Unresolved non-hydrogen planarities: 452 Chain: "D" Number of atoms: 1973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1973 Classifications: {'RNA': 92} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 46, 'rna3p_pyr': 32} Link IDs: {'rna2p': 14, 'rna3p': 77} Time building chain proxies: 2.12, per 1000 atoms: 0.18 Number of scatterers: 11645 At special positions: 0 Unit cell: (88.3386, 120.658, 122.812, 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 20 16.00 P 92 15.00 O 2491 8.00 N 2034 7.00 C 7008 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 549.9 milliseconds 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2456 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 6 sheets defined 49.0% alpha, 8.0% beta 18 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 33 through 43 Processing helix chain 'A' and resid 67 through 71 Processing helix chain 'C' and resid 59 through 94 removed outlier: 5.169A pdb=" N ASN C 88 " --> pdb=" O GLU C 84 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N GLU C 89 " --> pdb=" O ILE C 85 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS C 92 " --> pdb=" O ASN C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 103 Processing helix chain 'C' and resid 121 through 132 Processing helix chain 'C' and resid 134 through 145 removed outlier: 3.632A pdb=" N LEU C 138 " --> pdb=" O THR C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 164 Processing helix chain 'C' and resid 180 through 195 Processing helix chain 'C' and resid 208 through 213 removed outlier: 3.514A pdb=" N SER C 213 " --> pdb=" O LYS C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 229 removed outlier: 3.695A pdb=" N ARG C 221 " --> pdb=" O SER C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 237 through 247 Processing helix chain 'C' and resid 270 through 282 removed outlier: 4.364A pdb=" N ASP C 274 " --> pdb=" O THR C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 283 through 286 Processing helix chain 'C' and resid 287 through 302 removed outlier: 3.585A pdb=" N LEU C 302 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 315 through 343 Processing helix chain 'C' and resid 346 through 352 Processing helix chain 'C' and resid 358 through 364 Processing helix chain 'C' and resid 368 through 382 Proline residue: C 378 - end of helix Processing helix chain 'C' and resid 388 through 395 Processing helix chain 'C' and resid 404 through 410 removed outlier: 3.857A pdb=" N GLY C 408 " --> pdb=" O PHE C 405 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER C 409 " --> pdb=" O ASP C 406 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 427 removed outlier: 3.954A pdb=" N HIS C 415 " --> pdb=" O PRO C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 431 through 436 removed outlier: 3.527A pdb=" N ASP C 435 " --> pdb=" O PRO C 431 " (cutoff:3.500A) Processing helix chain 'C' and resid 436 through 446 Processing helix chain 'C' and resid 477 through 482 Processing helix chain 'C' and resid 483 through 496 removed outlier: 3.622A pdb=" N THR C 496 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing helix chain 'C' and resid 512 through 525 Processing helix chain 'C' and resid 541 through 551 removed outlier: 3.791A pdb=" N LYS C 545 " --> pdb=" O SER C 541 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS C 546 " --> pdb=" O GLY C 542 " (cutoff:3.500A) removed outlier: 5.540A pdb=" N ALA C 547 " --> pdb=" O GLU C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 569 Processing helix chain 'C' and resid 591 through 602 Processing helix chain 'C' and resid 612 through 626 Processing helix chain 'C' and resid 628 through 637 Processing helix chain 'C' and resid 638 through 640 No H-bonds generated for 'chain 'C' and resid 638 through 640' Processing helix chain 'C' and resid 644 through 652 Processing helix chain 'C' and resid 663 through 669 Processing helix chain 'C' and resid 678 through 685 Processing helix chain 'C' and resid 692 through 698 Processing helix chain 'C' and resid 703 through 710 Processing helix chain 'C' and resid 730 through 751 removed outlier: 3.590A pdb=" N GLY C 736 " --> pdb=" O ALA C 732 " (cutoff:3.500A) Processing helix chain 'C' and resid 920 through 924 removed outlier: 3.892A pdb=" N GLU C 923 " --> pdb=" O GLN C 920 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N THR C 924 " --> pdb=" O LEU C 921 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 920 through 924' Processing helix chain 'C' and resid 927 through 940 Processing helix chain 'C' and resid 962 through 970 Processing helix chain 'C' and resid 980 through 1001 removed outlier: 4.465A pdb=" N ALA C 984 " --> pdb=" O ASN C 980 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYS C 999 " --> pdb=" O THR C 995 " (cutoff:3.500A) Processing helix chain 'C' and resid 1004 through 1009 removed outlier: 4.493A pdb=" N PHE C1008 " --> pdb=" O LEU C1004 " (cutoff:3.500A) Processing helix chain 'C' and resid 1032 through 1044 removed outlier: 4.243A pdb=" N TYR C1039 " --> pdb=" O LYS C1035 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N SER C1040 " --> pdb=" O TYR C1036 " (cutoff:3.500A) Processing helix chain 'C' and resid 1045 through 1047 No H-bonds generated for 'chain 'C' and resid 1045 through 1047' Processing helix chain 'C' and resid 1078 through 1089 removed outlier: 3.564A pdb=" N THR C1082 " --> pdb=" O ARG C1078 " (cutoff:3.500A) Processing helix chain 'C' and resid 1127 through 1132 Processing helix chain 'C' and resid 1170 through 1177 removed outlier: 4.205A pdb=" N ASN C1177 " --> pdb=" O SER C1173 " (cutoff:3.500A) Processing helix chain 'C' and resid 1177 through 1185 removed outlier: 4.298A pdb=" N PHE C1181 " --> pdb=" O ASN C1177 " (cutoff:3.500A) Processing helix chain 'C' and resid 1191 through 1195 removed outlier: 3.976A pdb=" N ILE C1195 " --> pdb=" O LYS C1192 " (cutoff:3.500A) Processing helix chain 'C' and resid 1229 through 1241 Processing helix chain 'C' and resid 1248 through 1262 Processing helix chain 'C' and resid 1264 through 1280 removed outlier: 4.620A pdb=" N ILE C1270 " --> pdb=" O LEU C1266 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLU C1271 " --> pdb=" O ASP C1267 " (cutoff:3.500A) Processing helix chain 'C' and resid 1285 through 1296 Processing helix chain 'C' and resid 1301 through 1310 removed outlier: 3.894A pdb=" N GLU C1307 " --> pdb=" O ARG C1303 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE C1310 " --> pdb=" O ALA C1306 " (cutoff:3.500A) Processing helix chain 'C' and resid 1311 through 1316 Processing helix chain 'C' and resid 1339 through 1343 removed outlier: 3.666A pdb=" N LEU C1343 " --> pdb=" O LYS C1340 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 29 removed outlier: 7.031A pdb=" N ILE A 6 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LYS A 28 " --> pdb=" O PHE A 4 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N PHE A 4 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 954 through 957 removed outlier: 6.166A pdb=" N ILE C 759 " --> pdb=" O ILE C 956 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 46 removed outlier: 10.105A pdb=" N GLU C1357 " --> pdb=" O LYS C 31 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N LYS C 33 " --> pdb=" O GLU C1357 " (cutoff:3.500A) removed outlier: 7.695A pdb=" N ARG C1359 " --> pdb=" O LYS C 33 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N LEU C 35 " --> pdb=" O ARG C1359 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N ASP C1361 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU C1203 " --> pdb=" O ILE C1348 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER C1202 " --> pdb=" O LEU C1214 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU C1219 " --> pdb=" O ALA C1215 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 1120 through 1121 Processing sheet with id=AA5, first strand: chain 'C' and resid 1156 through 1167 removed outlier: 3.599A pdb=" N GLU C1162 " --> pdb=" O VAL C1145 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL C1145 " --> pdb=" O GLU C1162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 1324 through 1325 439 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 84 hydrogen bond angles 0 basepair planarities 18 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 1.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1783 1.31 - 1.43: 3684 1.43 - 1.56: 6365 1.56 - 1.69: 183 1.69 - 1.82: 38 Bond restraints: 12053 Sorted by residual: bond pdb=" C PRO C 176 " pdb=" O PRO C 176 " ideal model delta sigma weight residual 1.235 1.177 0.058 1.30e-02 5.92e+03 1.99e+01 bond pdb=" N LEU C 174 " pdb=" CA LEU C 174 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.25e-02 6.40e+03 6.83e+00 bond pdb=" N ASN C 175 " pdb=" CA ASN C 175 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.41e-02 5.03e+03 6.64e+00 bond pdb=" N ASP C 177 " pdb=" CA ASP C 177 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 6.11e+00 bond pdb=" C ASN C 175 " pdb=" O ASN C 175 " ideal model delta sigma weight residual 1.238 1.214 0.024 1.28e-02 6.10e+03 3.53e+00 ... (remaining 12048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 16682 2.73 - 5.47: 131 5.47 - 8.20: 12 8.20 - 10.94: 2 10.94 - 13.67: 2 Bond angle restraints: 16829 Sorted by residual: angle pdb=" C PRO C 176 " pdb=" CA PRO C 176 " pdb=" CB PRO C 176 " ideal model delta sigma weight residual 111.56 97.89 13.67 1.65e+00 3.67e-01 6.87e+01 angle pdb=" C1' U D 24 " pdb=" N1 U D 24 " pdb=" C2 U D 24 " ideal model delta sigma weight residual 117.70 124.56 -6.86 1.20e+00 6.94e-01 3.27e+01 angle pdb=" O5' A D 28 " pdb=" C5' A D 28 " pdb=" C4' A D 28 " ideal model delta sigma weight residual 109.40 112.87 -3.47 8.00e-01 1.56e+00 1.88e+01 angle pdb=" O2 U D 24 " pdb=" C2 U D 24 " pdb=" N3 U D 24 " ideal model delta sigma weight residual 122.20 119.26 2.94 7.00e-01 2.04e+00 1.77e+01 angle pdb=" O4' U D 24 " pdb=" C1' U D 24 " pdb=" N1 U D 24 " ideal model delta sigma weight residual 108.50 111.32 -2.82 7.00e-01 2.04e+00 1.63e+01 ... (remaining 16824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.39: 6914 35.39 - 70.78: 349 70.78 - 106.18: 24 106.18 - 141.57: 4 141.57 - 176.96: 1 Dihedral angle restraints: 7292 sinusoidal: 3507 harmonic: 3785 Sorted by residual: dihedral pdb=" O4' U D 24 " pdb=" C1' U D 24 " pdb=" N1 U D 24 " pdb=" C2 U D 24 " ideal model delta sinusoidal sigma weight residual 200.00 23.04 176.96 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" C PRO C 176 " pdb=" N PRO C 176 " pdb=" CA PRO C 176 " pdb=" CB PRO C 176 " ideal model delta harmonic sigma weight residual -120.70 -105.43 -15.27 0 2.50e+00 1.60e-01 3.73e+01 dihedral pdb=" CA ILE C 305 " pdb=" C ILE C 305 " pdb=" N LEU C 306 " pdb=" CA LEU C 306 " ideal model delta harmonic sigma weight residual 180.00 153.69 26.31 0 5.00e+00 4.00e-02 2.77e+01 ... (remaining 7289 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1375 0.039 - 0.078: 430 0.078 - 0.117: 125 0.117 - 0.156: 87 0.156 - 0.195: 9 Chirality restraints: 2026 Sorted by residual: chirality pdb=" C3' A D 42 " pdb=" C4' A D 42 " pdb=" O3' A D 42 " pdb=" C2' A D 42 " both_signs ideal model delta sigma weight residual False -2.48 -2.28 -0.19 2.00e-01 2.50e+01 9.49e-01 chirality pdb=" CA TYR C 450 " pdb=" N TYR C 450 " pdb=" C TYR C 450 " pdb=" CB TYR C 450 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.89e-01 chirality pdb=" CA ASN C 175 " pdb=" N ASN C 175 " pdb=" C ASN C 175 " pdb=" CB ASN C 175 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.41e-01 ... (remaining 2023 not shown) Planarity restraints: 1838 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 249 " 0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO C 250 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO C 250 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 250 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 502 " 0.032 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO C 503 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO C 503 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 503 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A D 12 " 0.027 2.00e-02 2.50e+03 1.17e-02 3.76e+00 pdb=" N9 A D 12 " -0.026 2.00e-02 2.50e+03 pdb=" C8 A D 12 " -0.005 2.00e-02 2.50e+03 pdb=" N7 A D 12 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A D 12 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A D 12 " 0.002 2.00e-02 2.50e+03 pdb=" N6 A D 12 " 0.008 2.00e-02 2.50e+03 pdb=" N1 A D 12 " 0.001 2.00e-02 2.50e+03 pdb=" C2 A D 12 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A D 12 " -0.004 2.00e-02 2.50e+03 pdb=" C4 A D 12 " -0.003 2.00e-02 2.50e+03 ... (remaining 1835 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2070 2.77 - 3.30: 10742 3.30 - 3.83: 20374 3.83 - 4.37: 23685 4.37 - 4.90: 38017 Nonbonded interactions: 94888 Sorted by model distance: nonbonded pdb=" OD1 ASP C 936 " pdb=" ND2 ASN C 940 " model vdw 2.235 3.120 nonbonded pdb=" CD2 HIS C 412 " pdb=" CE1 HIS C 412 " model vdw 2.242 2.784 nonbonded pdb=" O ARG C 307 " pdb=" OG1 THR C 310 " model vdw 2.248 3.040 nonbonded pdb=" O ALA C 149 " pdb=" OH TYR C 430 " model vdw 2.264 3.040 nonbonded pdb=" ND2 ASN C 556 " pdb=" OE1 GLN C 563 " model vdw 2.265 3.120 ... (remaining 94883 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: 1.420 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: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.580 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:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 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 0.058 12053 Z= 0.197 Angle : 0.721 13.673 16829 Z= 0.485 Chirality : 0.048 0.195 2026 Planarity : 0.004 0.052 1838 Dihedral : 18.656 176.960 4836 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.39 % Allowed : 5.30 % Favored : 94.31 % Rotamer: Outliers : 2.43 % Allowed : 20.49 % Favored : 77.09 % Cbeta Deviations : 0.08 % 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: -0.61 (0.24), residues: 1282 helix: 0.63 (0.23), residues: 543 sheet: 0.33 (0.51), residues: 118 loop : -1.53 (0.24), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 75 TYR 0.024 0.002 TYR C 450 PHE 0.014 0.001 PHE C1235 TRP 0.012 0.002 TRP A 51 HIS 0.008 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.20 (12053) covalent geometry : angle 0.72077 / 0.49 (16829) hydrogen bonds : bond 0.16170 / 10.74 ( 483) hydrogen bonds : angle 6.31841 / 4.31 ( 1347) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 121 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 201 ILE cc_start: -0.0913 (OUTLIER) cc_final: -0.1605 (pt) outliers start: 23 outliers final: 7 residues processed: 143 average time/residue: 0.5242 time to fit residues: 81.0230 Evaluate side-chains 88 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 735 LYS Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 998 ILE Chi-restraints excluded: chain C residue 1358 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 ASN C 758 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.082708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.056120 restraints weight = 39911.024| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 4.27 r_work: 0.2814 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 12053 Z= 0.246 Angle : 0.682 8.767 16829 Z= 0.360 Chirality : 0.043 0.272 2026 Planarity : 0.005 0.054 1838 Dihedral : 17.905 176.320 2787 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.77 % Favored : 94.07 % Rotamer: Outliers : 3.38 % Allowed : 21.12 % Favored : 75.50 % 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 (0.23), residues: 1282 helix: 0.63 (0.23), residues: 558 sheet: 0.13 (0.49), residues: 120 loop : -1.57 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 35 TYR 0.029 0.002 TYR C 450 PHE 0.018 0.002 PHE A 47 TRP 0.012 0.002 TRP A 51 HIS 0.006 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.25 (12053) covalent geometry : angle 0.68236 / 0.36 (16829) hydrogen bonds : bond 0.04824 / 3.17 ( 483) hydrogen bonds : angle 5.31384 / 3.58 ( 1347) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9187 (mp0) cc_final: 0.8867 (mp0) REVERT: A 35 ARG cc_start: 0.8981 (ttm110) cc_final: 0.8688 (tpp80) REVERT: A 36 GLU cc_start: 0.9311 (tt0) cc_final: 0.8796 (pt0) REVERT: A 39 LYS cc_start: 0.9410 (mttp) cc_final: 0.9113 (mttp) REVERT: C 169 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9353 (pp) REVERT: C 201 ILE cc_start: -0.0849 (OUTLIER) cc_final: -0.1151 (pt) REVERT: C 349 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8697 (tp30) REVERT: C 455 LEU cc_start: 0.9562 (OUTLIER) cc_final: 0.9337 (mt) REVERT: C 569 PHE cc_start: 0.9452 (m-80) cc_final: 0.9110 (m-80) REVERT: C 751 MET cc_start: 0.9341 (mmm) cc_final: 0.8965 (mtm) REVERT: C 986 ASP cc_start: 0.9191 (m-30) cc_final: 0.8813 (m-30) outliers start: 32 outliers final: 5 residues processed: 106 average time/residue: 0.4500 time to fit residues: 52.0052 Evaluate side-chains 83 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 455 LEU Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 662 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 54 optimal weight: 4.9990 chunk 79 optimal weight: 0.0670 chunk 1 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 96 optimal weight: 20.0000 chunk 43 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 135 optimal weight: 30.0000 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 497 ASN C1305 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.083026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.056445 restraints weight = 39894.409| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 4.37 r_work: 0.2828 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 12053 Z= 0.160 Angle : 0.624 12.121 16829 Z= 0.330 Chirality : 0.041 0.259 2026 Planarity : 0.004 0.051 1838 Dihedral : 17.850 176.460 2776 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.30 % Favored : 94.54 % Rotamer: Outliers : 3.17 % Allowed : 21.96 % Favored : 74.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.24), residues: 1282 helix: 0.74 (0.23), residues: 559 sheet: 0.19 (0.48), residues: 120 loop : -1.39 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 664 TYR 0.024 0.001 TYR C 450 PHE 0.012 0.001 PHE A 47 TRP 0.010 0.001 TRP A 51 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 (12053) covalent geometry : angle 0.62419 / 0.33 (16829) hydrogen bonds : bond 0.04347 / 2.85 ( 483) hydrogen bonds : angle 5.05116 / 3.39 ( 1347) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 81 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9177 (mp0) cc_final: 0.8798 (mp0) REVERT: A 35 ARG cc_start: 0.8713 (ttm110) cc_final: 0.8376 (tpp80) REVERT: A 52 LYS cc_start: 0.9139 (mmmt) cc_final: 0.8894 (mmpt) REVERT: C 169 LEU cc_start: 0.9637 (OUTLIER) cc_final: 0.9368 (pp) REVERT: C 184 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9090 (mm) REVERT: C 201 ILE cc_start: -0.0765 (OUTLIER) cc_final: -0.1096 (pt) REVERT: C 349 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8696 (tp30) REVERT: C 569 PHE cc_start: 0.9368 (m-80) cc_final: 0.9070 (m-80) REVERT: C 751 MET cc_start: 0.9324 (mmm) cc_final: 0.8831 (mtm) REVERT: C 986 ASP cc_start: 0.9162 (m-30) cc_final: 0.8783 (m-30) REVERT: C 1135 ASP cc_start: 0.8894 (t0) cc_final: 0.8580 (p0) outliers start: 30 outliers final: 7 residues processed: 103 average time/residue: 0.4810 time to fit residues: 54.1889 Evaluate side-chains 88 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 1342 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 57 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 86 optimal weight: 0.4980 chunk 118 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 107 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 27 optimal weight: 0.7980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1066 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.083185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.056834 restraints weight = 39999.565| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 4.29 r_work: 0.2841 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12053 Z= 0.128 Angle : 0.590 11.772 16829 Z= 0.310 Chirality : 0.039 0.254 2026 Planarity : 0.003 0.048 1838 Dihedral : 17.815 176.454 2776 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 3.06 % Allowed : 21.54 % Favored : 75.40 % 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: -0.33 (0.24), residues: 1282 helix: 0.78 (0.23), residues: 558 sheet: 0.27 (0.48), residues: 120 loop : -1.28 (0.25), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 664 TYR 0.020 0.001 TYR C 450 PHE 0.012 0.001 PHE C 966 TRP 0.009 0.001 TRP A 51 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 (12053) covalent geometry : angle 0.59048 / 0.31 (16829) hydrogen bonds : bond 0.03961 / 2.61 ( 483) hydrogen bonds : angle 4.90688 / 3.29 ( 1347) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 85 time to evaluate : 0.417 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9189 (mp0) cc_final: 0.8783 (mp0) REVERT: A 52 LYS cc_start: 0.9212 (mmmt) cc_final: 0.8973 (mmpt) REVERT: C 184 LEU cc_start: 0.9301 (OUTLIER) cc_final: 0.8969 (mm) REVERT: C 201 ILE cc_start: -0.0411 (OUTLIER) cc_final: -0.0747 (pt) REVERT: C 327 GLU cc_start: 0.8832 (OUTLIER) cc_final: 0.8205 (pp20) REVERT: C 349 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8692 (tp30) REVERT: C 371 GLU cc_start: 0.8954 (mt-10) cc_final: 0.8680 (mt-10) REVERT: C 568 TYR cc_start: 0.7894 (t80) cc_final: 0.7691 (t80) REVERT: C 569 PHE cc_start: 0.9372 (m-80) cc_final: 0.9046 (m-80) REVERT: C 927 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9117 (tp) REVERT: C 986 ASP cc_start: 0.9165 (m-30) cc_final: 0.8783 (m-30) REVERT: C 1135 ASP cc_start: 0.8881 (t0) cc_final: 0.8584 (p0) outliers start: 29 outliers final: 10 residues processed: 108 average time/residue: 0.5383 time to fit residues: 63.3346 Evaluate side-chains 89 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 356 LYS Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 935 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 121 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 32 optimal weight: 0.4980 chunk 49 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 29 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 ASN C 167 HIS C1241 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.083669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.057395 restraints weight = 40067.699| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 4.32 r_work: 0.2856 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 12053 Z= 0.115 Angle : 0.588 12.346 16829 Z= 0.305 Chirality : 0.039 0.248 2026 Planarity : 0.003 0.047 1838 Dihedral : 17.777 176.685 2776 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 3.59 % Allowed : 21.44 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.26 (0.24), residues: 1282 helix: 0.80 (0.23), residues: 560 sheet: 0.38 (0.48), residues: 120 loop : -1.23 (0.25), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 35 TYR 0.015 0.001 TYR C 450 PHE 0.010 0.001 PHE C 966 TRP 0.009 0.001 TRP A 51 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.11 (12053) covalent geometry : angle 0.58821 / 0.31 (16829) hydrogen bonds : bond 0.03633 / 2.40 ( 483) hydrogen bonds : angle 4.76367 / 3.20 ( 1347) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 83 time to evaluate : 0.379 Fit side-chains REVERT: A 16 GLU cc_start: 0.9195 (mp0) cc_final: 0.8775 (mp0) REVERT: A 35 ARG cc_start: 0.8640 (mtp-110) cc_final: 0.8421 (ttm110) REVERT: A 39 LYS cc_start: 0.9343 (mmmm) cc_final: 0.9024 (mtmm) REVERT: A 40 LYS cc_start: 0.9494 (tptp) cc_final: 0.9157 (tptp) REVERT: A 52 LYS cc_start: 0.9208 (mmmt) cc_final: 0.8928 (mmmt) REVERT: A 56 ARG cc_start: 0.9261 (pmm-80) cc_final: 0.9057 (pmm-80) REVERT: C 184 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.8939 (mm) REVERT: C 201 ILE cc_start: -0.0407 (OUTLIER) cc_final: -0.0704 (pt) REVERT: C 224 ASN cc_start: 0.8932 (t0) cc_final: 0.8293 (m110) REVERT: C 327 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8231 (pp20) REVERT: C 349 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8564 (tp30) REVERT: C 371 GLU cc_start: 0.8956 (mt-10) cc_final: 0.8712 (mt-10) REVERT: C 568 TYR cc_start: 0.7816 (t80) cc_final: 0.7575 (t80) REVERT: C 569 PHE cc_start: 0.9376 (m-80) cc_final: 0.9028 (m-80) REVERT: C 751 MET cc_start: 0.9236 (mmm) cc_final: 0.8990 (mtp) REVERT: C 986 ASP cc_start: 0.9142 (m-30) cc_final: 0.8721 (m-30) REVERT: C 1043 MET cc_start: 0.6355 (tpt) cc_final: 0.6042 (tpt) REVERT: C 1135 ASP cc_start: 0.8876 (t0) cc_final: 0.8573 (p0) outliers start: 34 outliers final: 9 residues processed: 111 average time/residue: 0.4220 time to fit residues: 51.6972 Evaluate side-chains 92 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 1228 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 33 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 132 optimal weight: 10.0000 chunk 74 optimal weight: 9.9990 chunk 136 optimal weight: 20.0000 chunk 107 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 ASN C 497 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.079034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.052585 restraints weight = 41084.154| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 4.29 r_work: 0.2735 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 12053 Z= 0.342 Angle : 0.744 12.458 16829 Z= 0.385 Chirality : 0.046 0.292 2026 Planarity : 0.005 0.044 1838 Dihedral : 17.741 176.270 2776 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.93 % Favored : 93.99 % Rotamer: Outliers : 3.17 % Allowed : 22.07 % Favored : 74.76 % 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: -0.40 (0.24), residues: 1282 helix: 0.78 (0.23), residues: 554 sheet: -0.10 (0.44), residues: 138 loop : -1.32 (0.26), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 35 TYR 0.036 0.002 TYR C 450 PHE 0.027 0.002 PHE A 38 TRP 0.012 0.002 TRP A 69 HIS 0.008 0.002 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00720 / 0.34 (12053) covalent geometry : angle 0.74384 / 0.38 (16829) hydrogen bonds : bond 0.04974 / 3.35 ( 483) hydrogen bonds : angle 5.05500 / 3.40 ( 1347) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.395 Fit side-chains REVERT: A 16 GLU cc_start: 0.9186 (mp0) cc_final: 0.8847 (mp0) REVERT: A 35 ARG cc_start: 0.8850 (mtp-110) cc_final: 0.8612 (ttm110) REVERT: A 39 LYS cc_start: 0.9508 (mmmm) cc_final: 0.9270 (mmmm) REVERT: A 40 LYS cc_start: 0.9528 (tptp) cc_final: 0.9209 (tptp) REVERT: C 201 ILE cc_start: 0.0629 (OUTLIER) cc_final: 0.0358 (pt) REVERT: C 327 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8304 (pp20) REVERT: C 349 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8620 (tp30) REVERT: C 569 PHE cc_start: 0.9530 (m-80) cc_final: 0.9051 (m-80) REVERT: C 751 MET cc_start: 0.9317 (mmm) cc_final: 0.8961 (mtm) REVERT: C 763 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7585 (mmm) REVERT: C 961 LYS cc_start: 0.8675 (tppt) cc_final: 0.8319 (pmtt) REVERT: C 986 ASP cc_start: 0.9311 (m-30) cc_final: 0.8872 (m-30) REVERT: C 1043 MET cc_start: 0.6517 (tpt) cc_final: 0.6266 (mmm) REVERT: C 1135 ASP cc_start: 0.8929 (t0) cc_final: 0.8609 (p0) REVERT: C 1170 GLU cc_start: 0.9290 (OUTLIER) cc_final: 0.9033 (pt0) outliers start: 30 outliers final: 10 residues processed: 98 average time/residue: 0.5091 time to fit residues: 54.4224 Evaluate side-chains 86 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 GLU Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 763 MET Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 1170 GLU Chi-restraints excluded: chain C residue 1228 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 64 optimal weight: 6.9990 chunk 21 optimal weight: 0.4980 chunk 89 optimal weight: 0.0980 chunk 73 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 32 optimal weight: 0.1980 chunk 18 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 497 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.081907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.055582 restraints weight = 40095.553| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 4.30 r_work: 0.2826 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12053 Z= 0.123 Angle : 0.632 14.001 16829 Z= 0.325 Chirality : 0.041 0.260 2026 Planarity : 0.003 0.045 1838 Dihedral : 17.787 176.171 2776 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.99 % Favored : 94.93 % Rotamer: Outliers : 2.53 % Allowed : 22.81 % Favored : 74.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.24), residues: 1282 helix: 0.97 (0.23), residues: 554 sheet: -0.00 (0.45), residues: 134 loop : -1.16 (0.25), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 35 TYR 0.021 0.001 TYR A 27 PHE 0.010 0.001 PHE A 47 TRP 0.010 0.001 TRP A 51 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (12053) covalent geometry : angle 0.63198 / 0.33 (16829) hydrogen bonds : bond 0.03807 / 2.48 ( 483) hydrogen bonds : angle 4.78503 / 3.19 ( 1347) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9247 (mp0) cc_final: 0.8775 (mp0) REVERT: A 27 TYR cc_start: 0.8893 (t80) cc_final: 0.8542 (t80) REVERT: A 40 LYS cc_start: 0.9474 (tptp) cc_final: 0.9072 (tptp) REVERT: C 184 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9023 (mm) REVERT: C 201 ILE cc_start: 0.0534 (OUTLIER) cc_final: 0.0243 (pt) REVERT: C 327 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8257 (pp20) REVERT: C 349 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8705 (tp30) REVERT: C 404 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8859 (p) REVERT: C 569 PHE cc_start: 0.9457 (m-80) cc_final: 0.8989 (m-80) REVERT: C 751 MET cc_start: 0.9285 (mmm) cc_final: 0.9017 (mtm) REVERT: C 927 ILE cc_start: 0.9331 (OUTLIER) cc_final: 0.9128 (tp) REVERT: C 986 ASP cc_start: 0.9179 (m-30) cc_final: 0.8709 (m-30) REVERT: C 1135 ASP cc_start: 0.8866 (t0) cc_final: 0.8593 (p0) REVERT: C 1170 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.9078 (pt0) outliers start: 24 outliers final: 7 residues processed: 95 average time/residue: 0.5597 time to fit residues: 57.8507 Evaluate side-chains 87 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 1170 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 36 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 31 optimal weight: 0.0970 chunk 91 optimal weight: 0.0980 chunk 0 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 136 optimal weight: 20.0000 chunk 32 optimal weight: 0.0470 chunk 73 optimal weight: 7.9990 chunk 45 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 overall best weight: 1.0480 ------------------------------------------------------------------------------- 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 = 0.3696 r_free = 0.3696 target = 0.081625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.055254 restraints weight = 40479.690| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 4.30 r_work: 0.2828 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12053 Z= 0.133 Angle : 0.622 14.829 16829 Z= 0.319 Chirality : 0.040 0.282 2026 Planarity : 0.003 0.057 1838 Dihedral : 17.712 176.407 2776 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.70 % Rotamer: Outliers : 2.85 % Allowed : 22.39 % Favored : 74.76 % 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: -0.11 (0.24), residues: 1282 helix: 1.06 (0.23), residues: 549 sheet: 0.09 (0.45), residues: 130 loop : -1.19 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 35 TYR 0.021 0.001 TYR A 27 PHE 0.012 0.001 PHE A 47 TRP 0.014 0.001 TRP A 51 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 (12053) covalent geometry : angle 0.62171 / 0.32 (16829) hydrogen bonds : bond 0.03716 / 2.42 ( 483) hydrogen bonds : angle 4.69942 / 3.14 ( 1347) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 79 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9266 (mp0) cc_final: 0.8770 (mp0) REVERT: A 28 LYS cc_start: 0.9356 (mmmm) cc_final: 0.9141 (mmmt) REVERT: A 36 GLU cc_start: 0.9002 (OUTLIER) cc_final: 0.8651 (pm20) REVERT: A 39 LYS cc_start: 0.9406 (mmtt) cc_final: 0.9042 (mttp) REVERT: C 184 LEU cc_start: 0.9258 (OUTLIER) cc_final: 0.9015 (mm) REVERT: C 201 ILE cc_start: 0.0576 (OUTLIER) cc_final: 0.0308 (pt) REVERT: C 327 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8306 (pp20) REVERT: C 349 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8652 (tp30) REVERT: C 404 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8815 (p) REVERT: C 495 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8158 (tpp) REVERT: C 694 MET cc_start: 0.9017 (pmm) cc_final: 0.8679 (tmt) REVERT: C 751 MET cc_start: 0.9267 (mmm) cc_final: 0.8991 (mtm) REVERT: C 927 ILE cc_start: 0.9382 (OUTLIER) cc_final: 0.9129 (tp) REVERT: C 986 ASP cc_start: 0.9184 (m-30) cc_final: 0.8699 (m-30) REVERT: C 1135 ASP cc_start: 0.8861 (t0) cc_final: 0.8529 (p0) outliers start: 27 outliers final: 8 residues processed: 101 average time/residue: 0.5385 time to fit residues: 59.5711 Evaluate side-chains 90 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 GLU Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 928 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 2 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 83 optimal weight: 0.0970 chunk 104 optimal weight: 1.9990 chunk 107 optimal weight: 10.0000 chunk 133 optimal weight: 10.0000 chunk 123 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 31 optimal weight: 0.0170 chunk 50 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 overall best weight: 0.8220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.082125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.055945 restraints weight = 40090.035| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 4.35 r_work: 0.2846 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12053 Z= 0.124 Angle : 0.635 13.934 16829 Z= 0.325 Chirality : 0.040 0.326 2026 Planarity : 0.003 0.040 1838 Dihedral : 17.685 176.839 2776 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 2.01 % Allowed : 23.97 % Favored : 74.02 % 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: -0.12 (0.24), residues: 1282 helix: 0.95 (0.23), residues: 561 sheet: 0.20 (0.45), residues: 130 loop : -1.15 (0.26), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 56 TYR 0.015 0.001 TYR C 450 PHE 0.024 0.001 PHE C 569 TRP 0.012 0.001 TRP A 51 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (12053) covalent geometry : angle 0.63484 / 0.33 (16829) hydrogen bonds : bond 0.03589 / 2.32 ( 483) hydrogen bonds : angle 4.66008 / 3.11 ( 1347) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9306 (mp0) cc_final: 0.8824 (mp0) REVERT: A 39 LYS cc_start: 0.9407 (mmtt) cc_final: 0.9128 (mptp) REVERT: C 184 LEU cc_start: 0.9256 (OUTLIER) cc_final: 0.9012 (mm) REVERT: C 201 ILE cc_start: 0.0643 (OUTLIER) cc_final: 0.0393 (pt) REVERT: C 327 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8302 (pp20) REVERT: C 349 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8631 (tp30) REVERT: C 404 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8782 (p) REVERT: C 495 MET cc_start: 0.8456 (OUTLIER) cc_final: 0.8146 (tpp) REVERT: C 569 PHE cc_start: 0.9215 (m-80) cc_final: 0.8959 (m-80) REVERT: C 694 MET cc_start: 0.9027 (pmm) cc_final: 0.8678 (tmt) REVERT: C 751 MET cc_start: 0.9243 (mmm) cc_final: 0.8962 (mtm) REVERT: C 927 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9085 (tp) REVERT: C 986 ASP cc_start: 0.9153 (m-30) cc_final: 0.8717 (m-30) REVERT: C 1135 ASP cc_start: 0.8857 (t0) cc_final: 0.8570 (p0) outliers start: 19 outliers final: 8 residues processed: 95 average time/residue: 0.5728 time to fit residues: 59.3561 Evaluate side-chains 90 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 928 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 58 optimal weight: 0.7980 chunk 104 optimal weight: 0.0070 chunk 9 optimal weight: 10.0000 chunk 86 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 89 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.082681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.056539 restraints weight = 40431.304| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 4.36 r_work: 0.2870 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12053 Z= 0.117 Angle : 0.640 13.247 16829 Z= 0.326 Chirality : 0.039 0.251 2026 Planarity : 0.003 0.037 1838 Dihedral : 17.639 177.142 2776 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.84 % Favored : 95.09 % Rotamer: Outliers : 1.80 % Allowed : 23.65 % Favored : 74.55 % 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: -0.03 (0.24), residues: 1282 helix: 1.05 (0.23), residues: 556 sheet: 0.44 (0.47), residues: 120 loop : -1.14 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 35 TYR 0.016 0.001 TYR C 568 PHE 0.008 0.001 PHE C 966 TRP 0.010 0.001 TRP A 51 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 (12053) covalent geometry : angle 0.64006 / 0.33 (16829) hydrogen bonds : bond 0.03468 / 2.22 ( 483) hydrogen bonds : angle 4.60186 / 3.08 ( 1347) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2564 Ramachandran restraints generated. 1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9248 (mp0) cc_final: 0.8756 (mp0) REVERT: A 35 ARG cc_start: 0.8705 (ttm110) cc_final: 0.8486 (tpp80) REVERT: A 39 LYS cc_start: 0.9424 (mmtt) cc_final: 0.9157 (mttp) REVERT: C 184 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8996 (mm) REVERT: C 201 ILE cc_start: 0.0446 (OUTLIER) cc_final: 0.0210 (pt) REVERT: C 327 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8306 (pp20) REVERT: C 349 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8623 (tp30) REVERT: C 404 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8760 (p) REVERT: C 495 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8091 (tpp) REVERT: C 569 PHE cc_start: 0.9116 (m-80) cc_final: 0.8875 (m-80) REVERT: C 694 MET cc_start: 0.9086 (pmm) cc_final: 0.8680 (tmt) REVERT: C 751 MET cc_start: 0.9226 (mmm) cc_final: 0.8939 (mtm) REVERT: C 763 MET cc_start: 0.7980 (mmm) cc_final: 0.7331 (mtt) REVERT: C 927 ILE cc_start: 0.9381 (OUTLIER) cc_final: 0.9040 (tp) REVERT: C 986 ASP cc_start: 0.9094 (m-30) cc_final: 0.8668 (m-30) REVERT: C 1135 ASP cc_start: 0.8857 (t0) cc_final: 0.8588 (p0) outliers start: 17 outliers final: 9 residues processed: 91 average time/residue: 0.4725 time to fit residues: 47.0905 Evaluate side-chains 89 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 184 LEU Chi-restraints excluded: chain C residue 201 ILE Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 258 LEU Chi-restraints excluded: chain C residue 312 ILE Chi-restraints excluded: chain C residue 327 GLU Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 404 THR Chi-restraints excluded: chain C residue 419 LEU Chi-restraints excluded: chain C residue 450 TYR Chi-restraints excluded: chain C residue 495 MET Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 928 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 15 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 129 optimal weight: 10.0000 chunk 94 optimal weight: 30.0000 chunk 22 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 130 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 ASN ** C 497 ASN ** 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 = 0.3665 r_free = 0.3665 target = 0.079733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.053545 restraints weight = 40714.642| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 4.28 r_work: 0.2789 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.3320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12053 Z= 0.245 Angle : 0.683 11.858 16829 Z= 0.352 Chirality : 0.042 0.271 2026 Planarity : 0.004 0.040 1838 Dihedral : 17.545 176.379 2776 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 2.11 % Allowed : 23.86 % Favored : 74.02 % 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: 1282 helix: 1.11 (0.23), residues: 558 sheet: 0.44 (0.46), residues: 126 loop : -1.12 (0.25), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 35 TYR 0.025 0.002 TYR C 450 PHE 0.016 0.001 PHE A 47 TRP 0.010 0.002 TRP A 51 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.24 (12053) covalent geometry : angle 0.68289 / 0.35 (16829) hydrogen bonds : bond 0.04081 / 2.67 ( 483) hydrogen bonds : angle 4.70718 / 3.15 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3641.24 seconds wall clock time: 62 minutes 34.94 seconds (3754.94 seconds total)