Starting phenix.real_space_refine on Wed Feb 4 16:48:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lkj_63180/02_2026/9lkj_63180.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lkj_63180/02_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_63180/02_2026/9lkj_63180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lkj_63180/02_2026/9lkj_63180.map" model { file = "/net/cci-nas-00/data/ceres_data/9lkj_63180/02_2026/9lkj_63180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lkj_63180/02_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-2.0-5952/lib/python3.9/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: 2.13, 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: 0.91 Conformation dependent library (CDL) restraints added in 525.8 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: 1.22 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: 2.16 Time building geometry restraints manager: 1.26 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: 16693 2.73 - 5.47: 120 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=" CA TYR C 450 " pdb=" CB TYR C 450 " pdb=" CG TYR C 450 " ideal model delta sigma weight residual 113.90 120.86 -6.96 1.80e+00 3.09e-01 1.50e+01 angle pdb=" C GLY C 385 " pdb=" N THR C 386 " pdb=" CA THR C 386 " ideal model delta sigma weight residual 121.54 128.82 -7.28 1.91e+00 2.74e-01 1.45e+01 angle pdb=" CA GLN C 933 " pdb=" CB GLN C 933 " pdb=" CG GLN C 933 " ideal model delta sigma weight residual 114.10 121.68 -7.58 2.00e+00 2.50e-01 1.44e+01 angle pdb=" CA LEU C 174 " pdb=" C LEU C 174 " pdb=" O LEU C 174 " ideal model delta sigma weight residual 121.45 117.56 3.89 1.07e+00 8.73e-01 1.32e+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: 1474 0.039 - 0.078: 422 0.078 - 0.117: 108 0.117 - 0.156: 15 0.156 - 0.195: 7 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: 1.090 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.540 Find NCS groups from input model: 0.030 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:6.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 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= 0.160 Angle : 0.660 13.673 16829 Z= 0.385 Chirality : 0.040 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 covalent geometry : bond 0.00307 (12053) covalent geometry : angle 0.66002 (16829) hydrogen bonds : bond 0.16170 ( 483) hydrogen bonds : angle 6.31841 ( 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 : 0.393 Fit side-chains 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: 0.5405 time to fit residues: 83.4383 Evaluate side-chains 87 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3656 r_free = 0.3656 target = 0.080227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.053859 restraints weight = 40251.149| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 4.32 r_work: 0.2773 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 12053 Z= 0.261 Angle : 0.670 8.651 16829 Z= 0.351 Chirality : 0.042 0.250 2026 Planarity : 0.004 0.055 1838 Dihedral : 17.858 178.372 2787 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.01 % Favored : 93.84 % Rotamer: Outliers : 4.33 % Allowed : 19.43 % Favored : 76.24 % 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: -0.59 (0.23), residues: 1282 helix: 0.62 (0.23), residues: 570 sheet: 0.79 (0.55), residues: 95 loop : -1.60 (0.23), residues: 617 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 35 TYR 0.030 0.002 TYR C 450 PHE 0.013 0.002 PHE A 38 TRP 0.009 0.002 TRP A 69 HIS 0.007 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00559 (12053) covalent geometry : angle 0.66989 (16829) hydrogen bonds : bond 0.04437 ( 483) hydrogen bonds : angle 5.10105 ( 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 123 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 82 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9218 (mp0) cc_final: 0.8837 (mp0) REVERT: A 27 TYR cc_start: 0.9057 (t80) cc_final: 0.8829 (t80) REVERT: A 39 LYS cc_start: 0.9419 (mttp) cc_final: 0.9195 (mtmp) REVERT: A 52 LYS cc_start: 0.9319 (mmmt) cc_final: 0.8984 (mmmm) REVERT: C 169 LEU cc_start: 0.9649 (OUTLIER) cc_final: 0.9343 (pp) REVERT: C 201 ILE cc_start: 0.0478 (OUTLIER) cc_final: 0.0211 (pt) REVERT: C 327 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8279 (pp20) REVERT: C 349 GLU cc_start: 0.9047 (OUTLIER) cc_final: 0.8441 (tp30) REVERT: C 356 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8655 (mtpm) REVERT: C 569 PHE cc_start: 0.9425 (m-80) cc_final: 0.9100 (m-80) REVERT: C 751 MET cc_start: 0.9309 (mmm) cc_final: 0.9046 (mtm) REVERT: C 986 ASP cc_start: 0.9209 (m-30) cc_final: 0.8836 (m-30) REVERT: C 1170 GLU cc_start: 0.9337 (OUTLIER) cc_final: 0.9111 (pt0) outliers start: 41 outliers final: 5 residues processed: 116 average time/residue: 0.5186 time to fit residues: 65.3756 Evaluate side-chains 85 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain C residue 201 ILE 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 450 TYR Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 662 LEU Chi-restraints excluded: chain C residue 1170 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 54 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 33 optimal weight: 8.9990 chunk 46 optimal weight: 4.9990 chunk 96 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.080357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.054086 restraints weight = 40350.162| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 4.27 r_work: 0.2786 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12053 Z= 0.182 Angle : 0.605 12.640 16829 Z= 0.314 Chirality : 0.040 0.238 2026 Planarity : 0.004 0.042 1838 Dihedral : 17.794 178.231 2776 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.23 % Favored : 94.62 % Rotamer: Outliers : 3.38 % Allowed : 21.01 % Favored : 75.61 % 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: -0.38 (0.24), residues: 1282 helix: 0.86 (0.23), residues: 555 sheet: 0.10 (0.46), residues: 130 loop : -1.42 (0.25), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 35 TYR 0.022 0.001 TYR C 450 PHE 0.009 0.001 PHE C 966 TRP 0.008 0.001 TRP A 69 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00390 (12053) covalent geometry : angle 0.60528 (16829) hydrogen bonds : bond 0.03936 ( 483) hydrogen bonds : angle 4.79410 ( 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 116 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 84 time to evaluate : 0.426 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9627 (mmmm) cc_final: 0.9312 (mppt) REVERT: A 16 GLU cc_start: 0.9212 (mp0) cc_final: 0.8799 (mp0) REVERT: A 27 TYR cc_start: 0.9186 (t80) cc_final: 0.8942 (t80) REVERT: A 39 LYS cc_start: 0.9429 (mttp) cc_final: 0.8882 (mttp) REVERT: A 52 LYS cc_start: 0.9350 (mmmt) cc_final: 0.9139 (mmmt) REVERT: A 56 ARG cc_start: 0.9186 (ptp-110) cc_final: 0.8935 (ptp90) REVERT: C 169 LEU cc_start: 0.9623 (OUTLIER) cc_final: 0.9352 (pp) REVERT: C 184 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9074 (mm) REVERT: C 201 ILE cc_start: 0.0617 (OUTLIER) cc_final: 0.0324 (pt) REVERT: C 288 ASP cc_start: 0.8834 (m-30) cc_final: 0.8282 (OUTLIER) REVERT: C 327 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8317 (pp20) REVERT: C 349 GLU cc_start: 0.9021 (OUTLIER) cc_final: 0.8411 (tp30) REVERT: C 356 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8258 (tppp) REVERT: C 569 PHE cc_start: 0.9491 (m-80) cc_final: 0.9024 (m-80) REVERT: C 751 MET cc_start: 0.9272 (mmm) cc_final: 0.8811 (mtm) REVERT: C 986 ASP cc_start: 0.9231 (m-30) cc_final: 0.8756 (m-30) REVERT: C 1170 GLU cc_start: 0.9331 (OUTLIER) cc_final: 0.9118 (pt0) outliers start: 32 outliers final: 8 residues processed: 110 average time/residue: 0.5663 time to fit residues: 67.8956 Evaluate side-chains 89 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU 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 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 450 TYR Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 1170 GLU Chi-restraints excluded: chain C residue 1228 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 57 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 9.9990 chunk 86 optimal weight: 0.9980 chunk 118 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 107 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 0.0070 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 674 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.080698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.054221 restraints weight = 40655.088| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 4.32 r_work: 0.2809 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12053 Z= 0.151 Angle : 0.575 12.627 16829 Z= 0.299 Chirality : 0.039 0.236 2026 Planarity : 0.003 0.041 1838 Dihedral : 17.711 178.800 2776 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.68 % Favored : 95.24 % Rotamer: Outliers : 4.12 % Allowed : 19.75 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.24), residues: 1282 helix: 1.08 (0.23), residues: 548 sheet: 0.42 (0.47), residues: 123 loop : -1.35 (0.24), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 35 TYR 0.018 0.001 TYR C 450 PHE 0.008 0.001 PHE C 290 TRP 0.008 0.001 TRP A 69 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00324 (12053) covalent geometry : angle 0.57459 (16829) hydrogen bonds : bond 0.03542 ( 483) hydrogen bonds : angle 4.55557 ( 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 121 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 82 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9641 (mmmm) cc_final: 0.9299 (mppt) REVERT: A 16 GLU cc_start: 0.9278 (mp0) cc_final: 0.8795 (mp0) REVERT: A 39 LYS cc_start: 0.9263 (mttp) cc_final: 0.8959 (mtmp) REVERT: A 52 LYS cc_start: 0.9397 (mmmt) cc_final: 0.9171 (mmmt) REVERT: C 184 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.9027 (mm) REVERT: C 201 ILE cc_start: 0.0815 (OUTLIER) cc_final: 0.0567 (pt) REVERT: C 225 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7765 (pp) REVERT: C 266 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.7926 (mt) REVERT: C 288 ASP cc_start: 0.8890 (m-30) cc_final: 0.8353 (OUTLIER) REVERT: C 349 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8358 (tp30) REVERT: C 356 LYS cc_start: 0.8887 (OUTLIER) cc_final: 0.8568 (mtpm) REVERT: C 569 PHE cc_start: 0.9526 (m-80) cc_final: 0.9013 (m-80) REVERT: C 694 MET cc_start: 0.9023 (pmm) cc_final: 0.8691 (pmm) REVERT: C 986 ASP cc_start: 0.9174 (m-30) cc_final: 0.8740 (m-30) REVERT: C 1170 GLU cc_start: 0.9344 (OUTLIER) cc_final: 0.9122 (pt0) outliers start: 39 outliers final: 8 residues processed: 114 average time/residue: 0.5306 time to fit residues: 66.1186 Evaluate side-chains 92 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 225 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 266 LEU 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 927 ILE Chi-restraints excluded: chain C residue 1170 GLU Chi-restraints excluded: chain C residue 1228 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 121 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 109 optimal weight: 4.9990 chunk 75 optimal weight: 6.9990 chunk 126 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 49 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN C1066 ASN C1286 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.076597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.050340 restraints weight = 40552.829| |-----------------------------------------------------------------------------| r_work (start): 0.2877 rms_B_bonded: 4.21 r_work: 0.2716 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 12053 Z= 0.314 Angle : 0.695 12.966 16829 Z= 0.363 Chirality : 0.043 0.255 2026 Planarity : 0.004 0.043 1838 Dihedral : 17.827 177.526 2776 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.08 % Favored : 93.76 % Rotamer: Outliers : 3.80 % Allowed : 21.33 % 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: -0.42 (0.23), residues: 1282 helix: 0.77 (0.23), residues: 566 sheet: 0.14 (0.45), residues: 128 loop : -1.43 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 35 TYR 0.034 0.002 TYR C 450 PHE 0.016 0.001 PHE C 970 TRP 0.010 0.002 TRP C 476 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00668 (12053) covalent geometry : angle 0.69485 (16829) hydrogen bonds : bond 0.04649 ( 483) hydrogen bonds : angle 4.93693 ( 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 109 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 73 time to evaluate : 0.447 Fit side-chains REVERT: A 15 LYS cc_start: 0.9652 (mmmm) cc_final: 0.9292 (mppt) REVERT: A 16 GLU cc_start: 0.9312 (mp0) cc_final: 0.8806 (mp0) REVERT: A 39 LYS cc_start: 0.9263 (mtmp) cc_final: 0.8929 (mtmp) REVERT: C 169 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9396 (pp) REVERT: C 225 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7835 (pp) REVERT: C 327 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8419 (pp20) REVERT: C 349 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8469 (tp30) REVERT: C 569 PHE cc_start: 0.9569 (m-80) cc_final: 0.9066 (m-80) REVERT: C 587 PHE cc_start: 0.8366 (OUTLIER) cc_final: 0.8105 (m-10) REVERT: C 751 MET cc_start: 0.9275 (mmm) cc_final: 0.9048 (mtp) REVERT: C 961 LYS cc_start: 0.8611 (tppt) cc_final: 0.8353 (pmtt) REVERT: C 986 ASP cc_start: 0.9269 (m-30) cc_final: 0.8797 (m-30) REVERT: C 1170 GLU cc_start: 0.9342 (OUTLIER) cc_final: 0.9100 (pt0) outliers start: 36 outliers final: 8 residues processed: 104 average time/residue: 0.5363 time to fit residues: 60.6680 Evaluate side-chains 86 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ASN Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 169 LEU Chi-restraints excluded: chain C residue 225 LEU 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 450 TYR Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 1170 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 33 optimal weight: 6.9990 chunk 128 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 0.0980 chunk 132 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 93 optimal weight: 0.0870 overall best weight: 1.2160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN C 167 HIS C1308 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.078965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.052986 restraints weight = 40454.492| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 4.21 r_work: 0.2790 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12053 Z= 0.144 Angle : 0.610 13.745 16829 Z= 0.314 Chirality : 0.040 0.258 2026 Planarity : 0.003 0.059 1838 Dihedral : 17.682 179.004 2774 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 2.22 % Allowed : 23.97 % Favored : 73.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.18 (0.24), residues: 1282 helix: 1.00 (0.23), residues: 561 sheet: 0.47 (0.47), residues: 117 loop : -1.34 (0.24), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 35 TYR 0.018 0.001 TYR C 450 PHE 0.007 0.001 PHE A 47 TRP 0.008 0.001 TRP A 69 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00311 (12053) covalent geometry : angle 0.61011 (16829) hydrogen bonds : bond 0.03498 ( 483) hydrogen bonds : angle 4.57792 ( 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 104 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.379 Fit side-chains REVERT: A 15 LYS cc_start: 0.9632 (mmmm) cc_final: 0.9274 (mppt) REVERT: A 16 GLU cc_start: 0.9327 (mp0) cc_final: 0.8741 (mp0) REVERT: A 33 ASN cc_start: 0.9227 (p0) cc_final: 0.8265 (p0) REVERT: A 39 LYS cc_start: 0.9232 (mtmp) cc_final: 0.8730 (mtmp) REVERT: C 225 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7819 (pp) REVERT: C 327 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8384 (pp20) REVERT: C 349 GLU cc_start: 0.9090 (OUTLIER) cc_final: 0.8867 (tp30) REVERT: C 569 PHE cc_start: 0.9509 (m-80) cc_final: 0.8964 (m-80) REVERT: C 751 MET cc_start: 0.9237 (mmm) cc_final: 0.8978 (mtp) REVERT: C 763 MET cc_start: 0.8190 (mmm) cc_final: 0.7517 (mtt) REVERT: C 961 LYS cc_start: 0.8554 (tppt) cc_final: 0.8333 (pmtt) REVERT: C 986 ASP cc_start: 0.9152 (m-30) cc_final: 0.8738 (m-30) outliers start: 21 outliers final: 9 residues processed: 100 average time/residue: 0.5874 time to fit residues: 63.8811 Evaluate side-chains 90 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 241 LEU Chi-restraints excluded: chain C residue 288 ASP 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 927 ILE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 935 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 64 optimal weight: 20.0000 chunk 21 optimal weight: 6.9990 chunk 89 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 chunk 32 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 90 optimal weight: 0.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.076818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.050765 restraints weight = 40788.075| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 4.16 r_work: 0.2733 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.4079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 12053 Z= 0.244 Angle : 0.663 14.027 16829 Z= 0.342 Chirality : 0.042 0.275 2026 Planarity : 0.004 0.058 1838 Dihedral : 17.625 178.050 2772 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 3.59 % Allowed : 22.91 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.28 (0.24), residues: 1282 helix: 0.89 (0.23), residues: 565 sheet: 0.18 (0.45), residues: 132 loop : -1.37 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 56 TYR 0.028 0.002 TYR C 450 PHE 0.013 0.001 PHE A 47 TRP 0.009 0.001 TRP A 69 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00526 (12053) covalent geometry : angle 0.66334 (16829) hydrogen bonds : bond 0.04067 ( 483) hydrogen bonds : angle 4.75210 ( 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 112 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 78 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9638 (mmmm) cc_final: 0.9263 (mppt) REVERT: A 16 GLU cc_start: 0.9370 (mp0) cc_final: 0.8840 (mp0) REVERT: A 39 LYS cc_start: 0.9149 (mtmp) cc_final: 0.8693 (mppt) REVERT: C 225 LEU cc_start: 0.8159 (OUTLIER) cc_final: 0.7927 (pp) REVERT: C 288 ASP cc_start: 0.8994 (p0) cc_final: 0.8789 (p0) REVERT: C 327 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8446 (pp20) REVERT: C 349 GLU cc_start: 0.9100 (OUTLIER) cc_final: 0.8882 (tp30) REVERT: C 569 PHE cc_start: 0.9511 (m-80) cc_final: 0.8987 (m-80) REVERT: C 763 MET cc_start: 0.8251 (mmm) cc_final: 0.7456 (mtt) REVERT: C 961 LYS cc_start: 0.8681 (tppt) cc_final: 0.8454 (pmtt) REVERT: C 986 ASP cc_start: 0.9223 (m-30) cc_final: 0.8802 (m-30) REVERT: C 1170 GLU cc_start: 0.9341 (OUTLIER) cc_final: 0.9131 (pt0) outliers start: 34 outliers final: 9 residues processed: 107 average time/residue: 0.5217 time to fit residues: 61.1206 Evaluate side-chains 88 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 75 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 225 LEU Chi-restraints excluded: chain C residue 237 LEU Chi-restraints excluded: chain C residue 241 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 450 TYR Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 935 LEU 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: 2.9990 chunk 120 optimal weight: 3.9990 chunk 31 optimal weight: 0.1980 chunk 91 optimal weight: 0.1980 chunk 0 optimal weight: 7.9990 chunk 108 optimal weight: 0.7980 chunk 136 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.077595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.051698 restraints weight = 40670.954| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 4.14 r_work: 0.2774 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12053 Z= 0.163 Angle : 0.640 14.343 16829 Z= 0.327 Chirality : 0.040 0.258 2026 Planarity : 0.004 0.054 1838 Dihedral : 17.607 178.748 2772 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.38 % Favored : 94.54 % Rotamer: Outliers : 2.96 % Allowed : 23.97 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.99 (0.23), residues: 562 sheet: 0.38 (0.47), residues: 117 loop : -1.26 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 35 TYR 0.021 0.001 TYR C 450 PHE 0.013 0.001 PHE A 47 TRP 0.009 0.001 TRP A 51 HIS 0.004 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00355 (12053) covalent geometry : angle 0.63962 (16829) hydrogen bonds : bond 0.03593 ( 483) hydrogen bonds : angle 4.60695 ( 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 104 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9633 (mmmm) cc_final: 0.9246 (mppt) REVERT: A 16 GLU cc_start: 0.9346 (mp0) cc_final: 0.8757 (mp0) REVERT: A 40 LYS cc_start: 0.9441 (tptp) cc_final: 0.8992 (tptp) REVERT: C 184 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9115 (mm) REVERT: C 288 ASP cc_start: 0.8981 (p0) cc_final: 0.8732 (p0) REVERT: C 327 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8394 (pp20) REVERT: C 349 GLU cc_start: 0.9138 (OUTLIER) cc_final: 0.8883 (tp30) REVERT: C 569 PHE cc_start: 0.9457 (m-80) cc_final: 0.8877 (m-80) REVERT: C 634 GLU cc_start: 0.9427 (tp30) cc_final: 0.9207 (tm-30) REVERT: C 763 MET cc_start: 0.8342 (mmm) cc_final: 0.7700 (mtt) REVERT: C 961 LYS cc_start: 0.8703 (tppt) cc_final: 0.8477 (pmtt) REVERT: C 986 ASP cc_start: 0.9169 (m-30) cc_final: 0.8742 (m-30) REVERT: C 1170 GLU cc_start: 0.9349 (OUTLIER) cc_final: 0.9132 (pt0) outliers start: 28 outliers final: 10 residues processed: 96 average time/residue: 0.5700 time to fit residues: 59.4244 Evaluate side-chains 90 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 0.338 ------------------------------------------------------------------------------- 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 237 LEU Chi-restraints excluded: chain C residue 241 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 450 TYR Chi-restraints excluded: chain C residue 927 ILE Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 1170 GLU Chi-restraints excluded: chain C residue 1265 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 2 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 104 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 133 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 94 optimal weight: 20.0000 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.075398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.049464 restraints weight = 40913.831| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 4.11 r_work: 0.2708 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12053 Z= 0.277 Angle : 0.709 11.121 16829 Z= 0.366 Chirality : 0.043 0.268 2026 Planarity : 0.004 0.055 1838 Dihedral : 17.684 177.981 2772 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.40 % Favored : 93.53 % Rotamer: Outliers : 2.43 % Allowed : 24.50 % Favored : 73.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1282 helix: 0.73 (0.22), residues: 569 sheet: 0.16 (0.45), residues: 128 loop : -1.28 (0.25), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 35 TYR 0.031 0.002 TYR C 450 PHE 0.010 0.001 PHE C 970 TRP 0.011 0.002 TRP A 51 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00593 (12053) covalent geometry : angle 0.70917 (16829) hydrogen bonds : bond 0.04306 ( 483) hydrogen bonds : angle 4.86406 ( 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 99 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 76 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9639 (mmmm) cc_final: 0.9249 (mppt) REVERT: A 16 GLU cc_start: 0.9374 (mp0) cc_final: 0.8855 (mp0) REVERT: A 28 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8737 (mmmt) REVERT: C 288 ASP cc_start: 0.9081 (p0) cc_final: 0.8768 (p0) REVERT: C 327 GLU cc_start: 0.8980 (OUTLIER) cc_final: 0.8447 (pp20) REVERT: C 349 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8794 (tp30) REVERT: C 569 PHE cc_start: 0.9470 (m-80) cc_final: 0.8966 (m-80) REVERT: C 634 GLU cc_start: 0.9432 (tp30) cc_final: 0.9206 (tm-30) REVERT: C 763 MET cc_start: 0.8350 (mmm) cc_final: 0.7959 (mpp) REVERT: C 986 ASP cc_start: 0.9234 (m-30) cc_final: 0.8818 (m-30) REVERT: C 1170 GLU cc_start: 0.9359 (OUTLIER) cc_final: 0.9131 (pt0) outliers start: 23 outliers final: 12 residues processed: 96 average time/residue: 0.6348 time to fit residues: 66.1032 Evaluate side-chains 91 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 13 THR 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 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 450 TYR Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 1170 GLU Chi-restraints excluded: chain C residue 1265 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 86 optimal weight: 10.0000 chunk 46 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 89 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 77 ASN C 723 HIS C1256 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.078029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.052518 restraints weight = 40686.279| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 4.11 r_work: 0.2797 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.4627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12053 Z= 0.133 Angle : 0.659 11.137 16829 Z= 0.337 Chirality : 0.040 0.249 2026 Planarity : 0.004 0.079 1838 Dihedral : 17.613 179.537 2772 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 1.80 % Allowed : 25.03 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.24), residues: 1282 helix: 0.94 (0.23), residues: 569 sheet: 0.32 (0.47), residues: 117 loop : -1.07 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 35 TYR 0.021 0.001 TYR A 45 PHE 0.010 0.001 PHE A 47 TRP 0.009 0.001 TRP A 51 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd covalent geometry : bond 0.00298 (12053) covalent geometry : angle 0.65916 (16829) hydrogen bonds : bond 0.03415 ( 483) hydrogen bonds : angle 4.58524 ( 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 98 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9627 (mmmm) cc_final: 0.9230 (mppt) REVERT: A 16 GLU cc_start: 0.9350 (mp0) cc_final: 0.8733 (mp0) REVERT: C 288 ASP cc_start: 0.9035 (p0) cc_final: 0.8813 (p0) REVERT: C 327 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8391 (pp20) REVERT: C 349 GLU cc_start: 0.9068 (OUTLIER) cc_final: 0.8587 (tp30) REVERT: C 569 PHE cc_start: 0.9314 (m-80) cc_final: 0.8832 (m-80) REVERT: C 634 GLU cc_start: 0.9379 (tp30) cc_final: 0.9177 (tm-30) REVERT: C 746 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8745 (tp30) REVERT: C 763 MET cc_start: 0.8392 (mmm) cc_final: 0.7890 (mtt) REVERT: C 986 ASP cc_start: 0.9123 (m-30) cc_final: 0.8690 (m-30) outliers start: 17 outliers final: 6 residues processed: 94 average time/residue: 0.6168 time to fit residues: 62.9381 Evaluate side-chains 82 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 58 THR 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 746 GLU Chi-restraints excluded: chain C residue 928 THR Chi-restraints excluded: chain C residue 935 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 15 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 94 optimal weight: 40.0000 chunk 22 optimal weight: 0.5980 chunk 87 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 130 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1256 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.076186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.050483 restraints weight = 41133.182| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 4.09 r_work: 0.2744 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.4700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12053 Z= 0.210 Angle : 0.691 11.458 16829 Z= 0.351 Chirality : 0.041 0.263 2026 Planarity : 0.004 0.065 1838 Dihedral : 17.569 178.755 2772 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.30 % Favored : 94.62 % Rotamer: Outliers : 1.69 % Allowed : 25.45 % Favored : 72.86 % 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: -0.07 (0.24), residues: 1282 helix: 0.97 (0.23), residues: 569 sheet: 0.30 (0.47), residues: 117 loop : -1.12 (0.25), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 35 TYR 0.025 0.001 TYR A 45 PHE 0.013 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 covalent geometry : bond 0.00459 (12053) covalent geometry : angle 0.69076 (16829) hydrogen bonds : bond 0.03769 ( 483) hydrogen bonds : angle 4.67299 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4091.33 seconds wall clock time: 70 minutes 19.72 seconds (4219.72 seconds total)