Starting phenix.real_space_refine on Fri Jul 3 03:49:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lkj_63180/07_2026/9lkj_63180.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lkj_63180/07_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_63180/07_2026/9lkj_63180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lkj_63180/07_2026/9lkj_63180.map" model { file = "/net/cci-nas-00/data/ceres_data/9lkj_63180/07_2026/9lkj_63180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lkj_63180/07_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-dev-6108/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: 2.32, per 1000 atoms: 0.20 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: 0.92 Conformation dependent library (CDL) restraints added in 460.6 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: 1.16 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: 1.94 Time building geometry restraints manager: 1.25 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=" 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=" 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=" 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=" C1' U D 24 " pdb=" N1 U D 24 " pdb=" C6 U D 24 " ideal model delta sigma weight residual 121.20 115.79 5.41 1.40e+00 5.10e-01 1.49e+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: 0.970 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: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.050 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:5.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.090 ------------------------------------------------------------------------------- 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= 0.188 Angle : 0.660 13.673 16829 Z= 0.428 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/Z covalent geometry : bond 0.00307 / 0.19 (12053) covalent geometry : angle 0.66005 / 0.43 (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 : 0.379 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: 0.4936 time to fit residues: 76.4629 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 : 0.285 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.082998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.056629 restraints weight = 39919.022| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 4.20 r_work: 0.2816 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12053 Z= 0.249 Angle : 0.662 8.548 16829 Z= 0.356 Chirality : 0.043 0.241 2026 Planarity : 0.005 0.053 1838 Dihedral : 17.917 176.293 2787 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.46 % Favored : 94.38 % 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: -0.57 (0.24), residues: 1282 helix: 0.70 (0.23), residues: 552 sheet: 0.20 (0.49), residues: 120 loop : -1.54 (0.24), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG A 35 TYR 0.027 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 0.00526 / 0.25 (12053) covalent geometry : angle 0.66194 / 0.36 (16829) hydrogen bonds : bond 0.04931 / 3.25 ( 483) hydrogen bonds : angle 5.32138 / 3.59 ( 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 : 0.258 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9129 (mp0) cc_final: 0.8818 (mp0) REVERT: A 35 ARG cc_start: 0.9029 (ttm110) cc_final: 0.8797 (tpp80) REVERT: A 36 GLU cc_start: 0.9300 (tt0) cc_final: 0.8725 (pt0) REVERT: A 52 LYS cc_start: 0.9257 (mmmt) cc_final: 0.8927 (mmmm) REVERT: A 61 ILE cc_start: 0.8989 (mm) cc_final: 0.8659 (mp) REVERT: C 169 LEU cc_start: 0.9664 (OUTLIER) cc_final: 0.9346 (pp) REVERT: C 201 ILE cc_start: -0.0925 (OUTLIER) cc_final: -0.1240 (pt) REVERT: C 349 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8549 (tp30) REVERT: C 455 LEU cc_start: 0.9548 (OUTLIER) cc_final: 0.9316 (mt) REVERT: C 569 PHE cc_start: 0.9434 (m-80) cc_final: 0.9084 (m-80) REVERT: C 751 MET cc_start: 0.9322 (mmm) cc_final: 0.8933 (mtm) REVERT: C 986 ASP cc_start: 0.9186 (m-30) cc_final: 0.8805 (m-30) outliers start: 32 outliers final: 4 residues processed: 106 average time/residue: 0.5044 time to fit residues: 58.2845 Evaluate side-chains 82 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.323 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 79 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 96 optimal weight: 20.0000 chunk 43 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 135 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 C1305 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.083161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.056768 restraints weight = 40036.585| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 4.23 r_work: 0.2832 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12053 Z= 0.157 Angle : 0.614 12.139 16829 Z= 0.327 Chirality : 0.041 0.237 2026 Planarity : 0.004 0.050 1838 Dihedral : 17.873 176.616 2776 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.30 % Favored : 94.54 % Rotamer: Outliers : 2.96 % Allowed : 21.65 % 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: -0.45 (0.24), residues: 1282 helix: 0.72 (0.23), residues: 559 sheet: 0.20 (0.48), residues: 120 loop : -1.40 (0.25), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 56 TYR 0.023 0.001 TYR C 450 PHE 0.012 0.001 PHE C 966 TRP 0.011 0.001 TRP A 51 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 (12053) covalent geometry : angle 0.61350 / 0.33 (16829) hydrogen bonds : bond 0.04264 / 2.80 ( 483) hydrogen bonds : angle 5.03565 / 3.38 ( 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 110 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9161 (mp0) cc_final: 0.8774 (mp0) REVERT: A 35 ARG cc_start: 0.8695 (ttm110) cc_final: 0.8439 (tpp80) REVERT: A 36 GLU cc_start: 0.9294 (tt0) cc_final: 0.9064 (pp20) REVERT: A 39 LYS cc_start: 0.9440 (mttp) cc_final: 0.9001 (mtmp) REVERT: A 40 LYS cc_start: 0.9095 (mttt) cc_final: 0.8884 (mppt) REVERT: A 52 LYS cc_start: 0.9311 (mmmt) cc_final: 0.9046 (mmmm) REVERT: C 169 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9343 (pp) REVERT: C 184 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9107 (mm) REVERT: C 201 ILE cc_start: -0.0798 (OUTLIER) cc_final: -0.1130 (pt) REVERT: C 349 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8617 (tp30) REVERT: C 569 PHE cc_start: 0.9390 (m-80) cc_final: 0.9074 (m-80) REVERT: C 751 MET cc_start: 0.9302 (mmm) cc_final: 0.8808 (mtm) REVERT: C 986 ASP cc_start: 0.9153 (m-30) cc_final: 0.8792 (m-30) REVERT: C 1135 ASP cc_start: 0.8880 (t0) cc_final: 0.8601 (p0) outliers start: 28 outliers final: 8 residues processed: 104 average time/residue: 0.4765 time to fit residues: 54.3804 Evaluate side-chains 89 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR 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 419 LEU 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: 0.7980 chunk 74 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 118 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 107 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C1066 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.081476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.055043 restraints weight = 40318.790| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 4.37 r_work: 0.2794 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 12053 Z= 0.203 Angle : 0.604 11.042 16829 Z= 0.323 Chirality : 0.041 0.242 2026 Planarity : 0.004 0.048 1838 Dihedral : 17.821 176.915 2776 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.15 % Favored : 94.70 % Rotamer: Outliers : 3.38 % Allowed : 21.33 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.24), residues: 1282 helix: 0.80 (0.23), residues: 559 sheet: 0.18 (0.47), residues: 124 loop : -1.32 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.026 0.001 TYR C 450 PHE 0.013 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 0.00431 / 0.20 (12053) covalent geometry : angle 0.60418 / 0.32 (16829) hydrogen bonds : bond 0.04155 / 2.74 ( 483) hydrogen bonds : angle 4.89581 / 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 112 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 80 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 16 GLU cc_start: 0.9212 (mp0) cc_final: 0.8782 (mp0) REVERT: A 27 TYR cc_start: 0.9023 (t80) cc_final: 0.8684 (t80) REVERT: A 52 LYS cc_start: 0.9332 (mmmt) cc_final: 0.9026 (mmmm) REVERT: C 169 LEU cc_start: 0.9653 (OUTLIER) cc_final: 0.9321 (pp) REVERT: C 184 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9034 (mm) REVERT: C 201 ILE cc_start: 0.0003 (OUTLIER) cc_final: -0.0306 (pt) REVERT: C 327 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8269 (pp20) REVERT: C 349 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8597 (tp30) REVERT: C 751 MET cc_start: 0.9347 (mmm) cc_final: 0.9134 (mmm) REVERT: C 986 ASP cc_start: 0.9198 (m-30) cc_final: 0.8837 (m-30) REVERT: C 1135 ASP cc_start: 0.8903 (t0) cc_final: 0.8593 (p0) outliers start: 32 outliers final: 8 residues processed: 106 average time/residue: 0.4794 time to fit residues: 55.5273 Evaluate side-chains 87 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR 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 450 TYR Chi-restraints excluded: chain C residue 497 ASN Chi-restraints excluded: chain C residue 587 PHE Chi-restraints excluded: chain C residue 743 VAL Chi-restraints excluded: chain C residue 927 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 121 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 126 optimal weight: 5.9990 chunk 61 optimal weight: 7.9990 chunk 102 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 497 ASN C1241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.080613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.054309 restraints weight = 40510.339| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 4.27 r_work: 0.2780 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12053 Z= 0.227 Angle : 0.628 12.074 16829 Z= 0.334 Chirality : 0.041 0.244 2026 Planarity : 0.004 0.047 1838 Dihedral : 17.814 176.989 2776 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.38 % Favored : 94.54 % Rotamer: Outliers : 3.80 % Allowed : 20.80 % 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: -0.31 (0.24), residues: 1282 helix: 0.86 (0.23), residues: 559 sheet: 0.08 (0.45), residues: 134 loop : -1.32 (0.25), residues: 589 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 35 TYR 0.026 0.002 TYR C 450 PHE 0.013 0.001 PHE A 47 TRP 0.010 0.001 TRP A 51 HIS 0.005 0.001 HIS C1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.23 (12053) covalent geometry : angle 0.62770 / 0.33 (16829) hydrogen bonds : bond 0.04179 / 2.75 ( 483) hydrogen bonds : angle 4.88448 / 3.28 ( 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 111 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 75 time to evaluate : 0.246 Fit side-chains revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8677 (pp20) cc_final: 0.8455 (pp20) REVERT: A 15 LYS cc_start: 0.9589 (mmmm) cc_final: 0.9323 (mppt) REVERT: A 16 GLU cc_start: 0.9199 (mp0) cc_final: 0.8782 (mp0) REVERT: A 28 LYS cc_start: 0.9284 (mmmm) cc_final: 0.9074 (mmmm) REVERT: A 35 ARG cc_start: 0.8541 (ttm110) cc_final: 0.8307 (tpp80) REVERT: A 39 LYS cc_start: 0.9489 (mmtt) cc_final: 0.8904 (mtmp) REVERT: A 52 LYS cc_start: 0.9327 (mmmt) cc_final: 0.9057 (mmmm) REVERT: C 169 LEU cc_start: 0.9655 (OUTLIER) cc_final: 0.9354 (pp) REVERT: C 201 ILE cc_start: 0.0557 (OUTLIER) cc_final: 0.0271 (pt) REVERT: C 327 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8295 (pp20) REVERT: C 349 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8574 (tp30) REVERT: C 371 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8669 (mt-10) REVERT: C 495 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8361 (tpp) REVERT: C 986 ASP cc_start: 0.9171 (m-30) cc_final: 0.8805 (m-30) REVERT: C 1135 ASP cc_start: 0.8893 (t0) cc_final: 0.8616 (p0) REVERT: C 1170 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.9054 (pt0) outliers start: 36 outliers final: 12 residues processed: 103 average time/residue: 0.4570 time to fit residues: 51.3158 Evaluate side-chains 91 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.348 ------------------------------------------------------------------------------- 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 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 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 Chi-restraints excluded: chain C residue 1170 GLU 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: 8.9990 chunk 128 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 61 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 132 optimal weight: 8.9990 chunk 74 optimal weight: 8.9990 chunk 136 optimal weight: 20.0000 chunk 107 optimal weight: 7.9990 chunk 93 optimal weight: 0.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.079874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.053553 restraints weight = 40737.247| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 4.28 r_work: 0.2761 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.2833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 12053 Z= 0.227 Angle : 0.626 13.581 16829 Z= 0.331 Chirality : 0.042 0.244 2026 Planarity : 0.004 0.047 1838 Dihedral : 17.804 176.852 2776 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.38 % Rotamer: Outliers : 3.80 % Allowed : 22.07 % Favored : 74.13 % 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: -0.28 (0.24), residues: 1282 helix: 0.89 (0.23), residues: 561 sheet: -0.00 (0.45), residues: 134 loop : -1.29 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 35 TYR 0.026 0.002 TYR C 450 PHE 0.031 0.001 PHE C 569 TRP 0.009 0.001 TRP A 69 HIS 0.004 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.23 (12053) covalent geometry : angle 0.62555 / 0.33 (16829) hydrogen bonds : bond 0.04148 / 2.74 ( 483) hydrogen bonds : angle 4.78985 / 3.21 ( 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 114 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 78 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9597 (mmmm) cc_final: 0.9328 (mppt) REVERT: A 16 GLU cc_start: 0.9232 (mp0) cc_final: 0.8779 (mp0) REVERT: A 35 ARG cc_start: 0.8649 (ttm110) cc_final: 0.8266 (tpp80) REVERT: A 39 LYS cc_start: 0.9352 (mmtt) cc_final: 0.8985 (mtmm) REVERT: A 56 ARG cc_start: 0.9302 (pmm-80) cc_final: 0.9083 (pmm-80) REVERT: C 169 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9355 (pp) REVERT: C 184 LEU cc_start: 0.9339 (OUTLIER) cc_final: 0.9080 (mm) REVERT: C 201 ILE cc_start: 0.0562 (OUTLIER) cc_final: 0.0275 (pt) REVERT: C 266 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8090 (mt) REVERT: C 288 ASP cc_start: 0.8894 (m-30) cc_final: 0.8242 (OUTLIER) REVERT: C 327 GLU cc_start: 0.8981 (OUTLIER) cc_final: 0.8338 (pp20) REVERT: C 349 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8532 (tp30) REVERT: C 371 GLU cc_start: 0.8896 (mt-10) cc_final: 0.8571 (mt-10) REVERT: C 404 THR cc_start: 0.9226 (OUTLIER) cc_final: 0.8964 (p) REVERT: C 694 MET cc_start: 0.9034 (pmm) cc_final: 0.8749 (pmm) REVERT: C 927 ILE cc_start: 0.9339 (OUTLIER) cc_final: 0.9105 (tp) REVERT: C 986 ASP cc_start: 0.9254 (m-30) cc_final: 0.8827 (m-30) REVERT: C 1135 ASP cc_start: 0.8919 (t0) cc_final: 0.8664 (p0) REVERT: C 1170 GLU cc_start: 0.9300 (OUTLIER) cc_final: 0.9057 (pt0) outliers start: 36 outliers final: 13 residues processed: 107 average time/residue: 0.4730 time to fit residues: 55.5957 Evaluate side-chains 96 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR 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 266 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 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 Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 958 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: 5.9990 chunk 21 optimal weight: 0.6980 chunk 89 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 11 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 18 optimal weight: 5.9990 chunk 116 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 90 optimal weight: 1.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.078450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.052139 restraints weight = 40824.673| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 4.26 r_work: 0.2738 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 12053 Z= 0.290 Angle : 0.676 12.455 16829 Z= 0.357 Chirality : 0.043 0.252 2026 Planarity : 0.004 0.047 1838 Dihedral : 17.806 176.537 2776 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.23 % Favored : 94.62 % Rotamer: Outliers : 3.38 % Allowed : 22.91 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.24), residues: 1282 helix: 0.87 (0.23), residues: 558 sheet: -0.05 (0.45), residues: 134 loop : -1.30 (0.25), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.030 0.002 TYR C 450 PHE 0.012 0.001 PHE A 53 TRP 0.013 0.002 TRP A 51 HIS 0.005 0.001 HIS C 116 Details of bonding type rmsd/Z covalent geometry : bond 0.00618 / 0.29 (12053) covalent geometry : angle 0.67623 / 0.36 (16829) hydrogen bonds : bond 0.04426 / 2.93 ( 483) hydrogen bonds : angle 4.89269 / 3.29 ( 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 109 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 77 time to evaluate : 0.405 Fit side-chains revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9621 (mmmm) cc_final: 0.9330 (mppt) REVERT: A 16 GLU cc_start: 0.9268 (mp0) cc_final: 0.8827 (mp0) REVERT: A 35 ARG cc_start: 0.8682 (ttm110) cc_final: 0.8078 (tpp80) REVERT: A 39 LYS cc_start: 0.9350 (mmtt) cc_final: 0.8932 (mtmm) REVERT: A 52 LYS cc_start: 0.9152 (mmmt) cc_final: 0.8941 (mmpt) REVERT: A 56 ARG cc_start: 0.9328 (pmm-80) cc_final: 0.9112 (pmm-80) REVERT: C 169 LEU cc_start: 0.9661 (OUTLIER) cc_final: 0.9351 (pp) REVERT: C 184 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.9144 (mm) REVERT: C 201 ILE cc_start: 0.0620 (OUTLIER) cc_final: 0.0377 (pt) REVERT: C 266 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8528 (mt) REVERT: C 288 ASP cc_start: 0.8996 (m-30) cc_final: 0.8381 (OUTLIER) REVERT: C 327 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8359 (pp20) REVERT: C 349 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.8494 (tp30) REVERT: C 371 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8711 (mt-10) REVERT: C 404 THR cc_start: 0.9222 (OUTLIER) cc_final: 0.8966 (p) REVERT: C 569 PHE cc_start: 0.9234 (m-80) cc_final: 0.9019 (m-80) REVERT: C 694 MET cc_start: 0.9081 (pmm) cc_final: 0.8813 (pmm) REVERT: C 961 LYS cc_start: 0.8502 (tppt) cc_final: 0.8275 (pmtt) REVERT: C 986 ASP cc_start: 0.9281 (m-30) cc_final: 0.8849 (m-30) REVERT: C 1170 GLU cc_start: 0.9306 (OUTLIER) cc_final: 0.9076 (pt0) outliers start: 32 outliers final: 13 residues processed: 102 average time/residue: 0.4649 time to fit residues: 51.8902 Evaluate side-chains 94 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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 258 LEU Chi-restraints excluded: chain C residue 266 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 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 Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 958 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: 1.9990 chunk 120 optimal weight: 6.9990 chunk 31 optimal weight: 0.0970 chunk 91 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 32 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.079977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.053693 restraints weight = 40638.630| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.31 r_work: 0.2791 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12053 Z= 0.150 Angle : 0.630 14.220 16829 Z= 0.330 Chirality : 0.041 0.238 2026 Planarity : 0.003 0.044 1838 Dihedral : 17.817 176.791 2776 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.15 % Favored : 94.77 % Rotamer: Outliers : 2.85 % Allowed : 23.13 % Favored : 74.02 % 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: -0.22 (0.24), residues: 1282 helix: 0.93 (0.23), residues: 561 sheet: -0.02 (0.45), residues: 134 loop : -1.24 (0.25), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 42 TYR 0.023 0.001 TYR C 450 PHE 0.012 0.001 PHE C 966 TRP 0.011 0.001 TRP A 51 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (12053) covalent geometry : angle 0.63000 / 0.33 (16829) hydrogen bonds : bond 0.03904 / 2.56 ( 483) hydrogen bonds : angle 4.75429 / 3.20 ( 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 110 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 15 LYS cc_start: 0.9617 (mmmm) cc_final: 0.9290 (mppt) REVERT: A 16 GLU cc_start: 0.9272 (mp0) cc_final: 0.8733 (mp0) REVERT: A 35 ARG cc_start: 0.8638 (ttm110) cc_final: 0.8220 (tpp80) REVERT: A 39 LYS cc_start: 0.9339 (mmtt) cc_final: 0.9002 (mtmm) REVERT: A 40 LYS cc_start: 0.9568 (tptp) cc_final: 0.9104 (tptp) REVERT: A 52 LYS cc_start: 0.9167 (mmmt) cc_final: 0.8922 (mmpt) REVERT: A 56 ARG cc_start: 0.9329 (pmm-80) cc_final: 0.9127 (pmm-80) REVERT: C 184 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9082 (mm) REVERT: C 201 ILE cc_start: 0.0839 (OUTLIER) cc_final: 0.0600 (pt) REVERT: C 288 ASP cc_start: 0.8896 (m-30) cc_final: 0.8272 (OUTLIER) REVERT: C 327 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8314 (pp20) REVERT: C 349 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8502 (tp30) REVERT: C 404 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8819 (p) REVERT: C 694 MET cc_start: 0.9064 (pmm) cc_final: 0.8800 (pmm) REVERT: C 927 ILE cc_start: 0.9332 (OUTLIER) cc_final: 0.9102 (tp) REVERT: C 961 LYS cc_start: 0.8646 (tppt) cc_final: 0.8295 (pmtt) REVERT: C 986 ASP cc_start: 0.9188 (m-30) cc_final: 0.8727 (m-30) REVERT: C 1135 ASP cc_start: 0.8790 (t0) cc_final: 0.8517 (p0) REVERT: C 1170 GLU cc_start: 0.9353 (OUTLIER) cc_final: 0.9116 (pt0) outliers start: 27 outliers final: 10 residues processed: 104 average time/residue: 0.4654 time to fit residues: 52.9478 Evaluate side-chains 91 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 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 928 THR Chi-restraints excluded: chain C residue 935 LEU Chi-restraints excluded: chain C residue 1170 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 2 optimal weight: 6.9990 chunk 67 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 104 optimal weight: 0.9980 chunk 107 optimal weight: 7.9990 chunk 133 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 94 optimal weight: 40.0000 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.079249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.053034 restraints weight = 40400.505| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 4.26 r_work: 0.2774 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12053 Z= 0.209 Angle : 0.661 12.503 16829 Z= 0.347 Chirality : 0.042 0.326 2026 Planarity : 0.004 0.042 1838 Dihedral : 17.758 176.987 2776 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.77 % Favored : 94.15 % Rotamer: Outliers : 2.64 % Allowed : 23.86 % 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: -0.22 (0.24), residues: 1282 helix: 0.90 (0.23), residues: 563 sheet: -0.02 (0.45), residues: 134 loop : -1.21 (0.26), residues: 585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 42 TYR 0.025 0.002 TYR C 450 PHE 0.012 0.001 PHE C 569 TRP 0.009 0.001 TRP A 69 HIS 0.005 0.001 HIS C 328 Details of bonding type rmsd/Z covalent geometry : bond 0.00455 / 0.21 (12053) covalent geometry : angle 0.66099 / 0.35 (16829) hydrogen bonds : bond 0.04109 / 2.69 ( 483) hydrogen bonds : angle 4.79682 / 3.22 ( 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: 25 poor density : 75 time to evaluate : 0.397 Fit side-chains REVERT: A 15 LYS cc_start: 0.9623 (mmmm) cc_final: 0.9294 (mppt) REVERT: A 16 GLU cc_start: 0.9297 (mp0) cc_final: 0.8774 (mp0) REVERT: A 35 ARG cc_start: 0.8643 (ttm110) cc_final: 0.8150 (tpp80) REVERT: A 39 LYS cc_start: 0.9411 (mmtt) cc_final: 0.9054 (mtmm) REVERT: A 52 LYS cc_start: 0.9218 (mmmt) cc_final: 0.8958 (mmpt) REVERT: A 56 ARG cc_start: 0.9293 (pmm-80) cc_final: 0.9092 (pmm-80) REVERT: C 169 LEU cc_start: 0.9608 (OUTLIER) cc_final: 0.9401 (pp) REVERT: C 184 LEU cc_start: 0.9341 (OUTLIER) cc_final: 0.9114 (mm) REVERT: C 201 ILE cc_start: 0.0664 (OUTLIER) cc_final: 0.0443 (pt) REVERT: C 288 ASP cc_start: 0.8955 (m-30) cc_final: 0.8325 (OUTLIER) REVERT: C 327 GLU cc_start: 0.8930 (OUTLIER) cc_final: 0.8344 (pp20) REVERT: C 349 GLU cc_start: 0.8788 (OUTLIER) cc_final: 0.8458 (tp30) REVERT: C 404 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8815 (p) REVERT: C 694 MET cc_start: 0.9075 (pmm) cc_final: 0.8822 (pmm) REVERT: C 961 LYS cc_start: 0.8645 (tppt) cc_final: 0.8355 (pmtt) REVERT: C 986 ASP cc_start: 0.9218 (m-30) cc_final: 0.8748 (m-30) REVERT: C 1135 ASP cc_start: 0.8801 (t0) cc_final: 0.8495 (p0) REVERT: C 1170 GLU cc_start: 0.9346 (OUTLIER) cc_final: 0.9110 (pt0) outliers start: 25 outliers final: 12 residues processed: 94 average time/residue: 0.4907 time to fit residues: 50.5613 Evaluate side-chains 90 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 72 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 GLU 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 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 928 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 58 optimal weight: 0.8980 chunk 104 optimal weight: 0.7980 chunk 9 optimal weight: 10.0000 chunk 86 optimal weight: 0.0670 chunk 46 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 7.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 ASN ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.080416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.054182 restraints weight = 40741.390| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 4.32 r_work: 0.2808 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12053 Z= 0.131 Angle : 0.642 13.033 16829 Z= 0.336 Chirality : 0.041 0.391 2026 Planarity : 0.003 0.040 1838 Dihedral : 17.769 177.011 2776 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.91 % Favored : 95.01 % Rotamer: Outliers : 1.90 % Allowed : 24.50 % Favored : 73.60 % 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: -0.14 (0.24), residues: 1282 helix: 1.00 (0.23), residues: 555 sheet: 0.01 (0.45), residues: 134 loop : -1.18 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 35 TYR 0.020 0.001 TYR C 450 PHE 0.011 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 0.00286 / 0.13 (12053) covalent geometry : angle 0.64238 / 0.34 (16829) hydrogen bonds : bond 0.03802 / 2.44 ( 483) hydrogen bonds : angle 4.72819 / 3.17 ( 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 89 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.368 Fit side-chains REVERT: A 15 LYS cc_start: 0.9603 (mmmm) cc_final: 0.9263 (mppt) REVERT: A 16 GLU cc_start: 0.9282 (mp0) cc_final: 0.8765 (mp0) REVERT: A 20 GLU cc_start: 0.8834 (pm20) cc_final: 0.8615 (pp20) REVERT: A 27 TYR cc_start: 0.8944 (t80) cc_final: 0.8705 (t80) REVERT: A 35 ARG cc_start: 0.8603 (ttm110) cc_final: 0.8195 (tpp80) REVERT: A 39 LYS cc_start: 0.9410 (mmtt) cc_final: 0.9066 (mtmm) REVERT: A 52 LYS cc_start: 0.9228 (mmmt) cc_final: 0.8980 (mmpt) REVERT: A 56 ARG cc_start: 0.9325 (pmm-80) cc_final: 0.9121 (pmm-80) REVERT: C 184 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9073 (mm) REVERT: C 201 ILE cc_start: 0.0779 (OUTLIER) cc_final: 0.0567 (pt) REVERT: C 288 ASP cc_start: 0.8910 (m-30) cc_final: 0.8284 (OUTLIER) REVERT: C 327 GLU cc_start: 0.8932 (OUTLIER) cc_final: 0.8333 (pp20) REVERT: C 349 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8447 (tp30) REVERT: C 404 THR cc_start: 0.9029 (OUTLIER) cc_final: 0.8791 (p) REVERT: C 694 MET cc_start: 0.9056 (pmm) cc_final: 0.8792 (pmm) REVERT: C 927 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9125 (tp) REVERT: C 961 LYS cc_start: 0.8626 (tppt) cc_final: 0.8341 (pmtt) REVERT: C 986 ASP cc_start: 0.9152 (m-30) cc_final: 0.8726 (m-30) REVERT: C 1043 MET cc_start: 0.6785 (tpt) cc_final: 0.6585 (tpt) REVERT: C 1135 ASP cc_start: 0.8787 (t0) cc_final: 0.8499 (p0) REVERT: C 1170 GLU cc_start: 0.9337 (OUTLIER) cc_final: 0.9121 (pt0) outliers start: 18 outliers final: 10 residues processed: 86 average time/residue: 0.5141 time to fit residues: 47.8737 Evaluate side-chains 88 residues out of total 1152 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 9 LEU Chi-restraints excluded: chain C residue 175 ASN 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 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 928 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 137 random chunks: chunk 15 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 129 optimal weight: 8.9990 chunk 94 optimal weight: 40.0000 chunk 22 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 130 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.079904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.053844 restraints weight = 40466.864| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 4.21 r_work: 0.2800 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12053 Z= 0.170 Angle : 0.650 12.627 16829 Z= 0.337 Chirality : 0.041 0.372 2026 Planarity : 0.003 0.040 1838 Dihedral : 17.721 177.198 2776 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.46 % Favored : 94.46 % Rotamer: Outliers : 2.01 % Allowed : 24.50 % Favored : 73.50 % 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: -0.10 (0.24), residues: 1282 helix: 1.01 (0.23), residues: 556 sheet: 0.37 (0.46), residues: 127 loop : -1.20 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 35 TYR 0.021 0.001 TYR C 450 PHE 0.012 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/Z covalent geometry : bond 0.00374 / 0.17 (12053) covalent geometry : angle 0.64960 / 0.34 (16829) hydrogen bonds : bond 0.03880 / 2.49 ( 483) hydrogen bonds : angle 4.70987 / 3.16 ( 1347) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3450.51 seconds wall clock time: 59 minutes 24.47 seconds (3564.47 seconds total)