Starting phenix.real_space_refine on Wed Aug 5 15:15:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6s_41079/08_2026/8t6s_41079.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6s_41079/08_2026/8t6s_41079.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8t6s_41079/08_2026/8t6s_41079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6s_41079/08_2026/8t6s_41079.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8t6s_41079/08_2026/8t6s_41079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6s_41079/08_2026/8t6s_41079.map" } resolution = 3.28 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= -0.000 sd= 0.009 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 119 5.49 5 S 14 5.16 5 C 6185 2.51 5 N 1839 2.21 5 O 2243 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10400 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 962, 7878 Classifications: {'peptide': 962} Link IDs: {'PTRANS': 28, 'TRANS': 933} Chain breaks: 9 Chain: "B" Number of atoms: 1931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 1931 Classifications: {'RNA': 90} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 48, 'rna3p_pyr': 31} Link IDs: {'rna2p': 10, 'rna3p': 79} Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 406 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "D" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Time building chain proxies: 2.46, per 1000 atoms: 0.24 Number of scatterers: 10400 At special positions: 0 Unit cell: (87.486, 119.981, 119.981, 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 14 16.00 P 119 15.00 O 2243 8.00 N 1839 7.00 C 6185 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: 0.66 Conformation dependent library (CDL) restraints added in 210.6 milliseconds 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1832 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 5 sheets defined 56.4% alpha, 6.5% beta 41 base pairs and 70 stacking pairs defined. Time for finding SS restraints: 1.27 Creating SS restraints... Processing helix chain 'A' and resid 59 through 94 removed outlier: 4.694A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.679A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 175 through 179 removed outlier: 3.616A pdb=" N ASN A 178 " --> pdb=" O ASN A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 183 No H-bonds generated for 'chain 'A' and resid 181 through 183' Processing helix chain 'A' and resid 184 through 190 removed outlier: 3.928A pdb=" N LEU A 188 " --> pdb=" O LEU A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 Processing helix chain 'A' and resid 217 through 228 removed outlier: 3.521A pdb=" N GLN A 228 " --> pdb=" O ASN A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 removed outlier: 4.267A pdb=" N SER A 245 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 306 Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 344 through 353 removed outlier: 4.159A pdb=" N LYS A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N GLU A 349 " --> pdb=" O GLU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 383 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 4.080A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.105A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 3.843A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASN A 436 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 removed outlier: 3.672A pdb=" N ILE A 440 " --> pdb=" O ASN A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 494 removed outlier: 3.620A pdb=" N ILE A 492 " --> pdb=" O ALA A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 526 Processing helix chain 'A' and resid 593 through 602 removed outlier: 4.317A pdb=" N LEU A 598 " --> pdb=" O TYR A 594 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LYS A 599 " --> pdb=" O HIS A 595 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ILE A 600 " --> pdb=" O ASP A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 612 through 626 removed outlier: 3.796A pdb=" N LEU A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 Processing helix chain 'A' and resid 638 through 643 removed outlier: 5.144A pdb=" N HIS A 641 " --> pdb=" O THR A 638 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE A 643 " --> pdb=" O ALA A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 652 Processing helix chain 'A' and resid 678 through 684 Processing helix chain 'A' and resid 721 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 4.173A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 933 removed outlier: 3.520A pdb=" N LYS A 929 " --> pdb=" O ARG A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 933 through 938 Processing helix chain 'A' and resid 959 through 970 removed outlier: 4.201A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 980 through 1000 removed outlier: 4.409A pdb=" N ALA A 984 " --> pdb=" O ASN A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1079 through 1087 removed outlier: 4.526A pdb=" N ARG A1084 " --> pdb=" O PHE A1080 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N LYS A1085 " --> pdb=" O ALA A1081 " (cutoff:3.500A) Processing helix chain 'A' and resid 1127 through 1132 removed outlier: 3.572A pdb=" N GLY A1132 " --> pdb=" O PRO A1128 " (cutoff:3.500A) Processing helix chain 'A' and resid 1168 through 1177 removed outlier: 4.228A pdb=" N SER A1172 " --> pdb=" O ILE A1168 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N SER A1173 " --> pdb=" O MET A1169 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1207 through 1209 No H-bonds generated for 'chain 'A' and resid 1207 through 1209' Processing helix chain 'A' and resid 1229 through 1240 removed outlier: 3.534A pdb=" N VAL A1233 " --> pdb=" O PRO A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1260 Processing helix chain 'A' and resid 1261 through 1263 No H-bonds generated for 'chain 'A' and resid 1261 through 1263' Processing helix chain 'A' and resid 1264 through 1280 removed outlier: 4.759A pdb=" N ILE A1270 " --> pdb=" O LEU A1266 " (cutoff:3.500A) Processing helix chain 'A' and resid 1284 through 1297 removed outlier: 3.697A pdb=" N ASP A1288 " --> pdb=" O ASP A1284 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1313 Processing helix chain 'A' and resid 1339 through 1343 removed outlier: 3.554A pdb=" N VAL A1342 " --> pdb=" O THR A1339 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 11 removed outlier: 3.662A pdb=" N GLY A 17 " --> pdb=" O ASP A 10 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE A 48 " --> pdb=" O ASN A1093 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N VAL A1095 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N ALA A 50 " --> pdb=" O VAL A1095 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.583A pdb=" N LYS A 30 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 508 through 509 Processing sheet with id=AA4, first strand: chain 'A' and resid 1156 through 1167 removed outlier: 3.502A pdb=" N LYS A1151 " --> pdb=" O LYS A1156 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR A1141 " --> pdb=" O ILE A1166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1219 through 1222 removed outlier: 6.278A pdb=" N GLN A1219 " --> pdb=" O ALA A1215 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) 348 hydrogen bonds defined for protein. 999 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 200 hydrogen bond angles 0 basepair planarities 41 basepair parallelities 70 stacking parallelities Total time for adding SS restraints: 2.27 Time building geometry restraints manager: 0.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2222 1.33 - 1.45: 2904 1.45 - 1.57: 5454 1.57 - 1.69: 235 1.69 - 1.81: 27 Bond restraints: 10842 Sorted by residual: bond pdb=" C1' DC C 26 " pdb=" N1 DC C 26 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.95e+01 bond pdb=" C3' DC C 29 " pdb=" C2' DC C 29 " ideal model delta sigma weight residual 1.516 1.550 -0.034 8.00e-03 1.56e+04 1.82e+01 bond pdb=" C1' DT C 23 " pdb=" N1 DT C 23 " ideal model delta sigma weight residual 1.468 1.522 -0.054 1.40e-02 5.10e+03 1.51e+01 bond pdb=" CD1 TYR A 981 " pdb=" CE1 TYR A 981 " ideal model delta sigma weight residual 1.382 1.283 0.099 3.00e-02 1.11e+03 1.08e+01 bond pdb=" C1' DT C 25 " pdb=" N1 DT C 25 " ideal model delta sigma weight residual 1.468 1.509 -0.041 1.40e-02 5.10e+03 8.53e+00 ... (remaining 10837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 14875 3.22 - 6.45: 223 6.45 - 9.67: 40 9.67 - 12.89: 8 12.89 - 16.11: 5 Bond angle restraints: 15151 Sorted by residual: angle pdb=" O5' DA C 27 " pdb=" C5' DA C 27 " pdb=" C4' DA C 27 " ideal model delta sigma weight residual 109.40 114.51 -5.11 8.00e-01 1.56e+00 4.09e+01 angle pdb=" CG1 VAL A1092 " pdb=" CB VAL A1092 " pdb=" CG2 VAL A1092 " ideal model delta sigma weight residual 110.80 96.85 13.95 2.20e+00 2.07e-01 4.02e+01 angle pdb=" O4' DC C 26 " pdb=" C1' DC C 26 " pdb=" N1 DC C 26 " ideal model delta sigma weight residual 108.00 111.93 -3.93 7.00e-01 2.04e+00 3.16e+01 angle pdb=" C2' G B 11 " pdb=" C1' G B 11 " pdb=" N9 G B 11 " ideal model delta sigma weight residual 112.00 118.05 -6.05 1.10e+00 8.26e-01 3.03e+01 angle pdb=" CA ILE A 619 " pdb=" CB ILE A 619 " pdb=" CG1 ILE A 619 " ideal model delta sigma weight residual 110.40 119.30 -8.90 1.70e+00 3.46e-01 2.74e+01 ... (remaining 15146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.72: 6039 29.72 - 59.45: 464 59.45 - 89.17: 96 89.17 - 118.89: 1 118.89 - 148.62: 1 Dihedral angle restraints: 6601 sinusoidal: 3780 harmonic: 2821 Sorted by residual: dihedral pdb=" CA SER A1106 " pdb=" C SER A1106 " pdb=" N LYS A1107 " pdb=" CA LYS A1107 " ideal model delta harmonic sigma weight residual 180.00 153.54 26.46 0 5.00e+00 4.00e-02 2.80e+01 dihedral pdb=" CA SER A 512 " pdb=" C SER A 512 " pdb=" N LEU A 513 " pdb=" CA LEU A 513 " ideal model delta harmonic sigma weight residual -180.00 -154.86 -25.14 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA THR A 22 " pdb=" C THR A 22 " pdb=" N ASP A 23 " pdb=" CA ASP A 23 " ideal model delta harmonic sigma weight residual -180.00 -156.33 -23.67 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 6598 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 1583 0.109 - 0.217: 161 0.217 - 0.326: 11 0.326 - 0.434: 4 0.434 - 0.543: 2 Chirality restraints: 1761 Sorted by residual: chirality pdb=" CG LEU A1312 " pdb=" CB LEU A1312 " pdb=" CD1 LEU A1312 " pdb=" CD2 LEU A1312 " both_signs ideal model delta sigma weight residual False -2.59 -2.05 -0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" P DT C 23 " pdb=" OP1 DT C 23 " pdb=" OP2 DT C 23 " pdb=" O5' DT C 23 " both_signs ideal model delta sigma weight residual True 2.34 -2.83 -0.49 2.00e-01 2.50e+01 6.11e+00 chirality pdb=" CG LEU A 301 " pdb=" CB LEU A 301 " pdb=" CD1 LEU A 301 " pdb=" CD2 LEU A 301 " both_signs ideal model delta sigma weight residual False -2.59 -2.16 -0.43 2.00e-01 2.50e+01 4.62e+00 ... (remaining 1758 not shown) Planarity restraints: 1483 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC C 29 " 0.020 2.00e-02 2.50e+03 3.80e-02 3.25e+01 pdb=" N1 DC C 29 " -0.055 2.00e-02 2.50e+03 pdb=" C2 DC C 29 " 0.088 2.00e-02 2.50e+03 pdb=" O2 DC C 29 " -0.039 2.00e-02 2.50e+03 pdb=" N3 DC C 29 " -0.015 2.00e-02 2.50e+03 pdb=" C4 DC C 29 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC C 29 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DC C 29 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DC C 29 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 32 " 0.016 2.00e-02 2.50e+03 2.73e-02 1.31e+01 pdb=" CG PHE A 32 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 PHE A 32 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE A 32 " 0.030 2.00e-02 2.50e+03 pdb=" CE1 PHE A 32 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 32 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE A 32 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 66 " 0.023 2.00e-02 2.50e+03 2.41e-02 1.30e+01 pdb=" N1 U B 66 " -0.057 2.00e-02 2.50e+03 pdb=" C2 U B 66 " 0.035 2.00e-02 2.50e+03 pdb=" O2 U B 66 " -0.011 2.00e-02 2.50e+03 pdb=" N3 U B 66 " -0.004 2.00e-02 2.50e+03 pdb=" C4 U B 66 " 0.001 2.00e-02 2.50e+03 pdb=" O4 U B 66 " 0.002 2.00e-02 2.50e+03 pdb=" C5 U B 66 " 0.002 2.00e-02 2.50e+03 pdb=" C6 U B 66 " 0.008 2.00e-02 2.50e+03 ... (remaining 1480 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1363 2.75 - 3.29: 10315 3.29 - 3.83: 19208 3.83 - 4.36: 22535 4.36 - 4.90: 33906 Nonbonded interactions: 87327 Sorted by model distance: nonbonded pdb=" O ARG A 69 " pdb=" OG1 THR A 73 " model vdw 2.217 3.040 nonbonded pdb=" O ARG A1337 " pdb=" NH1 ARG A1337 " model vdw 2.221 3.120 nonbonded pdb=" OE2 GLU A 505 " pdb=" OG SER A 663 " model vdw 2.221 3.040 nonbonded pdb=" OH TYR A 373 " pdb=" O LEU A 398 " model vdw 2.223 3.040 nonbonded pdb=" OG SER A 512 " pdb=" OE1 GLU A 617 " model vdw 2.254 3.040 ... (remaining 87322 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=0.00 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: 3.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 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 : 0.006 0.099 10842 Z= 0.368 Angle : 1.118 16.113 15151 Z= 0.712 Chirality : 0.067 0.543 1761 Planarity : 0.008 0.106 1483 Dihedral : 19.307 148.617 4769 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.12 % Allowed : 20.02 % Favored : 79.86 % 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: -1.45 (0.26), residues: 942 helix: -0.96 (0.22), residues: 447 sheet: -0.79 (0.59), residues: 80 loop : -0.81 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG A1111 TYR 0.038 0.003 TYR A 136 PHE 0.060 0.003 PHE A 32 TRP 0.060 0.005 TRP A 18 HIS 0.017 0.002 HIS A1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.37 (10842) covalent geometry : angle 1.11816 / 0.71 (15151) hydrogen bonds : bond 0.15669 / 10.58 ( 450) hydrogen bonds : angle 6.54012 / 4.51 ( 1199) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.9064 (mt) cc_final: 0.8710 (tt) REVERT: A 498 PHE cc_start: 0.8173 (m-80) cc_final: 0.7924 (m-10) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.1194 time to fit residues: 13.9847 Evaluate side-chains 71 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 930 HIS A1093 ASN A1219 GLN A1350 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.103888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.074528 restraints weight = 36551.396| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 4.10 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10842 Z= 0.224 Angle : 0.700 8.128 15151 Z= 0.380 Chirality : 0.044 0.249 1761 Planarity : 0.005 0.065 1483 Dihedral : 19.795 154.247 2723 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.01 % Allowed : 16.90 % Favored : 80.09 % 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: -0.80 (0.26), residues: 942 helix: -0.13 (0.23), residues: 449 sheet: -0.32 (0.70), residues: 61 loop : -0.89 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 165 TYR 0.017 0.002 TYR A 981 PHE 0.015 0.002 PHE A 972 TRP 0.021 0.002 TRP A 18 HIS 0.007 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.22 (10842) covalent geometry : angle 0.70019 / 0.38 (15151) hydrogen bonds : bond 0.05881 / 4.06 ( 450) hydrogen bonds : angle 5.37156 / 3.72 ( 1199) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.9153 (mt) cc_final: 0.8894 (tt) REVERT: A 498 PHE cc_start: 0.8115 (m-80) cc_final: 0.7852 (m-80) REVERT: A 649 LYS cc_start: 0.9537 (mttm) cc_final: 0.9320 (ptmm) REVERT: A 1297 HIS cc_start: 0.8758 (m90) cc_final: 0.8484 (m90) REVERT: A 1337 ARG cc_start: 0.7224 (tpt90) cc_final: 0.6958 (tpt90) outliers start: 26 outliers final: 16 residues processed: 93 average time/residue: 0.1146 time to fit residues: 14.9029 Evaluate side-chains 87 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 88 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 982 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 = 0.4193 r_free = 0.4193 target = 0.102779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.073523 restraints weight = 37113.570| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 4.20 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10842 Z= 0.225 Angle : 0.660 7.674 15151 Z= 0.361 Chirality : 0.043 0.244 1761 Planarity : 0.005 0.063 1483 Dihedral : 19.782 154.621 2723 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.12 % Allowed : 17.13 % Favored : 79.75 % 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: -0.73 (0.26), residues: 942 helix: 0.02 (0.24), residues: 450 sheet: -0.29 (0.69), residues: 60 loop : -0.96 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 139 TYR 0.020 0.002 TYR A1237 PHE 0.021 0.002 PHE A 32 TRP 0.012 0.002 TRP A 18 HIS 0.010 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.23 (10842) covalent geometry : angle 0.66026 / 0.36 (15151) hydrogen bonds : bond 0.05701 / 3.98 ( 450) hydrogen bonds : angle 5.28249 / 3.69 ( 1199) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.9217 (mt) cc_final: 0.9014 (tt) REVERT: A 498 PHE cc_start: 0.8101 (m-80) cc_final: 0.7838 (m-80) REVERT: A 1297 HIS cc_start: 0.8861 (m90) cc_final: 0.8562 (m90) REVERT: A 1337 ARG cc_start: 0.7231 (tpt90) cc_final: 0.6849 (tpt90) outliers start: 27 outliers final: 21 residues processed: 96 average time/residue: 0.1148 time to fit residues: 15.4067 Evaluate side-chains 91 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 70 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 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 = 0.4194 r_free = 0.4194 target = 0.102831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.073651 restraints weight = 37025.519| |-----------------------------------------------------------------------------| r_work (start): 0.3519 rms_B_bonded: 4.19 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 10842 Z= 0.207 Angle : 0.625 9.676 15151 Z= 0.342 Chirality : 0.041 0.244 1761 Planarity : 0.004 0.063 1483 Dihedral : 19.786 154.676 2723 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.63 % Allowed : 16.67 % Favored : 78.70 % 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 (0.27), residues: 942 helix: 0.16 (0.24), residues: 450 sheet: -0.41 (0.69), residues: 60 loop : -0.90 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 139 TYR 0.014 0.002 TYR A 515 PHE 0.039 0.002 PHE A1313 TRP 0.012 0.002 TRP A1136 HIS 0.009 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.21 (10842) covalent geometry : angle 0.62452 / 0.34 (15151) hydrogen bonds : bond 0.05336 / 3.73 ( 450) hydrogen bonds : angle 5.09762 / 3.56 ( 1199) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 70 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.9327 (mt) cc_final: 0.9108 (tt) REVERT: A 301 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8675 (mm) REVERT: A 498 PHE cc_start: 0.8014 (m-80) cc_final: 0.7755 (m-80) REVERT: A 1087 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7945 (mt) REVERT: A 1271 GLU cc_start: 0.9547 (OUTLIER) cc_final: 0.9208 (tm-30) REVERT: A 1297 HIS cc_start: 0.8868 (m90) cc_final: 0.8547 (m90) REVERT: A 1337 ARG cc_start: 0.7303 (tpt90) cc_final: 0.6850 (tpt90) outliers start: 40 outliers final: 28 residues processed: 98 average time/residue: 0.1024 time to fit residues: 14.6627 Evaluate side-chains 99 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 68 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 981 TYR Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1087 LEU Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 0.1980 chunk 22 optimal weight: 20.0000 chunk 63 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 0.0000 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 0.0070 chunk 47 optimal weight: 5.9990 chunk 94 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.8406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 GLN ** A 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 HIS ** A1350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.104532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.075628 restraints weight = 36498.870| |-----------------------------------------------------------------------------| r_work (start): 0.3570 rms_B_bonded: 4.12 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10842 Z= 0.131 Angle : 0.574 9.509 15151 Z= 0.314 Chirality : 0.039 0.242 1761 Planarity : 0.004 0.058 1483 Dihedral : 19.711 152.986 2723 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.82 % Allowed : 17.25 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.27), residues: 942 helix: 0.36 (0.24), residues: 450 sheet: -0.29 (0.69), residues: 60 loop : -0.77 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 61 TYR 0.023 0.002 TYR A 25 PHE 0.030 0.002 PHE A1313 TRP 0.013 0.001 TRP A1136 HIS 0.006 0.001 HIS A1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (10842) covalent geometry : angle 0.57411 / 0.31 (15151) hydrogen bonds : bond 0.04730 / 3.32 ( 450) hydrogen bonds : angle 4.93411 / 3.46 ( 1199) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 75 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.9344 (mt) cc_final: 0.9103 (tt) REVERT: A 82 LEU cc_start: 0.9335 (OUTLIER) cc_final: 0.9031 (tt) REVERT: A 301 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8643 (mm) REVERT: A 498 PHE cc_start: 0.8086 (m-80) cc_final: 0.7826 (m-80) REVERT: A 1271 GLU cc_start: 0.9515 (OUTLIER) cc_final: 0.9213 (tm-30) REVERT: A 1297 HIS cc_start: 0.8821 (m90) cc_final: 0.8479 (m90) REVERT: A 1337 ARG cc_start: 0.7233 (tpt90) cc_final: 0.6707 (tpt90) outliers start: 33 outliers final: 24 residues processed: 100 average time/residue: 0.1078 time to fit residues: 15.4770 Evaluate side-chains 96 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 69 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 43 optimal weight: 0.0670 chunk 83 optimal weight: 9.9990 chunk 26 optimal weight: 0.0670 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 78 optimal weight: 0.0980 chunk 5 optimal weight: 6.9990 chunk 100 optimal weight: 10.0000 overall best weight: 1.0458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.104203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.075102 restraints weight = 36691.282| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 4.17 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10842 Z= 0.136 Angle : 0.565 7.801 15151 Z= 0.310 Chirality : 0.038 0.237 1761 Planarity : 0.004 0.058 1483 Dihedral : 19.667 153.093 2723 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.36 % Allowed : 17.94 % Favored : 78.70 % 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: -0.27 (0.27), residues: 942 helix: 0.42 (0.24), residues: 451 sheet: -0.38 (0.67), residues: 60 loop : -0.71 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 61 TYR 0.021 0.002 TYR A 25 PHE 0.021 0.001 PHE A1313 TRP 0.020 0.001 TRP A1136 HIS 0.013 0.001 HIS A1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.14 (10842) covalent geometry : angle 0.56489 / 0.31 (15151) hydrogen bonds : bond 0.04624 / 3.25 ( 450) hydrogen bonds : angle 4.82610 / 3.39 ( 1199) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.9375 (mt) cc_final: 0.9158 (tt) REVERT: A 301 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8638 (mm) REVERT: A 498 PHE cc_start: 0.8097 (m-80) cc_final: 0.7844 (m-80) REVERT: A 1271 GLU cc_start: 0.9519 (OUTLIER) cc_final: 0.9216 (tm-30) REVERT: A 1297 HIS cc_start: 0.8839 (m90) cc_final: 0.8506 (m90) REVERT: A 1337 ARG cc_start: 0.7233 (tpt90) cc_final: 0.6685 (tpt90) outliers start: 29 outliers final: 25 residues processed: 95 average time/residue: 0.1009 time to fit residues: 13.7742 Evaluate side-chains 95 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 68 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 1 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 71 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 89 optimal weight: 5.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1350 GLN ** 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 = 0.4195 r_free = 0.4195 target = 0.102561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.073417 restraints weight = 36824.957| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 4.19 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10842 Z= 0.210 Angle : 0.619 8.915 15151 Z= 0.336 Chirality : 0.040 0.234 1761 Planarity : 0.004 0.057 1483 Dihedral : 19.708 154.092 2723 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.70 % Allowed : 18.29 % Favored : 78.01 % 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 (0.27), residues: 942 helix: 0.36 (0.24), residues: 450 sheet: -0.50 (0.67), residues: 60 loop : -0.78 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 61 TYR 0.023 0.002 TYR A1242 PHE 0.022 0.002 PHE A1105 TRP 0.016 0.001 TRP A1136 HIS 0.022 0.002 HIS A1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.21 (10842) covalent geometry : angle 0.61885 / 0.34 (15151) hydrogen bonds : bond 0.05044 / 3.54 ( 450) hydrogen bonds : angle 4.95087 / 3.48 ( 1199) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 67 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.9387 (mt) cc_final: 0.9179 (tt) REVERT: A 498 PHE cc_start: 0.8106 (m-80) cc_final: 0.7862 (m-80) REVERT: A 1271 GLU cc_start: 0.9524 (OUTLIER) cc_final: 0.9204 (tm-30) REVERT: A 1297 HIS cc_start: 0.8872 (m90) cc_final: 0.8533 (m90) REVERT: A 1337 ARG cc_start: 0.7383 (tpt90) cc_final: 0.6829 (tpt90) outliers start: 32 outliers final: 30 residues processed: 90 average time/residue: 0.1060 time to fit residues: 13.7285 Evaluate side-chains 97 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 66 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 507 VAL Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 622 THR Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 19 optimal weight: 0.9980 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 56 optimal weight: 0.2980 chunk 57 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 92 optimal weight: 6.9990 chunk 101 optimal weight: 8.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 980 ASN ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.103991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.075030 restraints weight = 35976.691| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 4.11 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10842 Z= 0.133 Angle : 0.576 8.502 15151 Z= 0.314 Chirality : 0.038 0.237 1761 Planarity : 0.004 0.056 1483 Dihedral : 19.694 152.932 2723 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.36 % Allowed : 19.68 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.24 (0.27), residues: 942 helix: 0.42 (0.24), residues: 457 sheet: -0.38 (0.68), residues: 60 loop : -0.66 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 61 TYR 0.016 0.002 TYR A 25 PHE 0.020 0.001 PHE A1105 TRP 0.019 0.001 TRP A1136 HIS 0.007 0.001 HIS A1241 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (10842) covalent geometry : angle 0.57637 / 0.31 (15151) hydrogen bonds : bond 0.04514 / 3.16 ( 450) hydrogen bonds : angle 4.77057 / 3.36 ( 1199) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 68 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 PHE cc_start: 0.8036 (m-80) cc_final: 0.7777 (m-80) REVERT: A 1271 GLU cc_start: 0.9517 (OUTLIER) cc_final: 0.9186 (tm-30) REVERT: A 1297 HIS cc_start: 0.8847 (m90) cc_final: 0.8504 (m90) REVERT: A 1337 ARG cc_start: 0.7356 (tpt90) cc_final: 0.6755 (tpt90) outliers start: 29 outliers final: 25 residues processed: 91 average time/residue: 0.0984 time to fit residues: 13.1615 Evaluate side-chains 92 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 66 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 18 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 79 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 19 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 GLN ** 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 = 0.4189 r_free = 0.4189 target = 0.102136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.073009 restraints weight = 36580.370| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 4.20 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10842 Z= 0.213 Angle : 0.625 8.559 15151 Z= 0.338 Chirality : 0.040 0.235 1761 Planarity : 0.004 0.056 1483 Dihedral : 19.763 154.553 2723 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.59 % Allowed : 19.33 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.27), residues: 942 helix: 0.29 (0.24), residues: 461 sheet: -0.57 (0.67), residues: 60 loop : -0.75 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 61 TYR 0.017 0.002 TYR A 25 PHE 0.019 0.002 PHE A 972 TRP 0.012 0.001 TRP A1136 HIS 0.009 0.001 HIS A 167 Details of bonding type rmsd/Z covalent geometry : bond 0.00433 / 0.21 (10842) covalent geometry : angle 0.62507 / 0.34 (15151) hydrogen bonds : bond 0.05213 / 3.66 ( 450) hydrogen bonds : angle 4.91726 / 3.45 ( 1199) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 PHE cc_start: 0.7968 (m-80) cc_final: 0.7727 (m-10) REVERT: A 1271 GLU cc_start: 0.9511 (OUTLIER) cc_final: 0.9160 (tm-30) REVERT: A 1297 HIS cc_start: 0.8921 (m90) cc_final: 0.8579 (m90) REVERT: A 1325 LYS cc_start: 0.8888 (tmmt) cc_final: 0.8632 (tmmt) REVERT: A 1337 ARG cc_start: 0.7469 (tpt90) cc_final: 0.6907 (tpt90) outliers start: 31 outliers final: 27 residues processed: 88 average time/residue: 0.1074 time to fit residues: 13.7609 Evaluate side-chains 92 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 27 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 22 optimal weight: 0.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 97 optimal weight: 10.0000 chunk 90 optimal weight: 1.9990 chunk 47 optimal weight: 10.0000 chunk 3 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 GLN ** 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 = 0.4213 r_free = 0.4213 target = 0.103400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.074403 restraints weight = 36152.178| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 4.10 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10842 Z= 0.147 Angle : 0.595 10.830 15151 Z= 0.320 Chirality : 0.038 0.239 1761 Planarity : 0.004 0.055 1483 Dihedral : 19.755 153.320 2723 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.59 % Allowed : 19.68 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.25 (0.27), residues: 942 helix: 0.40 (0.24), residues: 456 sheet: -0.48 (0.68), residues: 60 loop : -0.65 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 61 TYR 0.015 0.001 TYR A 155 PHE 0.018 0.001 PHE A 972 TRP 0.015 0.001 TRP A1136 HIS 0.014 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.15 (10842) covalent geometry : angle 0.59522 / 0.32 (15151) hydrogen bonds : bond 0.04612 / 3.22 ( 450) hydrogen bonds : angle 4.80354 / 3.38 ( 1199) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1884 Ramachandran restraints generated. 942 Oldfield, 0 Emsley, 942 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 64 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 PHE cc_start: 0.8082 (m-80) cc_final: 0.7825 (m-80) REVERT: A 1271 GLU cc_start: 0.9508 (OUTLIER) cc_final: 0.9171 (tm-30) REVERT: A 1297 HIS cc_start: 0.8931 (m90) cc_final: 0.8582 (m90) REVERT: A 1337 ARG cc_start: 0.7451 (tpt90) cc_final: 0.6849 (tpt90) outliers start: 31 outliers final: 27 residues processed: 87 average time/residue: 0.0980 time to fit residues: 12.0200 Evaluate side-chains 92 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 64 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 99 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 518 PHE Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 637 LYS Chi-restraints excluded: chain A residue 639 TYR Chi-restraints excluded: chain A residue 738 LEU Chi-restraints excluded: chain A residue 743 VAL Chi-restraints excluded: chain A residue 990 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1108 GLU Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1167 THR Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1342 VAL Chi-restraints excluded: chain A residue 1353 THR Chi-restraints excluded: chain A residue 1355 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 56 optimal weight: 30.0000 chunk 79 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 0.0570 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 overall best weight: 1.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 GLN ** 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 = 0.4220 r_free = 0.4220 target = 0.103811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.074881 restraints weight = 36427.904| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 4.14 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10842 Z= 0.144 Angle : 0.605 10.970 15151 Z= 0.321 Chirality : 0.039 0.289 1761 Planarity : 0.004 0.055 1483 Dihedral : 19.746 153.143 2723 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 3.12 % Allowed : 20.02 % Favored : 76.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % 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: -0.20 (0.27), residues: 942 helix: 0.44 (0.24), residues: 457 sheet: -0.56 (0.67), residues: 60 loop : -0.60 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 61 TYR 0.016 0.001 TYR A 155 PHE 0.024 0.001 PHE A1105 TRP 0.016 0.001 TRP A1136 HIS 0.014 0.001 HIS A 137 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (10842) covalent geometry : angle 0.60522 / 0.32 (15151) hydrogen bonds : bond 0.04514 / 3.15 ( 450) hydrogen bonds : angle 4.75314 / 3.34 ( 1199) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2491.81 seconds wall clock time: 43 minutes 38.42 seconds (2618.42 seconds total)