Starting phenix.real_space_refine on Wed Feb 4 11:20:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8t6s_41079/02_2026/8t6s_41079.cif Found real_map, /net/cci-nas-00/data/ceres_data/8t6s_41079/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8t6s_41079/02_2026/8t6s_41079.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8t6s_41079/02_2026/8t6s_41079.map" model { file = "/net/cci-nas-00/data/ceres_data/8t6s_41079/02_2026/8t6s_41079.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8t6s_41079/02_2026/8t6s_41079.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.93, per 1000 atoms: 0.19 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 331.3 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: 0.93 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: 1.83 Time building geometry restraints manager: 0.86 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=" 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=" CB TYR A 981 " pdb=" CG TYR A 981 " ideal model delta sigma weight residual 1.512 1.454 0.058 2.20e-02 2.07e+03 6.89e+00 bond pdb=" CG1 ILE A 619 " pdb=" CD1 ILE A 619 " ideal model delta sigma weight residual 1.513 1.425 0.088 3.90e-02 6.57e+02 5.04e+00 bond pdb=" CB VAL A1092 " pdb=" CG1 VAL A1092 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.67e+00 bond pdb=" CB ARG A 976 " pdb=" CG ARG A 976 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 3.00e+00 ... (remaining 10837 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.22: 14887 3.22 - 6.45: 211 6.45 - 9.67: 40 9.67 - 12.89: 8 12.89 - 16.11: 5 Bond angle restraints: 15151 Sorted by residual: 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=" 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 angle pdb=" CB MET A 648 " pdb=" CG MET A 648 " pdb=" SD MET A 648 " ideal model delta sigma weight residual 112.70 127.59 -14.89 3.00e+00 1.11e-01 2.46e+01 angle pdb=" O3' DG C 22 " pdb=" P DT C 23 " pdb=" OP1 DT C 23 " ideal model delta sigma weight residual 108.00 121.87 -13.87 3.00e+00 1.11e-01 2.14e+01 angle pdb=" CA LEU A1312 " pdb=" CB LEU A1312 " pdb=" CG LEU A1312 " ideal model delta sigma weight residual 116.30 132.41 -16.11 3.50e+00 8.16e-02 2.12e+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: 1666 0.109 - 0.217: 78 0.217 - 0.326: 10 0.326 - 0.434: 5 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 2.35 -2.83 -0.48 2.00e-01 2.50e+01 5.86e+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: 3.450 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.290 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 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= 0.255 Angle : 1.062 16.113 15151 Z= 0.541 Chirality : 0.060 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 covalent geometry : bond 0.00568 (10842) covalent geometry : angle 1.06220 (15151) hydrogen bonds : bond 0.15669 ( 450) hydrogen bonds : angle 6.54012 ( 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 : 0.265 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: 0.7923 (m-10) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.0951 time to fit residues: 11.0703 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 : 0.207 ------------------------------------------------------------------------------- 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: 3.9990 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: 4.9990 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1093 ASN A1219 GLN A1350 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.103030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.073689 restraints weight = 36904.202| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 4.15 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10842 Z= 0.221 Angle : 0.673 7.803 15151 Z= 0.354 Chirality : 0.041 0.354 1761 Planarity : 0.004 0.059 1483 Dihedral : 19.751 156.599 2723 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.36 % Allowed : 15.86 % Favored : 80.79 % 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: -0.67 (0.27), residues: 942 helix: -0.01 (0.24), residues: 450 sheet: -0.37 (0.70), residues: 61 loop : -0.82 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 61 TYR 0.021 0.002 TYR A 515 PHE 0.024 0.002 PHE A 32 TRP 0.020 0.002 TRP A 18 HIS 0.009 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00464 (10842) covalent geometry : angle 0.67251 (15151) hydrogen bonds : bond 0.05128 ( 450) hydrogen bonds : angle 5.13845 ( 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 110 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 0.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 LEU cc_start: 0.9229 (mt) cc_final: 0.8974 (tt) REVERT: A 301 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8623 (mm) REVERT: A 498 PHE cc_start: 0.8050 (m-80) cc_final: 0.7776 (m-80) REVERT: A 649 LYS cc_start: 0.9548 (mttm) cc_final: 0.9341 (ptmm) REVERT: A 1297 HIS cc_start: 0.8823 (m90) cc_final: 0.8530 (m90) REVERT: A 1337 ARG cc_start: 0.7201 (tpt90) cc_final: 0.6893 (tpt90) outliers start: 29 outliers final: 19 residues processed: 100 average time/residue: 0.0977 time to fit residues: 13.5623 Evaluate side-chains 93 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 472 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 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 1149 VAL Chi-restraints excluded: chain A residue 1166 ILE 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: 7.9990 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 739 GLN ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 982 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1093 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4198 r_free = 0.4198 target = 0.102582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.073194 restraints weight = 36682.410| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 4.22 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10842 Z= 0.199 Angle : 0.623 7.163 15151 Z= 0.329 Chirality : 0.039 0.268 1761 Planarity : 0.004 0.060 1483 Dihedral : 19.710 155.198 2723 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.94 % Allowed : 16.78 % Favored : 79.28 % 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: -0.42 (0.27), residues: 942 helix: 0.31 (0.24), residues: 451 sheet: -0.48 (0.69), residues: 60 loop : -0.78 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 61 TYR 0.015 0.002 TYR A 515 PHE 0.030 0.002 PHE A1313 TRP 0.014 0.002 TRP A1136 HIS 0.008 0.001 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00417 (10842) covalent geometry : angle 0.62268 (15151) hydrogen bonds : bond 0.04726 ( 450) hydrogen bonds : angle 4.88970 ( 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 113 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 PHE cc_start: 0.7932 (m-80) cc_final: 0.7666 (m-80) REVERT: A 1210 ARG cc_start: 0.7446 (ptm160) cc_final: 0.7232 (ptm-80) REVERT: A 1297 HIS cc_start: 0.8882 (m90) cc_final: 0.8602 (m90) REVERT: A 1337 ARG cc_start: 0.7363 (tpt90) cc_final: 0.7072 (tpt90) outliers start: 34 outliers final: 26 residues processed: 104 average time/residue: 0.0868 time to fit residues: 12.9797 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 : 0.235 ------------------------------------------------------------------------------- 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 472 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 990 ASN Chi-restraints excluded: chain A residue 1102 THR Chi-restraints excluded: chain A residue 1166 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1264 HIS Chi-restraints excluded: chain A residue 1270 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 0.0770 chunk 58 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 60 optimal weight: 0.0670 chunk 28 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 14 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 930 HIS ** 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 = 0.4258 r_free = 0.4258 target = 0.105490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.076765 restraints weight = 36187.760| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 4.14 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10842 Z= 0.116 Angle : 0.554 9.343 15151 Z= 0.291 Chirality : 0.037 0.212 1761 Planarity : 0.004 0.057 1483 Dihedral : 19.534 153.100 2723 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.55 % Allowed : 18.17 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.27), residues: 942 helix: 0.64 (0.24), residues: 452 sheet: -0.40 (0.67), residues: 60 loop : -0.63 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 61 TYR 0.024 0.001 TYR A 25 PHE 0.018 0.001 PHE A1105 TRP 0.017 0.001 TRP A1136 HIS 0.009 0.001 HIS A1241 Details of bonding type rmsd covalent geometry : bond 0.00241 (10842) covalent geometry : angle 0.55416 (15151) hydrogen bonds : bond 0.03852 ( 450) hydrogen bonds : angle 4.55759 ( 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 101 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 PHE cc_start: 0.8001 (m-80) cc_final: 0.7720 (m-80) REVERT: A 599 LYS cc_start: 0.9488 (tptp) cc_final: 0.9203 (mmtm) REVERT: A 1297 HIS cc_start: 0.8961 (m90) cc_final: 0.8684 (m90) REVERT: A 1337 ARG cc_start: 0.7355 (tpt90) cc_final: 0.6781 (tpt90) REVERT: A 1356 TYR cc_start: 0.8126 (m-80) cc_final: 0.7491 (m-10) outliers start: 22 outliers final: 16 residues processed: 94 average time/residue: 0.0878 time to fit residues: 11.8519 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 : 0.249 ------------------------------------------------------------------------------- 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 355 SER Chi-restraints excluded: chain A residue 606 PHE Chi-restraints excluded: chain A residue 639 TYR 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 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 1355 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 9.9990 chunk 22 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 70 optimal weight: 4.9990 chunk 45 optimal weight: 0.0670 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 47 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 18 optimal weight: 0.0020 chunk 46 optimal weight: 3.9990 overall best weight: 2.6132 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 930 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 = 0.4177 r_free = 0.4177 target = 0.101079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.071444 restraints weight = 37418.105| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 4.28 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10842 Z= 0.252 Angle : 0.655 7.819 15151 Z= 0.344 Chirality : 0.040 0.227 1761 Planarity : 0.005 0.060 1483 Dihedral : 19.768 156.772 2723 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % 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: -0.32 (0.27), residues: 942 helix: 0.41 (0.24), residues: 458 sheet: -0.68 (0.68), residues: 60 loop : -0.75 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 139 TYR 0.017 0.002 TYR A 25 PHE 0.029 0.002 PHE A1105 TRP 0.009 0.001 TRP A1136 HIS 0.018 0.002 HIS A1241 Details of bonding type rmsd covalent geometry : bond 0.00523 (10842) covalent geometry : angle 0.65481 (15151) hydrogen bonds : bond 0.04987 ( 450) hydrogen bonds : angle 4.83239 ( 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 100 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 67 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 PHE cc_start: 0.7987 (m-80) cc_final: 0.7728 (m-80) REVERT: A 1297 HIS cc_start: 0.8990 (m90) cc_final: 0.8716 (m90) REVERT: A 1337 ARG cc_start: 0.7608 (tpt90) cc_final: 0.7173 (tpt90) outliers start: 33 outliers final: 24 residues processed: 90 average time/residue: 0.0917 time to fit residues: 11.6585 Evaluate side-chains 86 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 62 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 322 ILE 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 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 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU 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: 3.9990 chunk 83 optimal weight: 10.0000 chunk 26 optimal weight: 0.9990 chunk 25 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 100 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 930 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 = 0.4154 r_free = 0.4154 target = 0.099441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.069973 restraints weight = 38264.067| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 4.24 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 10842 Z= 0.280 Angle : 0.695 8.557 15151 Z= 0.364 Chirality : 0.041 0.267 1761 Planarity : 0.005 0.060 1483 Dihedral : 20.031 157.475 2723 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 17.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 4.17 % Allowed : 17.25 % Favored : 78.59 % 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: -0.53 (0.27), residues: 942 helix: 0.17 (0.24), residues: 453 sheet: -0.85 (0.67), residues: 60 loop : -0.74 (0.31), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 61 TYR 0.019 0.002 TYR A 25 PHE 0.020 0.002 PHE A 972 TRP 0.009 0.001 TRP A1136 HIS 0.011 0.002 HIS A 167 Details of bonding type rmsd covalent geometry : bond 0.00584 (10842) covalent geometry : angle 0.69541 (15151) hydrogen bonds : bond 0.05318 ( 450) hydrogen bonds : angle 5.00386 ( 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 99 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 63 time to evaluate : 0.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 HIS cc_start: 0.8026 (OUTLIER) cc_final: 0.7658 (t-170) REVERT: A 648 MET cc_start: 0.8353 (ppp) cc_final: 0.8064 (ppp) REVERT: A 1297 HIS cc_start: 0.9026 (m90) cc_final: 0.8745 (m90) REVERT: A 1337 ARG cc_start: 0.7720 (tpt90) cc_final: 0.7227 (tpt90) REVERT: A 1352 ILE cc_start: 0.8986 (mp) cc_final: 0.8681 (tp) outliers start: 36 outliers final: 27 residues processed: 87 average time/residue: 0.0918 time to fit residues: 11.5026 Evaluate side-chains 85 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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 99 HIS Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 322 ILE 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 502 LEU 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 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 1190 VAL Chi-restraints excluded: chain A residue 1228 LEU Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1260 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 1 optimal weight: 10.0000 chunk 46 optimal weight: 0.6980 chunk 91 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 930 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 = 0.4217 r_free = 0.4217 target = 0.103031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.073649 restraints weight = 36860.442| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 4.18 r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10842 Z= 0.128 Angle : 0.570 8.940 15151 Z= 0.297 Chirality : 0.037 0.240 1761 Planarity : 0.004 0.056 1483 Dihedral : 19.770 153.486 2723 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 3.12 % Allowed : 18.40 % Favored : 78.47 % 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: -0.21 (0.27), residues: 942 helix: 0.52 (0.24), residues: 456 sheet: -1.08 (0.65), residues: 52 loop : -0.64 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 61 TYR 0.018 0.001 TYR A 155 PHE 0.019 0.001 PHE A1105 TRP 0.015 0.001 TRP A1136 HIS 0.007 0.001 HIS A1241 Details of bonding type rmsd covalent geometry : bond 0.00271 (10842) covalent geometry : angle 0.56994 (15151) hydrogen bonds : bond 0.03910 ( 450) hydrogen bonds : angle 4.50353 ( 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: 27 poor density : 72 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7580 (tp) cc_final: 0.7022 (tp) REVERT: A 750 VAL cc_start: 0.9157 (m) cc_final: 0.8844 (m) REVERT: A 1297 HIS cc_start: 0.9073 (m90) cc_final: 0.8804 (m90) REVERT: A 1337 ARG cc_start: 0.7551 (tpt90) cc_final: 0.6945 (tpt90) REVERT: A 1356 TYR cc_start: 0.8169 (m-80) cc_final: 0.7696 (m-80) outliers start: 27 outliers final: 22 residues processed: 91 average time/residue: 0.0892 time to fit residues: 11.5947 Evaluate side-chains 88 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 66 time to evaluate : 0.248 ------------------------------------------------------------------------------- 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 301 LEU Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 622 THR 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 1190 VAL Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1260 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 19 optimal weight: 10.0000 chunk 69 optimal weight: 6.9990 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 67 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 27 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4168 r_free = 0.4168 target = 0.100480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.071244 restraints weight = 36970.505| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 4.14 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 10842 Z= 0.229 Angle : 0.648 8.987 15151 Z= 0.337 Chirality : 0.039 0.239 1761 Planarity : 0.004 0.057 1483 Dihedral : 19.898 156.263 2723 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.47 % Allowed : 18.63 % Favored : 77.89 % 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: -0.32 (0.27), residues: 942 helix: 0.40 (0.24), residues: 457 sheet: -1.23 (0.65), residues: 52 loop : -0.65 (0.31), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 61 TYR 0.017 0.002 TYR A 988 PHE 0.020 0.002 PHE A1105 TRP 0.009 0.001 TRP A1136 HIS 0.009 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00480 (10842) covalent geometry : angle 0.64780 (15151) hydrogen bonds : bond 0.04860 ( 450) hydrogen bonds : angle 4.71426 ( 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 91 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 498 PHE cc_start: 0.8304 (m-10) cc_final: 0.7995 (m-80) REVERT: A 661 ARG cc_start: 0.6902 (ttt180) cc_final: 0.6025 (tpt170) REVERT: A 1297 HIS cc_start: 0.9037 (m90) cc_final: 0.8737 (m90) REVERT: A 1312 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9250 (mm) REVERT: A 1337 ARG cc_start: 0.7670 (tpt90) cc_final: 0.7157 (tpt90) REVERT: A 1352 ILE cc_start: 0.8939 (mp) cc_final: 0.8648 (tp) outliers start: 30 outliers final: 25 residues processed: 80 average time/residue: 0.0890 time to fit residues: 10.5553 Evaluate side-chains 86 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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 355 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 502 LEU 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 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 1190 VAL Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1312 LEU 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: 5.9990 chunk 66 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 98 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 57 optimal weight: 8.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 930 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 = 0.4193 r_free = 0.4193 target = 0.101781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.072763 restraints weight = 36649.651| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 4.08 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10842 Z= 0.164 Angle : 0.596 8.889 15151 Z= 0.309 Chirality : 0.038 0.233 1761 Planarity : 0.004 0.055 1483 Dihedral : 19.846 154.996 2723 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.36 % Allowed : 18.40 % Favored : 78.24 % 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: -0.20 (0.27), residues: 942 helix: 0.48 (0.24), residues: 462 sheet: -1.25 (0.64), residues: 52 loop : -0.55 (0.31), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 61 TYR 0.016 0.002 TYR A 155 PHE 0.016 0.001 PHE A 972 TRP 0.011 0.001 TRP A1136 HIS 0.015 0.001 HIS A1241 Details of bonding type rmsd covalent geometry : bond 0.00349 (10842) covalent geometry : angle 0.59569 (15151) hydrogen bonds : bond 0.04231 ( 450) hydrogen bonds : angle 4.54156 ( 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 92 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 63 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 ILE cc_start: 0.7656 (tp) cc_final: 0.7130 (tp) REVERT: A 498 PHE cc_start: 0.8343 (m-10) cc_final: 0.7994 (m-80) REVERT: A 661 ARG cc_start: 0.6801 (ttt180) cc_final: 0.5938 (tpt170) REVERT: A 1271 GLU cc_start: 0.9545 (OUTLIER) cc_final: 0.9116 (tm-30) REVERT: A 1297 HIS cc_start: 0.9054 (m90) cc_final: 0.8767 (m90) REVERT: A 1312 LEU cc_start: 0.9438 (OUTLIER) cc_final: 0.9236 (mm) REVERT: A 1337 ARG cc_start: 0.7662 (tpt90) cc_final: 0.7129 (tpt90) outliers start: 29 outliers final: 23 residues processed: 82 average time/residue: 0.0895 time to fit residues: 10.5566 Evaluate side-chains 85 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 60 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 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 355 SER Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain A residue 472 THR Chi-restraints excluded: chain A residue 502 LEU 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 1166 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1271 GLU Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1312 LEU 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: 6.9990 chunk 76 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 6.9990 chunk 97 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 GLN ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1241 HIS ** A1256 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 = 0.4173 r_free = 0.4173 target = 0.100588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.071400 restraints weight = 36937.023| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 4.15 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10842 Z= 0.214 Angle : 0.632 9.169 15151 Z= 0.328 Chirality : 0.039 0.234 1761 Planarity : 0.004 0.056 1483 Dihedral : 19.911 156.001 2723 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.12 % Allowed : 18.87 % Favored : 78.01 % 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: 0.43 (0.24), residues: 453 sheet: -1.38 (0.64), residues: 52 loop : -0.55 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 61 TYR 0.015 0.002 TYR A 25 PHE 0.018 0.002 PHE A1105 TRP 0.009 0.001 TRP A1136 HIS 0.011 0.001 HIS A1241 Details of bonding type rmsd covalent geometry : bond 0.00449 (10842) covalent geometry : angle 0.63221 (15151) hydrogen bonds : bond 0.04672 ( 450) hydrogen bonds : angle 4.64651 ( 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 88 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 498 PHE cc_start: 0.8406 (m-10) cc_final: 0.8113 (m-80) REVERT: A 1297 HIS cc_start: 0.9069 (m90) cc_final: 0.8768 (m90) REVERT: A 1312 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9248 (mm) REVERT: A 1337 ARG cc_start: 0.7714 (tpt90) cc_final: 0.7188 (tpt90) REVERT: A 1352 ILE cc_start: 0.8921 (mp) cc_final: 0.8650 (tp) outliers start: 27 outliers final: 23 residues processed: 80 average time/residue: 0.0683 time to fit residues: 8.0148 Evaluate side-chains 83 residues out of total 864 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.233 ------------------------------------------------------------------------------- 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 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 502 LEU 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 1166 ILE Chi-restraints excluded: chain A residue 1190 VAL Chi-restraints excluded: chain A residue 1241 HIS Chi-restraints excluded: chain A residue 1245 LEU Chi-restraints excluded: chain A residue 1260 GLU Chi-restraints excluded: chain A residue 1294 TYR Chi-restraints excluded: chain A residue 1312 LEU 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: 20.0000 chunk 79 optimal weight: 0.0570 chunk 29 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 chunk 48 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 46 optimal weight: 0.0970 chunk 24 optimal weight: 5.9990 chunk 67 optimal weight: 9.9990 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS ** A 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 930 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4241 r_free = 0.4241 target = 0.104454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.076338 restraints weight = 36547.132| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 4.02 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10842 Z= 0.114 Angle : 0.570 10.046 15151 Z= 0.293 Chirality : 0.037 0.202 1761 Planarity : 0.004 0.053 1483 Dihedral : 19.738 152.895 2723 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.43 % Allowed : 19.56 % 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: -0.05 (0.27), residues: 942 helix: 0.66 (0.24), residues: 453 sheet: -1.30 (0.64), residues: 52 loop : -0.52 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 61 TYR 0.019 0.002 TYR A 155 PHE 0.016 0.001 PHE A 972 TRP 0.013 0.001 TRP A1136 HIS 0.014 0.001 HIS A1241 Details of bonding type rmsd covalent geometry : bond 0.00243 (10842) covalent geometry : angle 0.56994 (15151) hydrogen bonds : bond 0.03729 ( 450) hydrogen bonds : angle 4.33471 ( 1199) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1994.20 seconds wall clock time: 35 minutes 0.20 seconds (2100.20 seconds total)